diff --git a/blast/blast.json b/blast/blast.json index bf9bec3..241776b 100644 --- a/blast/blast.json +++ b/blast/blast.json @@ -1,4 +1,3 @@ - { "define": { @@ -12,7 +11,7 @@ }, "rules": [ - + { "command":"./split_fasta 10 small.fasta", "inputs": @@ -43,9 +42,10 @@ "small.fasta.18", "small.fasta.19" ], - "local_job":true + "local_job":true, + "category": "preprocessing" }, - + { "command":"./blastall -p blastn -d nt/nt -i small.fasta.0 -o small.fasta.0.out 2> small.fasta.0.err", "inputs": @@ -58,9 +58,16 @@ [ "small.fasta.0.out", "small.fasta.0.err" - ] + ], + "resources" : { + "cores":1, + "memory":1000, + "disk":1400, + "wall-time":40 + }, + "category": "simulation" }, - + { "command":"./blastall -p blastn -d nt/nt -i small.fasta.1 -o small.fasta.1.out 2> small.fasta.1.err", "inputs": @@ -73,9 +80,16 @@ [ "small.fasta.1.out", "small.fasta.1.err" - ] + ], + "resources" : { + "cores":1, + "memory":1000, + "disk":1400, + "wall-time":40 + }, + "category": "simulation" }, - + { "command":"./blastall -p blastn -d nt/nt -i small.fasta.2 -o small.fasta.2.out 2> small.fasta.2.err", "inputs": @@ -88,9 +102,16 @@ [ "small.fasta.2.out", "small.fasta.2.err" - ] + ], + "resources" : { + "cores":1, + "memory":1000, + "disk":1400, + "wall-time":40 + }, + "category": "simulation" }, - + { "command":"./blastall -p blastn -d nt/nt -i small.fasta.3 -o small.fasta.3.out 2> small.fasta.3.err", "inputs": @@ -103,9 +124,16 @@ [ "small.fasta.3.out", "small.fasta.3.err" - ] + ], + "resources" : { + "cores":1, + "memory":1000, + "disk":1400, + "wall-time":40 + }, + "category": "simulation" }, - + { "command":"./blastall -p blastn -d nt/nt -i small.fasta.4 -o small.fasta.4.out 2> small.fasta.4.err", "inputs": @@ -118,9 +146,16 @@ [ "small.fasta.4.out", "small.fasta.4.err" - ] + ], + "resources" : { + "cores":1, + "memory":1000, + "disk":1400, + "wall-time":40 + }, + "category": "simulation" }, - + { "command":"./blastall -p blastn -d nt/nt -i small.fasta.5 -o small.fasta.5.out 2> small.fasta.5.err", "inputs": @@ -133,9 +168,16 @@ [ "small.fasta.5.out", "small.fasta.5.err" - ] + ], + "resources" : { + "cores":1, + "memory":1000, + "disk":1400, + "wall-time":40 + }, + "category": "simulation" }, - + { "command":"./blastall -p blastn -d nt/nt -i small.fasta.6 -o small.fasta.6.out 2> small.fasta.6.err", "inputs": @@ -148,9 +190,16 @@ [ "small.fasta.6.out", "small.fasta.6.err" - ] + ], + "resources" : { + "cores":1, + "memory":1000, + "disk":1400, + "wall-time":40 + }, + "category": "simulation" }, - + { "command":"./blastall -p blastn -d nt/nt -i small.fasta.7 -o small.fasta.7.out 2> small.fasta.7.err", "inputs": @@ -163,9 +212,16 @@ [ "small.fasta.7.out", "small.fasta.7.err" - ] + ], + "resources" : { + "cores":1, + "memory":1000, + "disk":1400, + "wall-time":40 + }, + "category": "simulation" }, - + { "command":"./blastall -p blastn -d nt/nt -i small.fasta.8 -o small.fasta.8.out 2> small.fasta.8.err", "inputs": @@ -178,9 +234,16 @@ [ "small.fasta.8.out", "small.fasta.8.err" - ] + ], + "resources" : { + "cores":1, + "memory":1000, + "disk":1400, + "wall-time":40 + }, + "category": "simulation" }, - + { "command":"./blastall -p blastn -d nt/nt -i small.fasta.9 -o small.fasta.9.out 2> small.fasta.9.err", "inputs": @@ -193,9 +256,16 @@ [ "small.fasta.9.out", "small.fasta.9.err" - ] + ], + "resources" : { + "cores":1, + "memory":1000, + "disk":1400, + "wall-time":40 + }, + "category": "simulation" }, - + { "command":"./blastall -p blastn -d nt/nt -i small.fasta.10 -o small.fasta.10.out 2> small.fasta.10.err", "inputs": @@ -208,9 +278,16 @@ [ "small.fasta.10.out", "small.fasta.10.err" - ] + ], + "resources" : { + "cores":1, + "memory":1000, + "disk":1400, + "wall-time":40 + }, + "category": "simulation" }, - + { "command":"./blastall -p blastn -d nt/nt -i small.fasta.11 -o small.fasta.11.out 2> small.fasta.11.err", "inputs": @@ -223,9 +300,16 @@ [ "small.fasta.11.out", "small.fasta.11.err" - ] + ], + "resources" : { + "cores":1, + "memory":1000, + "disk":1400, + "wall-time":40 + }, + "category": "simulation" }, - + { "command":"./blastall -p blastn -d nt/nt -i small.fasta.12 -o small.fasta.12.out 2> small.fasta.12.err", "inputs": @@ -238,9 +322,16 @@ [ "small.fasta.12.out", "small.fasta.12.err" - ] + ], + "resources" : { + "cores":1, + "memory":1000, + "disk":1400, + "wall-time":40 + }, + "category": "simulation" }, - + { "command":"./blastall -p blastn -d nt/nt -i small.fasta.13 -o small.fasta.13.out 2> small.fasta.13.err", "inputs": @@ -253,9 +344,16 @@ [ "small.fasta.13.out", "small.fasta.13.err" - ] + ], + "resources" : { + "cores":1, + "memory":1000, + "disk":1400, + "wall-time":40 + }, + "category": "simulation" }, - + { "command":"./blastall -p blastn -d nt/nt -i small.fasta.14 -o small.fasta.14.out 2> small.fasta.14.err", "inputs": @@ -268,9 +366,16 @@ [ "small.fasta.14.out", "small.fasta.14.err" - ] + ], + "resources" : { + "cores":1, + "memory":1000, + "disk":1400, + "wall-time":40 + }, + "category": "simulation" }, - + { "command":"./blastall -p blastn -d nt/nt -i small.fasta.15 -o small.fasta.15.out 2> small.fasta.15.err", "inputs": @@ -283,9 +388,16 @@ [ "small.fasta.15.out", "small.fasta.15.err" - ] + ], + "resources" : { + "cores":1, + "memory":1000, + "disk":1400, + "wall-time":40 + }, + "category": "simulation" }, - + { "command":"./blastall -p blastn -d nt/nt -i small.fasta.16 -o small.fasta.16.out 2> small.fasta.16.err", "inputs": @@ -298,9 +410,16 @@ [ "small.fasta.16.out", "small.fasta.16.err" - ] + ], + "resources" : { + "cores":1, + "memory":1000, + "disk":1400, + "wall-time":40 + }, + "category": "simulation" }, - + { "command":"./blastall -p blastn -d nt/nt -i small.fasta.17 -o small.fasta.17.out 2> small.fasta.17.err", "inputs": @@ -313,9 +432,16 @@ [ "small.fasta.17.out", "small.fasta.17.err" - ] + ], + "resources" : { + "cores":1, + "memory":1000, + "disk":1400, + "wall-time":40 + }, + "category": "simulation" }, - + { "command":"./blastall -p blastn -d nt/nt -i small.fasta.18 -o small.fasta.18.out 2> small.fasta.18.err", "inputs": @@ -328,9 +454,16 @@ [ "small.fasta.18.out", "small.fasta.18.err" - ] + ], + "resources" : { + "cores":1, + "memory":1000, + "disk":1400, + "wall-time":40 + }, + "category": "simulation" }, - + { "command":"./blastall -p blastn -d nt/nt -i small.fasta.19 -o small.fasta.19.out 2> small.fasta.19.err", "inputs": @@ -343,9 +476,16 @@ [ "small.fasta.19.out", "small.fasta.19.err" - ] + ], + "resources" : { + "cores":1, + "memory":1000, + "disk":1400, + "wall-time":40 + }, + "category": "simulation" }, - + { "command":"./cat_blast output.fasta small.fasta.0.out small.fasta.1.out small.fasta.2.out small.fasta.3.out small.fasta.4.out small.fasta.5.out small.fasta.6.out small.fasta.7.out small.fasta.8.out small.fasta.9.out small.fasta.10.out small.fasta.11.out small.fasta.12.out small.fasta.13.out small.fasta.14.out small.fasta.15.out small.fasta.16.out small.fasta.17.out small.fasta.18.out small.fasta.19.out", "inputs": @@ -376,9 +516,10 @@ [ "output.fasta" ], - "local_job":true + "local_job":true, + "category":"analysis" }, - + { "command":"cat small.fasta.0.err small.fasta.1.err small.fasta.2.err small.fasta.3.err small.fasta.4.err small.fasta.5.err small.fasta.6.err small.fasta.7.err small.fasta.8.err small.fasta.9.err small.fasta.10.err small.fasta.11.err small.fasta.12.err small.fasta.13.err small.fasta.14.err small.fasta.15.err small.fasta.16.err small.fasta.17.err small.fasta.18.err small.fasta.19.err > output.fasta.err", "inputs": @@ -408,7 +549,8 @@ [ "output.fasta.err" ], - "local_job":true + "local_job":true, + "category":"analysis" } ] } diff --git a/blast/blast.jx b/blast/blast.jx index c94e529..4f22c10 100644 --- a/blast/blast.jx +++ b/blast/blast.jx @@ -22,6 +22,7 @@ ], "outputs": [format("small.fasta.%d", x) for x in range(ceil(TOTAL_SEQ/SEQ_PER_SPLIT))], "local_job": true, + "category": "preprocessing" }, { "command": format( @@ -41,14 +42,21 @@ "outputs": [ format("small.fasta.%d.out", x), format("small.fasta.%d.err", x), - ] + ], + "resources" : { + "cores":1, + "memory":1000, + "disk":1400, + "wall-time":40 + }, + "category": "simulation" } for x in range(ceil(TOTAL_SEQ/SEQ_PER_SPLIT)), { "command": format( "%s output.fasta %s", CAT_BLAST, join([format("small.fasta.%d.out", x) for x in range(ceil(TOTAL_SEQ/SEQ_PER_SPLIT))]), - ), + ), "inputs": [ CAT_BLAST, format("small.fasta.%d.out", x) for x in range(ceil(TOTAL_SEQ/SEQ_PER_SPLIT)), @@ -57,12 +65,13 @@ "output.fasta" ], "local_job": true, + "category": "analysis", }, { "command": format( "cat %s > output.fasta.err", join([format("small.fasta.%d.err", x) for x in range(ceil(TOTAL_SEQ/SEQ_PER_SPLIT))]), - ), + ), "inputs": [ format("small.fasta.%d.err", x) for x in range(ceil(TOTAL_SEQ/SEQ_PER_SPLIT)), ], @@ -70,6 +79,7 @@ "output.fasta.err" ], "local_job": true, + "category": "analysis" }, ], } diff --git a/blast/blast.mf b/blast/blast.mf index 9c62d77..648f94f 100644 --- a/blast/blast.mf +++ b/blast/blast.mf @@ -1,8 +1,14 @@ - +CATEGORY=preprocessing small.fasta.0 small.fasta.1 small.fasta.2 small.fasta.3 small.fasta.4 small.fasta.5 small.fasta.6 small.fasta.7 small.fasta.8 small.fasta.9 small.fasta.10 small.fasta.11 small.fasta.12 small.fasta.13 small.fasta.14 small.fasta.15 small.fasta.16 small.fasta.17 small.fasta.18 small.fasta.19 : small.fasta split_fasta LOCAL ./split_fasta 10 small.fasta +CATEGORY=simulation +CORES=1 +MEMORY=1000 +DISK=1400 +WALLTIME=40 + small.fasta.0.out small.fasta.0.err : blastall small.fasta.0 nt ./blastall -p blastn -d nt/nt -i small.fasta.0 -o small.fasta.0.out 2> small.fasta.0.err @@ -63,6 +69,8 @@ small.fasta.18.out small.fasta.18.err : blastall small.fasta.18 nt small.fasta.19.out small.fasta.19.err : blastall small.fasta.19 nt ./blastall -p blastn -d nt/nt -i small.fasta.19 -o small.fasta.19.out 2> small.fasta.19.err +CATEGORY=analysis + output.fasta : cat_blast small.fasta.0.out small.fasta.1.out small.fasta.2.out small.fasta.3.out small.fasta.4.out small.fasta.5.out small.fasta.6.out small.fasta.7.out small.fasta.8.out small.fasta.9.out small.fasta.10.out small.fasta.11.out small.fasta.12.out small.fasta.13.out small.fasta.14.out small.fasta.15.out small.fasta.16.out small.fasta.17.out small.fasta.18.out small.fasta.19.out LOCAL ./cat_blast output.fasta small.fasta.0.out small.fasta.1.out small.fasta.2.out small.fasta.3.out small.fasta.4.out small.fasta.5.out small.fasta.6.out small.fasta.7.out small.fasta.8.out small.fasta.9.out small.fasta.10.out small.fasta.11.out small.fasta.12.out small.fasta.13.out small.fasta.14.out small.fasta.15.out small.fasta.16.out small.fasta.17.out small.fasta.18.out small.fasta.19.out diff --git a/bwa/bwa.json b/bwa/bwa.json index cde18f6..d7d144a 100644 --- a/bwa/bwa.json +++ b/bwa/bwa.json @@ -1,2268 +1,2658 @@ - { - "define": - { - "BWA":"./bwa", - "ARGS":"mem", - "SPLIT":"./fastq_reduce", - "CONCAT":"./cat_bwa", - "REF":"ref.fastq", - "REF_INDEX": - [ - "ref.fastq.amb", - "ref.fastq.ann", - "ref.fastq.bwt", - "ref.fastq.pac", - "ref.fastq.sa" - ], - "INPUT_PRE":"query.fastq", - "SEQ_PER_SPLIT":10, - "TOTAL_SEQ":1000 - }, - "rules": - [ - - { - "command":"./fastq_reduce query.fastq 10", - "outputs": - [ - "query.fastq.0", - "query.fastq.1", - "query.fastq.2", - "query.fastq.3", - "query.fastq.4", - "query.fastq.5", - "query.fastq.6", - "query.fastq.7", - "query.fastq.8", - "query.fastq.9", - "query.fastq.10", - "query.fastq.11", - "query.fastq.12", - "query.fastq.13", - "query.fastq.14", - "query.fastq.15", - "query.fastq.16", - "query.fastq.17", - "query.fastq.18", - "query.fastq.19", - "query.fastq.20", - "query.fastq.21", - "query.fastq.22", - "query.fastq.23", - "query.fastq.24", - "query.fastq.25", - "query.fastq.26", - "query.fastq.27", - "query.fastq.28", - "query.fastq.29", - "query.fastq.30", - "query.fastq.31", - "query.fastq.32", - "query.fastq.33", - "query.fastq.34", - "query.fastq.35", - "query.fastq.36", - "query.fastq.37", - "query.fastq.38", - "query.fastq.39", - "query.fastq.40", - "query.fastq.41", - "query.fastq.42", - "query.fastq.43", - "query.fastq.44", - "query.fastq.45", - "query.fastq.46", - "query.fastq.47", - "query.fastq.48", - "query.fastq.49", - "query.fastq.50", - "query.fastq.51", - "query.fastq.52", - "query.fastq.53", - "query.fastq.54", - "query.fastq.55", - "query.fastq.56", - "query.fastq.57", - "query.fastq.58", - "query.fastq.59", - "query.fastq.60", - "query.fastq.61", - "query.fastq.62", - "query.fastq.63", - "query.fastq.64", - "query.fastq.65", - "query.fastq.66", - "query.fastq.67", - "query.fastq.68", - "query.fastq.69", - "query.fastq.70", - "query.fastq.71", - "query.fastq.72", - "query.fastq.73", - "query.fastq.74", - "query.fastq.75", - "query.fastq.76", - "query.fastq.77", - "query.fastq.78", - "query.fastq.79", - "query.fastq.80", - "query.fastq.81", - "query.fastq.82", - "query.fastq.83", - "query.fastq.84", - "query.fastq.85", - "query.fastq.86", - "query.fastq.87", - "query.fastq.88", - "query.fastq.89", - "query.fastq.90", - "query.fastq.91", - "query.fastq.92", - "query.fastq.93", - "query.fastq.94", - "query.fastq.95", - "query.fastq.96", - "query.fastq.97", - "query.fastq.98", - "query.fastq.99" - ], - "inputs": - [ - "./fastq_reduce", - "query.fastq" - ], - "local_job":true - }, - - { - "command":"./bwa index ref.fastq", - "inputs": - [ - "./bwa", - "ref.fastq" - ], - "outputs": - [ - "ref.fastq.amb", - "ref.fastq.ann", - "ref.fastq.bwt", - "ref.fastq.pac", - "ref.fastq.sa" - ], - "local job":true - }, - - { - "command":"./bwa mem ref.fastq query.fastq.0 > query.fastq.0.sam 2> query.fastq.0.err", - "outputs": - [ - "query.fastq.0.sam", - "query.fastq.0.err" - ], - "inputs": - [ - "./bwa", - "ref.fastq", - "ref.fastq.amb", - "ref.fastq.ann", - "ref.fastq.bwt", - "ref.fastq.pac", - "ref.fastq.sa", - "query.fastq.0" - ] - }, - - { - "command":"./bwa mem ref.fastq query.fastq.1 > query.fastq.1.sam 2> query.fastq.1.err", - "outputs": - [ - "query.fastq.1.sam", - "query.fastq.1.err" - ], - "inputs": - [ - "./bwa", - "ref.fastq", - "ref.fastq.amb", - "ref.fastq.ann", - "ref.fastq.bwt", - "ref.fastq.pac", - "ref.fastq.sa", - "query.fastq.1" - ] - }, - - { - "command":"./bwa mem ref.fastq query.fastq.2 > query.fastq.2.sam 2> query.fastq.2.err", - "outputs": - [ - "query.fastq.2.sam", - "query.fastq.2.err" - ], - "inputs": - [ - "./bwa", - "ref.fastq", - "ref.fastq.amb", - "ref.fastq.ann", - "ref.fastq.bwt", - "ref.fastq.pac", - "ref.fastq.sa", - "query.fastq.2" - ] - }, - - { - "command":"./bwa mem ref.fastq query.fastq.3 > query.fastq.3.sam 2> query.fastq.3.err", - "outputs": - [ - "query.fastq.3.sam", - "query.fastq.3.err" - ], - "inputs": - [ - "./bwa", - "ref.fastq", - "ref.fastq.amb", - "ref.fastq.ann", - "ref.fastq.bwt", - "ref.fastq.pac", - "ref.fastq.sa", - "query.fastq.3" - ] - }, - - { - "command":"./bwa mem ref.fastq query.fastq.4 > query.fastq.4.sam 2> query.fastq.4.err", - "outputs": - [ - "query.fastq.4.sam", - "query.fastq.4.err" - ], - "inputs": - [ - "./bwa", - "ref.fastq", - "ref.fastq.amb", - "ref.fastq.ann", - "ref.fastq.bwt", - "ref.fastq.pac", - "ref.fastq.sa", - "query.fastq.4" - ] - }, - - { - "command":"./bwa mem ref.fastq query.fastq.5 > query.fastq.5.sam 2> query.fastq.5.err", - "outputs": - [ - "query.fastq.5.sam", - "query.fastq.5.err" - ], - "inputs": - [ - "./bwa", - "ref.fastq", - "ref.fastq.amb", - "ref.fastq.ann", - "ref.fastq.bwt", - "ref.fastq.pac", - "ref.fastq.sa", - "query.fastq.5" - ] - }, - - { - "command":"./bwa mem ref.fastq query.fastq.6 > query.fastq.6.sam 2> query.fastq.6.err", - "outputs": - [ - "query.fastq.6.sam", - "query.fastq.6.err" - ], - "inputs": - [ - "./bwa", - "ref.fastq", - "ref.fastq.amb", - "ref.fastq.ann", - "ref.fastq.bwt", - "ref.fastq.pac", - "ref.fastq.sa", - "query.fastq.6" - ] - }, - - { - "command":"./bwa mem ref.fastq query.fastq.7 > query.fastq.7.sam 2> query.fastq.7.err", - "outputs": - [ - "query.fastq.7.sam", - "query.fastq.7.err" - ], - "inputs": - [ - 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{ + "category":"simulation", + "outputs":[ + "query.fastq.85.sam", + "query.fastq.85.err" + ], + "command":"./bwa mem ref.fastq query.fastq.85 > query.fastq.85.sam 2> query.fastq.85.err", + "resources":{ + "cores":1, + "disk":3800, + "wall-time":5, + "memory":100 + }, + "inputs":[ + "./bwa", + "ref.fastq", + "ref.fastq.amb", + "ref.fastq.ann", + "ref.fastq.bwt", + "ref.fastq.pac", + "ref.fastq.sa", + "query.fastq.85" + ] + }, + { + "category":"simulation", + "outputs":[ + "query.fastq.86.sam", + "query.fastq.86.err" + ], + "command":"./bwa mem ref.fastq query.fastq.86 > query.fastq.86.sam 2> query.fastq.86.err", + "resources":{ + "cores":1, + "disk":3800, + "wall-time":5, + "memory":100 + }, + "inputs":[ + "./bwa", + "ref.fastq", + "ref.fastq.amb", + "ref.fastq.ann", + "ref.fastq.bwt", + "ref.fastq.pac", + "ref.fastq.sa", + "query.fastq.86" + ] + }, + { + "category":"simulation", + "outputs":[ + "query.fastq.87.sam", + "query.fastq.87.err" + ], + "command":"./bwa mem ref.fastq query.fastq.87 > query.fastq.87.sam 2> query.fastq.87.err", + "resources":{ + "cores":1, + "disk":3800, + "wall-time":5, + "memory":100 + }, + "inputs":[ + "./bwa", + "ref.fastq", + "ref.fastq.amb", + "ref.fastq.ann", + "ref.fastq.bwt", + "ref.fastq.pac", + "ref.fastq.sa", + "query.fastq.87" + ] + }, + { + "category":"simulation", + "outputs":[ + "query.fastq.88.sam", + "query.fastq.88.err" + ], + "command":"./bwa mem ref.fastq query.fastq.88 > query.fastq.88.sam 2> query.fastq.88.err", + "resources":{ + "cores":1, + "disk":3800, + "wall-time":5, + "memory":100 + }, + "inputs":[ + "./bwa", + "ref.fastq", + "ref.fastq.amb", + "ref.fastq.ann", + "ref.fastq.bwt", + "ref.fastq.pac", + "ref.fastq.sa", + "query.fastq.88" + ] + }, + { + "category":"simulation", + "outputs":[ + "query.fastq.89.sam", + "query.fastq.89.err" + ], + "command":"./bwa mem ref.fastq query.fastq.89 > query.fastq.89.sam 2> query.fastq.89.err", + "resources":{ + "cores":1, + "disk":3800, + "wall-time":5, + "memory":100 + }, + "inputs":[ + "./bwa", + "ref.fastq", + "ref.fastq.amb", + "ref.fastq.ann", + "ref.fastq.bwt", + "ref.fastq.pac", + "ref.fastq.sa", + "query.fastq.89" + ] + }, + { + "category":"simulation", + "outputs":[ + "query.fastq.90.sam", + "query.fastq.90.err" + ], + "command":"./bwa mem ref.fastq query.fastq.90 > query.fastq.90.sam 2> query.fastq.90.err", + "resources":{ + "cores":1, + "disk":3800, + "wall-time":5, + "memory":100 + }, + "inputs":[ + "./bwa", + "ref.fastq", + "ref.fastq.amb", + "ref.fastq.ann", + "ref.fastq.bwt", + "ref.fastq.pac", + "ref.fastq.sa", + "query.fastq.90" + ] + }, + { + "category":"simulation", + "outputs":[ + "query.fastq.91.sam", + "query.fastq.91.err" + ], + "command":"./bwa mem ref.fastq query.fastq.91 > query.fastq.91.sam 2> query.fastq.91.err", + "resources":{ + "cores":1, + "disk":3800, + "wall-time":5, + "memory":100 + }, + "inputs":[ + "./bwa", + "ref.fastq", + "ref.fastq.amb", + "ref.fastq.ann", + "ref.fastq.bwt", + "ref.fastq.pac", + "ref.fastq.sa", + "query.fastq.91" + ] + }, + { + "category":"simulation", + "outputs":[ + "query.fastq.92.sam", + "query.fastq.92.err" + ], + "command":"./bwa mem ref.fastq query.fastq.92 > query.fastq.92.sam 2> query.fastq.92.err", + "resources":{ + "cores":1, + "disk":3800, + "wall-time":5, + "memory":100 + }, + "inputs":[ + "./bwa", + "ref.fastq", + "ref.fastq.amb", + "ref.fastq.ann", + "ref.fastq.bwt", + "ref.fastq.pac", + "ref.fastq.sa", + "query.fastq.92" + ] + }, + { + "category":"simulation", + "outputs":[ + "query.fastq.93.sam", + "query.fastq.93.err" + ], + "command":"./bwa mem ref.fastq query.fastq.93 > query.fastq.93.sam 2> query.fastq.93.err", + "resources":{ + "cores":1, + "disk":3800, + "wall-time":5, + "memory":100 + }, + "inputs":[ + "./bwa", + "ref.fastq", + "ref.fastq.amb", + "ref.fastq.ann", + "ref.fastq.bwt", + "ref.fastq.pac", + "ref.fastq.sa", + "query.fastq.93" + ] + }, + { + "category":"simulation", + "outputs":[ + "query.fastq.94.sam", + "query.fastq.94.err" + ], + "command":"./bwa mem ref.fastq query.fastq.94 > query.fastq.94.sam 2> query.fastq.94.err", + "resources":{ + "cores":1, + "disk":3800, + "wall-time":5, + "memory":100 + }, + "inputs":[ + "./bwa", + "ref.fastq", + "ref.fastq.amb", + "ref.fastq.ann", + "ref.fastq.bwt", + "ref.fastq.pac", + "ref.fastq.sa", + "query.fastq.94" + ] + }, + { + "category":"simulation", + "outputs":[ + "query.fastq.95.sam", + "query.fastq.95.err" + ], + "command":"./bwa mem ref.fastq query.fastq.95 > query.fastq.95.sam 2> query.fastq.95.err", + "resources":{ + "cores":1, + "disk":3800, + "wall-time":5, + "memory":100 + }, + "inputs":[ + "./bwa", + "ref.fastq", + "ref.fastq.amb", + "ref.fastq.ann", + "ref.fastq.bwt", + "ref.fastq.pac", + "ref.fastq.sa", + "query.fastq.95" + ] + }, + { + "category":"simulation", + "outputs":[ + "query.fastq.96.sam", + "query.fastq.96.err" + ], + "command":"./bwa mem ref.fastq query.fastq.96 > query.fastq.96.sam 2> query.fastq.96.err", + "resources":{ + "cores":1, + "disk":3800, + "wall-time":5, + "memory":100 + }, + "inputs":[ + "./bwa", + "ref.fastq", + "ref.fastq.amb", + "ref.fastq.ann", + "ref.fastq.bwt", + "ref.fastq.pac", + "ref.fastq.sa", + "query.fastq.96" + ] + }, + { + "category":"simulation", + "outputs":[ + "query.fastq.97.sam", + "query.fastq.97.err" + ], + "command":"./bwa mem ref.fastq query.fastq.97 > query.fastq.97.sam 2> query.fastq.97.err", + "resources":{ + "cores":1, + "disk":3800, + "wall-time":5, + "memory":100 + }, + "inputs":[ + "./bwa", + "ref.fastq", + "ref.fastq.amb", + "ref.fastq.ann", + "ref.fastq.bwt", + "ref.fastq.pac", + "ref.fastq.sa", + "query.fastq.97" + ] + }, + { + "category":"simulation", + "outputs":[ + "query.fastq.98.sam", + "query.fastq.98.err" + ], + "command":"./bwa mem ref.fastq query.fastq.98 > query.fastq.98.sam 2> query.fastq.98.err", + "resources":{ + "cores":1, + "disk":3800, + "wall-time":5, + "memory":100 + }, + "inputs":[ + "./bwa", + "ref.fastq", + "ref.fastq.amb", + "ref.fastq.ann", + "ref.fastq.bwt", + "ref.fastq.pac", + "ref.fastq.sa", + "query.fastq.98" + ] + }, + { + "category":"simulation", + "outputs":[ + "query.fastq.99.sam", + "query.fastq.99.err" + ], + "command":"./bwa mem ref.fastq query.fastq.99 > query.fastq.99.sam 2> query.fastq.99.err", + "resources":{ + "cores":1, + "disk":3800, + "wall-time":5, + "memory":100 + }, + "inputs":[ + "./bwa", + "ref.fastq", + "ref.fastq.amb", + "ref.fastq.ann", + "ref.fastq.bwt", + "ref.fastq.pac", + "ref.fastq.sa", + "query.fastq.99" + ] + }, + { + "category":"analysis", + "outputs":[ + "query.fastq.sam" + ], + "command":"./cat_bwa query.fastq.sam query.fastq*.sam", + "inputs":[ + "./cat_bwa", + "query.fastq.0.sam", + "query.fastq.1.sam", + "query.fastq.2.sam", + "query.fastq.3.sam", + "query.fastq.4.sam", + "query.fastq.5.sam", + "query.fastq.6.sam", + "query.fastq.7.sam", + "query.fastq.8.sam", + "query.fastq.9.sam", + "query.fastq.10.sam", + "query.fastq.11.sam", + "query.fastq.12.sam", + "query.fastq.13.sam", + "query.fastq.14.sam", + "query.fastq.15.sam", + "query.fastq.16.sam", + "query.fastq.17.sam", + "query.fastq.18.sam", + "query.fastq.19.sam", + "query.fastq.20.sam", + "query.fastq.21.sam", + "query.fastq.22.sam", + "query.fastq.23.sam", + "query.fastq.24.sam", + "query.fastq.25.sam", + "query.fastq.26.sam", + "query.fastq.27.sam", + "query.fastq.28.sam", + "query.fastq.29.sam", + "query.fastq.30.sam", + "query.fastq.31.sam", + "query.fastq.32.sam", + "query.fastq.33.sam", + "query.fastq.34.sam", + "query.fastq.35.sam", + "query.fastq.36.sam", + "query.fastq.37.sam", + "query.fastq.38.sam", + "query.fastq.39.sam", + "query.fastq.40.sam", + "query.fastq.41.sam", + "query.fastq.42.sam", + "query.fastq.43.sam", + "query.fastq.44.sam", + "query.fastq.45.sam", + "query.fastq.46.sam", + "query.fastq.47.sam", + "query.fastq.48.sam", + "query.fastq.49.sam", + "query.fastq.50.sam", + "query.fastq.51.sam", + "query.fastq.52.sam", + "query.fastq.53.sam", + "query.fastq.54.sam", + "query.fastq.55.sam", + "query.fastq.56.sam", + "query.fastq.57.sam", + "query.fastq.58.sam", + "query.fastq.59.sam", + "query.fastq.60.sam", + "query.fastq.61.sam", + "query.fastq.62.sam", + "query.fastq.63.sam", + "query.fastq.64.sam", + "query.fastq.65.sam", + "query.fastq.66.sam", + "query.fastq.67.sam", + "query.fastq.68.sam", + "query.fastq.69.sam", + "query.fastq.70.sam", + "query.fastq.71.sam", + "query.fastq.72.sam", + "query.fastq.73.sam", + "query.fastq.74.sam", + "query.fastq.75.sam", + "query.fastq.76.sam", + "query.fastq.77.sam", + "query.fastq.78.sam", + "query.fastq.79.sam", + "query.fastq.80.sam", + "query.fastq.81.sam", + "query.fastq.82.sam", + "query.fastq.83.sam", + "query.fastq.84.sam", + "query.fastq.85.sam", + "query.fastq.86.sam", + "query.fastq.87.sam", + "query.fastq.88.sam", + "query.fastq.89.sam", + "query.fastq.90.sam", + "query.fastq.91.sam", + "query.fastq.92.sam", + "query.fastq.93.sam", + "query.fastq.94.sam", + "query.fastq.95.sam", + "query.fastq.96.sam", + "query.fastq.97.sam", + "query.fastq.98.sam", + "query.fastq.99.sam" + ] + } + ] } diff --git a/bwa/bwa.jx b/bwa/bwa.jx index a02e869..e3b5f67 100644 --- a/bwa/bwa.jx +++ b/bwa/bwa.jx @@ -17,7 +17,7 @@ }, "rules": [ - + { "command":format("%s %s %d",SPLIT,INPUT_PRE,SEQ_PER_SPLIT), "outputs": @@ -29,9 +29,10 @@ SPLIT, INPUT_PRE ], - "local_job":true + "local_job":true, + "category": "preprocessing" }, - + { "command":format("%s index %s",BWA,REF), "inputs": @@ -43,9 +44,10 @@ [ x for x in REF_INDEX ], - "local job":true + "local job":true, + "category": "preprocessing" }, - + { "command":format("%s %s %s %s.%d > %s.%d.sam 2> %s.%d.err",BWA,ARGS,REF,INPUT_PRE,i,INPUT_PRE,i,INPUT_PRE,i), "outputs": @@ -59,9 +61,17 @@ REF, x for x in REF_INDEX, format("%s.%d",INPUT_PRE,i) - ] + ], + "resources" : { + "cores":1, + "memory":100, + "disk":3800, + "wall-time":5 + }, + "category": "simulation" + } for i in range(ceil(TOTAL_SEQ/SEQ_PER_SPLIT)), - + { "command":format("%s %s.sam %s*.sam",CONCAT,INPUT_PRE,INPUT_PRE), "outputs": @@ -72,7 +82,8 @@ [ CONCAT, format("%s.%d.sam",INPUT_PRE,i) for i in range(ceil(TOTAL_SEQ/SEQ_PER_SPLIT)) - ] + ], + "category": "analysis" } ] } diff --git a/bwa/bwa.mf b/bwa/bwa.mf index 8e75a1d..504659d 100644 --- a/bwa/bwa.mf +++ b/bwa/bwa.mf @@ -1,43 +1,3021 @@ +CATEGORY=preprocessing - -query.fastq.0 query.fastq.1 query.fastq.2 query.fastq.3 query.fastq.4 query.fastq.5 query.fastq.6 query.fastq.7 query.fastq.8 query.fastq.9 : fastq_reduce query.fastq - LOCAL perl fastq_reduce query.fastq 100 +query.fastq.0 query.fastq.1 query.fastq.2 query.fastq.3 query.fastq.4 query.fastq.5 query.fastq.6 query.fastq.7 query.fastq.8 query.fastq.9 query.fastq.10 query.fastq.11 query.fastq.12 query.fastq.13 query.fastq.14 query.fastq.15 query.fastq.16 query.fastq.17 query.fastq.18 query.fastq.19 query.fastq.20 query.fastq.21 query.fastq.22 query.fastq.23 query.fastq.24 query.fastq.25 query.fastq.26 query.fastq.27 query.fastq.28 query.fastq.29 query.fastq.30 query.fastq.31 query.fastq.32 query.fastq.33 query.fastq.34 query.fastq.35 query.fastq.36 query.fastq.37 query.fastq.38 query.fastq.39 query.fastq.40 query.fastq.41 query.fastq.42 query.fastq.43 query.fastq.44 query.fastq.45 query.fastq.46 query.fastq.47 query.fastq.48 query.fastq.49 query.fastq.50 query.fastq.51 query.fastq.52 query.fastq.53 query.fastq.54 query.fastq.55 query.fastq.56 query.fastq.57 query.fastq.58 query.fastq.59 query.fastq.60 query.fastq.61 query.fastq.62 query.fastq.63 query.fastq.64 query.fastq.65 query.fastq.66 query.fastq.67 query.fastq.68 query.fastq.69 query.fastq.70 query.fastq.71 query.fastq.72 query.fastq.73 query.fastq.74 query.fastq.75 query.fastq.76 query.fastq.77 query.fastq.78 query.fastq.79 query.fastq.80 query.fastq.81 query.fastq.82 query.fastq.83 query.fastq.84 query.fastq.85 query.fastq.86 query.fastq.87 query.fastq.88 query.fastq.89 query.fastq.90 query.fastq.91 query.fastq.92 query.fastq.93 query.fastq.94 query.fastq.95 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query.fastq.964 query.fastq.965 query.fastq.966 query.fastq.967 query.fastq.968 query.fastq.969 query.fastq.970 query.fastq.971 query.fastq.972 query.fastq.973 query.fastq.974 query.fastq.975 query.fastq.976 query.fastq.977 query.fastq.978 query.fastq.979 query.fastq.980 query.fastq.981 query.fastq.982 query.fastq.983 query.fastq.984 query.fastq.985 query.fastq.986 query.fastq.987 query.fastq.988 query.fastq.989 query.fastq.990 query.fastq.991 query.fastq.992 query.fastq.993 query.fastq.994 query.fastq.995 query.fastq.996 query.fastq.997 query.fastq.998 query.fastq.999 : fastq_reduce query.fastq + LOCAL perl fastq_reduce query.fastq 1000 ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa : bwa ref.fastq LOCAL ./bwa index ref.fastq -query.fastq.0.sam query.fastq.0.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.0 +CATEGORY=simulation +CORES=1 +MEMORY=100 +DISK=3800 +WALLTIME=5 + +query.fastq.0.sam query.fastq.0.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.0 ./bwa mem -v 0 ref.fastq query.fastq.0 > query.fastq.0.sam 2> query.fastq.0.err -query.fastq.1.sam query.fastq.1.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.1 +query.fastq.1.sam query.fastq.1.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.1 ./bwa mem -v 0 ref.fastq query.fastq.1 > query.fastq.1.sam 2> query.fastq.1.err -query.fastq.2.sam query.fastq.2.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.2 +query.fastq.2.sam query.fastq.2.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.2 ./bwa mem -v 0 ref.fastq query.fastq.2 > query.fastq.2.sam 2> query.fastq.2.err -query.fastq.3.sam query.fastq.3.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.3 +query.fastq.3.sam query.fastq.3.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.3 ./bwa mem -v 0 ref.fastq query.fastq.3 > query.fastq.3.sam 2> query.fastq.3.err -query.fastq.4.sam query.fastq.4.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.4 +query.fastq.4.sam query.fastq.4.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.4 ./bwa mem -v 0 ref.fastq query.fastq.4 > query.fastq.4.sam 2> query.fastq.4.err -query.fastq.5.sam query.fastq.5.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.5 +query.fastq.5.sam query.fastq.5.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.5 ./bwa mem -v 0 ref.fastq query.fastq.5 > query.fastq.5.sam 2> query.fastq.5.err -query.fastq.6.sam query.fastq.6.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.6 +query.fastq.6.sam query.fastq.6.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.6 ./bwa mem -v 0 ref.fastq query.fastq.6 > query.fastq.6.sam 2> query.fastq.6.err -query.fastq.7.sam query.fastq.7.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.7 +query.fastq.7.sam query.fastq.7.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.7 ./bwa mem -v 0 ref.fastq query.fastq.7 > query.fastq.7.sam 2> query.fastq.7.err -query.fastq.8.sam query.fastq.8.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.8 +query.fastq.8.sam query.fastq.8.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.8 ./bwa mem -v 0 ref.fastq query.fastq.8 > query.fastq.8.sam 2> query.fastq.8.err -query.fastq.9.sam query.fastq.9.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.9 +query.fastq.9.sam query.fastq.9.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.9 ./bwa mem -v 0 ref.fastq query.fastq.9 > query.fastq.9.sam 2> query.fastq.9.err -query.sam : cat_bwa query.fastq.0.sam query.fastq.1.sam query.fastq.2.sam query.fastq.3.sam query.fastq.4.sam query.fastq.5.sam query.fastq.6.sam query.fastq.7.sam query.fastq.8.sam query.fastq.9.sam +query.fastq.10.sam query.fastq.10.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.10 + ./bwa mem -v 0 ref.fastq query.fastq.10 > query.fastq.10.sam 2> query.fastq.10.err + +query.fastq.11.sam query.fastq.11.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.11 + ./bwa mem -v 0 ref.fastq query.fastq.11 > query.fastq.11.sam 2> query.fastq.11.err + +query.fastq.12.sam query.fastq.12.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.12 + ./bwa mem -v 0 ref.fastq query.fastq.12 > query.fastq.12.sam 2> query.fastq.12.err + +query.fastq.13.sam query.fastq.13.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.13 + ./bwa mem -v 0 ref.fastq query.fastq.13 > query.fastq.13.sam 2> query.fastq.13.err + +query.fastq.14.sam query.fastq.14.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.14 + ./bwa mem -v 0 ref.fastq query.fastq.14 > query.fastq.14.sam 2> query.fastq.14.err + +query.fastq.15.sam query.fastq.15.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.15 + ./bwa mem -v 0 ref.fastq query.fastq.15 > query.fastq.15.sam 2> query.fastq.15.err + +query.fastq.16.sam query.fastq.16.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.16 + ./bwa mem -v 0 ref.fastq query.fastq.16 > query.fastq.16.sam 2> query.fastq.16.err + +query.fastq.17.sam query.fastq.17.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.17 + ./bwa mem -v 0 ref.fastq query.fastq.17 > query.fastq.17.sam 2> query.fastq.17.err + +query.fastq.18.sam query.fastq.18.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.18 + ./bwa mem -v 0 ref.fastq query.fastq.18 > query.fastq.18.sam 2> query.fastq.18.err + +query.fastq.19.sam query.fastq.19.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.19 + ./bwa mem -v 0 ref.fastq query.fastq.19 > query.fastq.19.sam 2> query.fastq.19.err + +query.fastq.20.sam query.fastq.20.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.20 + ./bwa mem -v 0 ref.fastq query.fastq.20 > query.fastq.20.sam 2> query.fastq.20.err + +query.fastq.21.sam query.fastq.21.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.21 + ./bwa mem -v 0 ref.fastq query.fastq.21 > query.fastq.21.sam 2> query.fastq.21.err + +query.fastq.22.sam query.fastq.22.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.22 + ./bwa mem -v 0 ref.fastq query.fastq.22 > query.fastq.22.sam 2> query.fastq.22.err + +query.fastq.23.sam query.fastq.23.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.23 + ./bwa mem -v 0 ref.fastq query.fastq.23 > query.fastq.23.sam 2> query.fastq.23.err + +query.fastq.24.sam query.fastq.24.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.24 + ./bwa mem -v 0 ref.fastq query.fastq.24 > query.fastq.24.sam 2> query.fastq.24.err + +query.fastq.25.sam query.fastq.25.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.25 + ./bwa mem -v 0 ref.fastq query.fastq.25 > query.fastq.25.sam 2> query.fastq.25.err + +query.fastq.26.sam query.fastq.26.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.26 + ./bwa mem -v 0 ref.fastq query.fastq.26 > query.fastq.26.sam 2> query.fastq.26.err + +query.fastq.27.sam query.fastq.27.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.27 + ./bwa mem -v 0 ref.fastq query.fastq.27 > query.fastq.27.sam 2> query.fastq.27.err + +query.fastq.28.sam query.fastq.28.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.28 + ./bwa mem -v 0 ref.fastq query.fastq.28 > query.fastq.28.sam 2> query.fastq.28.err + +query.fastq.29.sam query.fastq.29.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.29 + ./bwa mem -v 0 ref.fastq query.fastq.29 > query.fastq.29.sam 2> query.fastq.29.err + +query.fastq.30.sam query.fastq.30.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.30 + ./bwa mem -v 0 ref.fastq query.fastq.30 > query.fastq.30.sam 2> query.fastq.30.err + +query.fastq.31.sam query.fastq.31.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.31 + ./bwa mem -v 0 ref.fastq query.fastq.31 > query.fastq.31.sam 2> query.fastq.31.err + +query.fastq.32.sam query.fastq.32.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.32 + ./bwa mem -v 0 ref.fastq query.fastq.32 > query.fastq.32.sam 2> query.fastq.32.err + +query.fastq.33.sam query.fastq.33.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.33 + ./bwa mem -v 0 ref.fastq query.fastq.33 > query.fastq.33.sam 2> query.fastq.33.err + +query.fastq.34.sam query.fastq.34.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.34 + ./bwa mem -v 0 ref.fastq query.fastq.34 > query.fastq.34.sam 2> query.fastq.34.err + +query.fastq.35.sam query.fastq.35.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.35 + ./bwa mem -v 0 ref.fastq query.fastq.35 > query.fastq.35.sam 2> query.fastq.35.err + +query.fastq.36.sam query.fastq.36.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.36 + ./bwa mem -v 0 ref.fastq query.fastq.36 > query.fastq.36.sam 2> query.fastq.36.err + +query.fastq.37.sam query.fastq.37.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.37 + ./bwa mem -v 0 ref.fastq query.fastq.37 > query.fastq.37.sam 2> query.fastq.37.err + +query.fastq.38.sam query.fastq.38.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.38 + ./bwa mem -v 0 ref.fastq query.fastq.38 > query.fastq.38.sam 2> query.fastq.38.err + +query.fastq.39.sam query.fastq.39.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.39 + ./bwa mem -v 0 ref.fastq query.fastq.39 > query.fastq.39.sam 2> query.fastq.39.err + +query.fastq.40.sam query.fastq.40.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.40 + ./bwa mem -v 0 ref.fastq query.fastq.40 > query.fastq.40.sam 2> query.fastq.40.err + +query.fastq.41.sam query.fastq.41.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.41 + ./bwa mem -v 0 ref.fastq query.fastq.41 > query.fastq.41.sam 2> query.fastq.41.err + +query.fastq.42.sam query.fastq.42.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.42 + ./bwa mem -v 0 ref.fastq query.fastq.42 > query.fastq.42.sam 2> query.fastq.42.err + +query.fastq.43.sam query.fastq.43.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.43 + ./bwa mem -v 0 ref.fastq query.fastq.43 > query.fastq.43.sam 2> query.fastq.43.err + +query.fastq.44.sam query.fastq.44.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.44 + ./bwa mem -v 0 ref.fastq query.fastq.44 > query.fastq.44.sam 2> query.fastq.44.err + +query.fastq.45.sam query.fastq.45.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.45 + ./bwa mem -v 0 ref.fastq query.fastq.45 > query.fastq.45.sam 2> query.fastq.45.err + +query.fastq.46.sam query.fastq.46.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.46 + ./bwa mem -v 0 ref.fastq query.fastq.46 > query.fastq.46.sam 2> query.fastq.46.err + +query.fastq.47.sam query.fastq.47.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.47 + ./bwa mem -v 0 ref.fastq query.fastq.47 > query.fastq.47.sam 2> query.fastq.47.err + +query.fastq.48.sam query.fastq.48.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.48 + ./bwa mem -v 0 ref.fastq query.fastq.48 > query.fastq.48.sam 2> query.fastq.48.err + +query.fastq.49.sam query.fastq.49.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.49 + ./bwa mem -v 0 ref.fastq query.fastq.49 > query.fastq.49.sam 2> query.fastq.49.err + +query.fastq.50.sam query.fastq.50.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.50 + ./bwa mem -v 0 ref.fastq query.fastq.50 > query.fastq.50.sam 2> query.fastq.50.err + +query.fastq.51.sam query.fastq.51.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.51 + ./bwa mem -v 0 ref.fastq query.fastq.51 > query.fastq.51.sam 2> query.fastq.51.err + +query.fastq.52.sam query.fastq.52.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.52 + ./bwa mem -v 0 ref.fastq query.fastq.52 > query.fastq.52.sam 2> query.fastq.52.err + +query.fastq.53.sam query.fastq.53.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.53 + ./bwa mem -v 0 ref.fastq query.fastq.53 > query.fastq.53.sam 2> query.fastq.53.err + +query.fastq.54.sam query.fastq.54.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.54 + ./bwa mem -v 0 ref.fastq query.fastq.54 > query.fastq.54.sam 2> query.fastq.54.err + +query.fastq.55.sam query.fastq.55.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.55 + ./bwa mem -v 0 ref.fastq query.fastq.55 > query.fastq.55.sam 2> query.fastq.55.err + +query.fastq.56.sam query.fastq.56.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.56 + ./bwa mem -v 0 ref.fastq query.fastq.56 > query.fastq.56.sam 2> query.fastq.56.err + +query.fastq.57.sam query.fastq.57.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.57 + ./bwa mem -v 0 ref.fastq query.fastq.57 > query.fastq.57.sam 2> query.fastq.57.err + +query.fastq.58.sam query.fastq.58.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.58 + ./bwa mem -v 0 ref.fastq query.fastq.58 > query.fastq.58.sam 2> query.fastq.58.err + +query.fastq.59.sam query.fastq.59.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.59 + ./bwa mem -v 0 ref.fastq query.fastq.59 > query.fastq.59.sam 2> query.fastq.59.err + +query.fastq.60.sam query.fastq.60.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.60 + ./bwa mem -v 0 ref.fastq query.fastq.60 > query.fastq.60.sam 2> query.fastq.60.err + +query.fastq.61.sam query.fastq.61.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.61 + ./bwa mem -v 0 ref.fastq query.fastq.61 > query.fastq.61.sam 2> query.fastq.61.err + +query.fastq.62.sam query.fastq.62.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.62 + ./bwa mem -v 0 ref.fastq query.fastq.62 > query.fastq.62.sam 2> query.fastq.62.err + +query.fastq.63.sam query.fastq.63.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.63 + ./bwa mem -v 0 ref.fastq query.fastq.63 > query.fastq.63.sam 2> query.fastq.63.err + +query.fastq.64.sam query.fastq.64.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.64 + ./bwa mem -v 0 ref.fastq query.fastq.64 > query.fastq.64.sam 2> query.fastq.64.err + +query.fastq.65.sam query.fastq.65.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.65 + ./bwa mem -v 0 ref.fastq query.fastq.65 > query.fastq.65.sam 2> query.fastq.65.err + +query.fastq.66.sam query.fastq.66.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.66 + ./bwa mem -v 0 ref.fastq query.fastq.66 > query.fastq.66.sam 2> query.fastq.66.err + +query.fastq.67.sam query.fastq.67.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.67 + ./bwa mem -v 0 ref.fastq query.fastq.67 > query.fastq.67.sam 2> query.fastq.67.err + +query.fastq.68.sam query.fastq.68.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.68 + ./bwa mem -v 0 ref.fastq query.fastq.68 > query.fastq.68.sam 2> query.fastq.68.err + +query.fastq.69.sam query.fastq.69.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.69 + ./bwa mem -v 0 ref.fastq query.fastq.69 > query.fastq.69.sam 2> query.fastq.69.err + +query.fastq.70.sam query.fastq.70.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.70 + ./bwa mem -v 0 ref.fastq query.fastq.70 > query.fastq.70.sam 2> query.fastq.70.err + +query.fastq.71.sam query.fastq.71.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.71 + ./bwa mem -v 0 ref.fastq query.fastq.71 > query.fastq.71.sam 2> query.fastq.71.err + +query.fastq.72.sam query.fastq.72.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.72 + ./bwa mem -v 0 ref.fastq query.fastq.72 > query.fastq.72.sam 2> query.fastq.72.err + +query.fastq.73.sam query.fastq.73.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.73 + ./bwa mem -v 0 ref.fastq query.fastq.73 > query.fastq.73.sam 2> query.fastq.73.err + +query.fastq.74.sam query.fastq.74.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.74 + ./bwa mem -v 0 ref.fastq query.fastq.74 > query.fastq.74.sam 2> query.fastq.74.err + +query.fastq.75.sam query.fastq.75.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.75 + ./bwa mem -v 0 ref.fastq query.fastq.75 > query.fastq.75.sam 2> query.fastq.75.err + +query.fastq.76.sam query.fastq.76.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.76 + ./bwa mem -v 0 ref.fastq query.fastq.76 > query.fastq.76.sam 2> query.fastq.76.err + +query.fastq.77.sam query.fastq.77.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.77 + ./bwa mem -v 0 ref.fastq query.fastq.77 > query.fastq.77.sam 2> query.fastq.77.err + +query.fastq.78.sam query.fastq.78.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.78 + ./bwa mem -v 0 ref.fastq query.fastq.78 > query.fastq.78.sam 2> query.fastq.78.err + +query.fastq.79.sam query.fastq.79.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.79 + ./bwa mem -v 0 ref.fastq query.fastq.79 > query.fastq.79.sam 2> query.fastq.79.err + +query.fastq.80.sam query.fastq.80.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.80 + ./bwa mem -v 0 ref.fastq query.fastq.80 > query.fastq.80.sam 2> query.fastq.80.err + +query.fastq.81.sam query.fastq.81.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.81 + ./bwa mem -v 0 ref.fastq query.fastq.81 > query.fastq.81.sam 2> query.fastq.81.err + +query.fastq.82.sam query.fastq.82.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.82 + ./bwa mem -v 0 ref.fastq query.fastq.82 > query.fastq.82.sam 2> query.fastq.82.err + +query.fastq.83.sam query.fastq.83.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.83 + ./bwa mem -v 0 ref.fastq query.fastq.83 > query.fastq.83.sam 2> query.fastq.83.err + +query.fastq.84.sam query.fastq.84.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.84 + ./bwa mem -v 0 ref.fastq query.fastq.84 > query.fastq.84.sam 2> query.fastq.84.err + +query.fastq.85.sam query.fastq.85.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.85 + ./bwa mem -v 0 ref.fastq query.fastq.85 > query.fastq.85.sam 2> query.fastq.85.err + +query.fastq.86.sam query.fastq.86.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.86 + ./bwa mem -v 0 ref.fastq query.fastq.86 > query.fastq.86.sam 2> query.fastq.86.err + +query.fastq.87.sam query.fastq.87.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.87 + ./bwa mem -v 0 ref.fastq query.fastq.87 > query.fastq.87.sam 2> query.fastq.87.err + +query.fastq.88.sam query.fastq.88.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.88 + ./bwa mem -v 0 ref.fastq query.fastq.88 > query.fastq.88.sam 2> query.fastq.88.err + +query.fastq.89.sam query.fastq.89.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.89 + ./bwa mem -v 0 ref.fastq query.fastq.89 > query.fastq.89.sam 2> query.fastq.89.err + +query.fastq.90.sam query.fastq.90.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.90 + ./bwa mem -v 0 ref.fastq query.fastq.90 > query.fastq.90.sam 2> query.fastq.90.err + +query.fastq.91.sam query.fastq.91.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.91 + ./bwa mem -v 0 ref.fastq query.fastq.91 > query.fastq.91.sam 2> query.fastq.91.err + +query.fastq.92.sam query.fastq.92.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.92 + ./bwa mem -v 0 ref.fastq query.fastq.92 > query.fastq.92.sam 2> query.fastq.92.err + +query.fastq.93.sam query.fastq.93.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.93 + ./bwa mem -v 0 ref.fastq query.fastq.93 > query.fastq.93.sam 2> query.fastq.93.err + +query.fastq.94.sam query.fastq.94.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.94 + ./bwa mem -v 0 ref.fastq query.fastq.94 > query.fastq.94.sam 2> query.fastq.94.err + +query.fastq.95.sam query.fastq.95.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.95 + ./bwa mem -v 0 ref.fastq query.fastq.95 > query.fastq.95.sam 2> query.fastq.95.err + +query.fastq.96.sam query.fastq.96.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.96 + ./bwa mem -v 0 ref.fastq query.fastq.96 > query.fastq.96.sam 2> query.fastq.96.err + +query.fastq.97.sam query.fastq.97.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.97 + ./bwa mem -v 0 ref.fastq query.fastq.97 > query.fastq.97.sam 2> query.fastq.97.err + +query.fastq.98.sam query.fastq.98.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.98 + ./bwa mem -v 0 ref.fastq query.fastq.98 > query.fastq.98.sam 2> query.fastq.98.err + +query.fastq.99.sam query.fastq.99.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.99 + ./bwa mem -v 0 ref.fastq query.fastq.99 > query.fastq.99.sam 2> query.fastq.99.err + +query.fastq.100.sam query.fastq.100.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.100 + ./bwa mem -v 0 ref.fastq query.fastq.100 > query.fastq.100.sam 2> query.fastq.100.err + +query.fastq.101.sam query.fastq.101.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.101 + ./bwa mem -v 0 ref.fastq query.fastq.101 > query.fastq.101.sam 2> query.fastq.101.err + +query.fastq.102.sam query.fastq.102.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.102 + ./bwa mem -v 0 ref.fastq query.fastq.102 > query.fastq.102.sam 2> query.fastq.102.err + +query.fastq.103.sam query.fastq.103.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.103 + ./bwa mem -v 0 ref.fastq query.fastq.103 > query.fastq.103.sam 2> query.fastq.103.err + +query.fastq.104.sam query.fastq.104.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.104 + ./bwa mem -v 0 ref.fastq query.fastq.104 > query.fastq.104.sam 2> query.fastq.104.err + +query.fastq.105.sam query.fastq.105.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.105 + ./bwa mem -v 0 ref.fastq query.fastq.105 > query.fastq.105.sam 2> query.fastq.105.err + +query.fastq.106.sam query.fastq.106.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.106 + ./bwa mem -v 0 ref.fastq query.fastq.106 > query.fastq.106.sam 2> query.fastq.106.err + +query.fastq.107.sam query.fastq.107.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.107 + ./bwa mem -v 0 ref.fastq query.fastq.107 > query.fastq.107.sam 2> query.fastq.107.err + +query.fastq.108.sam query.fastq.108.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.108 + ./bwa mem -v 0 ref.fastq query.fastq.108 > query.fastq.108.sam 2> query.fastq.108.err + +query.fastq.109.sam query.fastq.109.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.109 + ./bwa mem -v 0 ref.fastq query.fastq.109 > query.fastq.109.sam 2> query.fastq.109.err + +query.fastq.110.sam query.fastq.110.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.110 + ./bwa mem -v 0 ref.fastq query.fastq.110 > query.fastq.110.sam 2> query.fastq.110.err + +query.fastq.111.sam query.fastq.111.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.111 + ./bwa mem -v 0 ref.fastq query.fastq.111 > query.fastq.111.sam 2> query.fastq.111.err + +query.fastq.112.sam query.fastq.112.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.112 + ./bwa mem -v 0 ref.fastq query.fastq.112 > query.fastq.112.sam 2> query.fastq.112.err + +query.fastq.113.sam query.fastq.113.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.113 + ./bwa mem -v 0 ref.fastq query.fastq.113 > query.fastq.113.sam 2> query.fastq.113.err + +query.fastq.114.sam query.fastq.114.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.114 + ./bwa mem -v 0 ref.fastq query.fastq.114 > query.fastq.114.sam 2> query.fastq.114.err + +query.fastq.115.sam query.fastq.115.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.115 + ./bwa mem -v 0 ref.fastq query.fastq.115 > query.fastq.115.sam 2> query.fastq.115.err + +query.fastq.116.sam query.fastq.116.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.116 + ./bwa mem -v 0 ref.fastq query.fastq.116 > query.fastq.116.sam 2> query.fastq.116.err + +query.fastq.117.sam query.fastq.117.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.117 + ./bwa mem -v 0 ref.fastq query.fastq.117 > query.fastq.117.sam 2> query.fastq.117.err + +query.fastq.118.sam query.fastq.118.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.118 + ./bwa mem -v 0 ref.fastq query.fastq.118 > query.fastq.118.sam 2> query.fastq.118.err + +query.fastq.119.sam query.fastq.119.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.119 + ./bwa mem -v 0 ref.fastq query.fastq.119 > query.fastq.119.sam 2> query.fastq.119.err + +query.fastq.120.sam query.fastq.120.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.120 + ./bwa mem -v 0 ref.fastq query.fastq.120 > query.fastq.120.sam 2> query.fastq.120.err + +query.fastq.121.sam query.fastq.121.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.121 + ./bwa mem -v 0 ref.fastq query.fastq.121 > query.fastq.121.sam 2> query.fastq.121.err + +query.fastq.122.sam query.fastq.122.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.122 + ./bwa mem -v 0 ref.fastq query.fastq.122 > query.fastq.122.sam 2> query.fastq.122.err + +query.fastq.123.sam query.fastq.123.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.123 + ./bwa mem -v 0 ref.fastq query.fastq.123 > query.fastq.123.sam 2> query.fastq.123.err + +query.fastq.124.sam query.fastq.124.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.124 + ./bwa mem -v 0 ref.fastq query.fastq.124 > query.fastq.124.sam 2> query.fastq.124.err + +query.fastq.125.sam query.fastq.125.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.125 + ./bwa mem -v 0 ref.fastq query.fastq.125 > query.fastq.125.sam 2> query.fastq.125.err + +query.fastq.126.sam query.fastq.126.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.126 + ./bwa mem -v 0 ref.fastq query.fastq.126 > query.fastq.126.sam 2> query.fastq.126.err + +query.fastq.127.sam query.fastq.127.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.127 + ./bwa mem -v 0 ref.fastq query.fastq.127 > query.fastq.127.sam 2> query.fastq.127.err + +query.fastq.128.sam query.fastq.128.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.128 + ./bwa mem -v 0 ref.fastq query.fastq.128 > query.fastq.128.sam 2> query.fastq.128.err + +query.fastq.129.sam query.fastq.129.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.129 + ./bwa mem -v 0 ref.fastq query.fastq.129 > query.fastq.129.sam 2> query.fastq.129.err + +query.fastq.130.sam query.fastq.130.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.130 + ./bwa mem -v 0 ref.fastq query.fastq.130 > query.fastq.130.sam 2> query.fastq.130.err + +query.fastq.131.sam query.fastq.131.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.131 + ./bwa mem -v 0 ref.fastq query.fastq.131 > query.fastq.131.sam 2> query.fastq.131.err + +query.fastq.132.sam query.fastq.132.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.132 + ./bwa mem -v 0 ref.fastq query.fastq.132 > query.fastq.132.sam 2> query.fastq.132.err + +query.fastq.133.sam query.fastq.133.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.133 + ./bwa mem -v 0 ref.fastq query.fastq.133 > query.fastq.133.sam 2> query.fastq.133.err + +query.fastq.134.sam query.fastq.134.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.134 + ./bwa mem -v 0 ref.fastq query.fastq.134 > query.fastq.134.sam 2> query.fastq.134.err + +query.fastq.135.sam query.fastq.135.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.135 + ./bwa mem -v 0 ref.fastq query.fastq.135 > query.fastq.135.sam 2> query.fastq.135.err + +query.fastq.136.sam query.fastq.136.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.136 + ./bwa mem -v 0 ref.fastq query.fastq.136 > query.fastq.136.sam 2> query.fastq.136.err + +query.fastq.137.sam query.fastq.137.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.137 + ./bwa mem -v 0 ref.fastq query.fastq.137 > query.fastq.137.sam 2> query.fastq.137.err + +query.fastq.138.sam query.fastq.138.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.138 + ./bwa mem -v 0 ref.fastq query.fastq.138 > query.fastq.138.sam 2> query.fastq.138.err + +query.fastq.139.sam query.fastq.139.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.139 + ./bwa mem -v 0 ref.fastq query.fastq.139 > query.fastq.139.sam 2> query.fastq.139.err + +query.fastq.140.sam query.fastq.140.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.140 + ./bwa mem -v 0 ref.fastq query.fastq.140 > query.fastq.140.sam 2> query.fastq.140.err + +query.fastq.141.sam query.fastq.141.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.141 + ./bwa mem -v 0 ref.fastq query.fastq.141 > query.fastq.141.sam 2> query.fastq.141.err + +query.fastq.142.sam query.fastq.142.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.142 + ./bwa mem -v 0 ref.fastq query.fastq.142 > query.fastq.142.sam 2> query.fastq.142.err + +query.fastq.143.sam query.fastq.143.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.143 + ./bwa mem -v 0 ref.fastq query.fastq.143 > query.fastq.143.sam 2> query.fastq.143.err + +query.fastq.144.sam query.fastq.144.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.144 + ./bwa mem -v 0 ref.fastq query.fastq.144 > query.fastq.144.sam 2> query.fastq.144.err + +query.fastq.145.sam query.fastq.145.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.145 + ./bwa mem -v 0 ref.fastq query.fastq.145 > query.fastq.145.sam 2> query.fastq.145.err + +query.fastq.146.sam query.fastq.146.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.146 + ./bwa mem -v 0 ref.fastq query.fastq.146 > query.fastq.146.sam 2> query.fastq.146.err + +query.fastq.147.sam query.fastq.147.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.147 + ./bwa mem -v 0 ref.fastq query.fastq.147 > query.fastq.147.sam 2> query.fastq.147.err + +query.fastq.148.sam query.fastq.148.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.148 + ./bwa mem -v 0 ref.fastq query.fastq.148 > query.fastq.148.sam 2> query.fastq.148.err + +query.fastq.149.sam query.fastq.149.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.149 + ./bwa mem -v 0 ref.fastq query.fastq.149 > query.fastq.149.sam 2> query.fastq.149.err + +query.fastq.150.sam query.fastq.150.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.150 + ./bwa mem -v 0 ref.fastq query.fastq.150 > query.fastq.150.sam 2> query.fastq.150.err + +query.fastq.151.sam query.fastq.151.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.151 + ./bwa mem -v 0 ref.fastq query.fastq.151 > query.fastq.151.sam 2> query.fastq.151.err + +query.fastq.152.sam query.fastq.152.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.152 + ./bwa mem -v 0 ref.fastq query.fastq.152 > query.fastq.152.sam 2> query.fastq.152.err + +query.fastq.153.sam query.fastq.153.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.153 + ./bwa mem -v 0 ref.fastq query.fastq.153 > query.fastq.153.sam 2> query.fastq.153.err + +query.fastq.154.sam query.fastq.154.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.154 + ./bwa mem -v 0 ref.fastq query.fastq.154 > query.fastq.154.sam 2> query.fastq.154.err + +query.fastq.155.sam query.fastq.155.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.155 + ./bwa mem -v 0 ref.fastq query.fastq.155 > query.fastq.155.sam 2> query.fastq.155.err + +query.fastq.156.sam query.fastq.156.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.156 + ./bwa mem -v 0 ref.fastq query.fastq.156 > query.fastq.156.sam 2> query.fastq.156.err + +query.fastq.157.sam query.fastq.157.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.157 + ./bwa mem -v 0 ref.fastq query.fastq.157 > query.fastq.157.sam 2> query.fastq.157.err + +query.fastq.158.sam query.fastq.158.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.158 + ./bwa mem -v 0 ref.fastq query.fastq.158 > query.fastq.158.sam 2> query.fastq.158.err + +query.fastq.159.sam query.fastq.159.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.159 + ./bwa mem -v 0 ref.fastq query.fastq.159 > query.fastq.159.sam 2> query.fastq.159.err + +query.fastq.160.sam query.fastq.160.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.160 + ./bwa mem -v 0 ref.fastq query.fastq.160 > query.fastq.160.sam 2> query.fastq.160.err + +query.fastq.161.sam query.fastq.161.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.161 + ./bwa mem -v 0 ref.fastq query.fastq.161 > query.fastq.161.sam 2> query.fastq.161.err + +query.fastq.162.sam query.fastq.162.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.162 + ./bwa mem -v 0 ref.fastq query.fastq.162 > query.fastq.162.sam 2> query.fastq.162.err + +query.fastq.163.sam query.fastq.163.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.163 + ./bwa mem -v 0 ref.fastq query.fastq.163 > query.fastq.163.sam 2> query.fastq.163.err + +query.fastq.164.sam query.fastq.164.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.164 + ./bwa mem -v 0 ref.fastq query.fastq.164 > query.fastq.164.sam 2> query.fastq.164.err + +query.fastq.165.sam query.fastq.165.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.165 + ./bwa mem -v 0 ref.fastq query.fastq.165 > query.fastq.165.sam 2> query.fastq.165.err + +query.fastq.166.sam query.fastq.166.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.166 + ./bwa mem -v 0 ref.fastq query.fastq.166 > query.fastq.166.sam 2> query.fastq.166.err + +query.fastq.167.sam query.fastq.167.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.167 + ./bwa mem -v 0 ref.fastq query.fastq.167 > query.fastq.167.sam 2> query.fastq.167.err + +query.fastq.168.sam query.fastq.168.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.168 + ./bwa mem -v 0 ref.fastq query.fastq.168 > query.fastq.168.sam 2> query.fastq.168.err + +query.fastq.169.sam query.fastq.169.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.169 + ./bwa mem -v 0 ref.fastq query.fastq.169 > query.fastq.169.sam 2> query.fastq.169.err + +query.fastq.170.sam query.fastq.170.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.170 + ./bwa mem -v 0 ref.fastq query.fastq.170 > query.fastq.170.sam 2> query.fastq.170.err + +query.fastq.171.sam query.fastq.171.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.171 + ./bwa mem -v 0 ref.fastq query.fastq.171 > query.fastq.171.sam 2> query.fastq.171.err + +query.fastq.172.sam query.fastq.172.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.172 + ./bwa mem -v 0 ref.fastq query.fastq.172 > query.fastq.172.sam 2> query.fastq.172.err + +query.fastq.173.sam query.fastq.173.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.173 + ./bwa mem -v 0 ref.fastq query.fastq.173 > query.fastq.173.sam 2> query.fastq.173.err + +query.fastq.174.sam query.fastq.174.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.174 + ./bwa mem -v 0 ref.fastq query.fastq.174 > query.fastq.174.sam 2> query.fastq.174.err + +query.fastq.175.sam query.fastq.175.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.175 + ./bwa mem -v 0 ref.fastq query.fastq.175 > query.fastq.175.sam 2> query.fastq.175.err + +query.fastq.176.sam query.fastq.176.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.176 + ./bwa mem -v 0 ref.fastq query.fastq.176 > query.fastq.176.sam 2> query.fastq.176.err + +query.fastq.177.sam query.fastq.177.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.177 + ./bwa mem -v 0 ref.fastq query.fastq.177 > query.fastq.177.sam 2> query.fastq.177.err + +query.fastq.178.sam query.fastq.178.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.178 + ./bwa mem -v 0 ref.fastq query.fastq.178 > query.fastq.178.sam 2> query.fastq.178.err + +query.fastq.179.sam query.fastq.179.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.179 + ./bwa mem -v 0 ref.fastq query.fastq.179 > query.fastq.179.sam 2> query.fastq.179.err + +query.fastq.180.sam query.fastq.180.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.180 + ./bwa mem -v 0 ref.fastq query.fastq.180 > query.fastq.180.sam 2> query.fastq.180.err + +query.fastq.181.sam query.fastq.181.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.181 + ./bwa mem -v 0 ref.fastq query.fastq.181 > query.fastq.181.sam 2> query.fastq.181.err + +query.fastq.182.sam query.fastq.182.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.182 + ./bwa mem -v 0 ref.fastq query.fastq.182 > query.fastq.182.sam 2> query.fastq.182.err + +query.fastq.183.sam query.fastq.183.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.183 + ./bwa mem -v 0 ref.fastq query.fastq.183 > query.fastq.183.sam 2> query.fastq.183.err + +query.fastq.184.sam query.fastq.184.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.184 + ./bwa mem -v 0 ref.fastq query.fastq.184 > query.fastq.184.sam 2> query.fastq.184.err + +query.fastq.185.sam query.fastq.185.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.185 + ./bwa mem -v 0 ref.fastq query.fastq.185 > query.fastq.185.sam 2> query.fastq.185.err + +query.fastq.186.sam query.fastq.186.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.186 + ./bwa mem -v 0 ref.fastq query.fastq.186 > query.fastq.186.sam 2> query.fastq.186.err + +query.fastq.187.sam query.fastq.187.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.187 + ./bwa mem -v 0 ref.fastq query.fastq.187 > query.fastq.187.sam 2> query.fastq.187.err + +query.fastq.188.sam query.fastq.188.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.188 + ./bwa mem -v 0 ref.fastq query.fastq.188 > query.fastq.188.sam 2> query.fastq.188.err + +query.fastq.189.sam query.fastq.189.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.189 + ./bwa mem -v 0 ref.fastq query.fastq.189 > query.fastq.189.sam 2> query.fastq.189.err + +query.fastq.190.sam query.fastq.190.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.190 + ./bwa mem -v 0 ref.fastq query.fastq.190 > query.fastq.190.sam 2> query.fastq.190.err + +query.fastq.191.sam query.fastq.191.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.191 + ./bwa mem -v 0 ref.fastq query.fastq.191 > query.fastq.191.sam 2> query.fastq.191.err + +query.fastq.192.sam query.fastq.192.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.192 + ./bwa mem -v 0 ref.fastq query.fastq.192 > query.fastq.192.sam 2> query.fastq.192.err + +query.fastq.193.sam query.fastq.193.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.193 + ./bwa mem -v 0 ref.fastq query.fastq.193 > query.fastq.193.sam 2> query.fastq.193.err + +query.fastq.194.sam query.fastq.194.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.194 + ./bwa mem -v 0 ref.fastq query.fastq.194 > query.fastq.194.sam 2> query.fastq.194.err + +query.fastq.195.sam query.fastq.195.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.195 + ./bwa mem -v 0 ref.fastq query.fastq.195 > query.fastq.195.sam 2> query.fastq.195.err + +query.fastq.196.sam query.fastq.196.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.196 + ./bwa mem -v 0 ref.fastq query.fastq.196 > query.fastq.196.sam 2> query.fastq.196.err + +query.fastq.197.sam query.fastq.197.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.197 + ./bwa mem -v 0 ref.fastq query.fastq.197 > query.fastq.197.sam 2> query.fastq.197.err + +query.fastq.198.sam query.fastq.198.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.198 + ./bwa mem -v 0 ref.fastq query.fastq.198 > query.fastq.198.sam 2> query.fastq.198.err + +query.fastq.199.sam query.fastq.199.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.199 + ./bwa mem -v 0 ref.fastq query.fastq.199 > query.fastq.199.sam 2> query.fastq.199.err + +query.fastq.200.sam query.fastq.200.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.200 + ./bwa mem -v 0 ref.fastq query.fastq.200 > query.fastq.200.sam 2> query.fastq.200.err + +query.fastq.201.sam query.fastq.201.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.201 + ./bwa mem -v 0 ref.fastq query.fastq.201 > query.fastq.201.sam 2> query.fastq.201.err + +query.fastq.202.sam query.fastq.202.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.202 + ./bwa mem -v 0 ref.fastq query.fastq.202 > query.fastq.202.sam 2> query.fastq.202.err + +query.fastq.203.sam query.fastq.203.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.203 + ./bwa mem -v 0 ref.fastq query.fastq.203 > query.fastq.203.sam 2> query.fastq.203.err + +query.fastq.204.sam query.fastq.204.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.204 + ./bwa mem -v 0 ref.fastq query.fastq.204 > query.fastq.204.sam 2> query.fastq.204.err + +query.fastq.205.sam query.fastq.205.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.205 + ./bwa mem -v 0 ref.fastq query.fastq.205 > query.fastq.205.sam 2> query.fastq.205.err + +query.fastq.206.sam query.fastq.206.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.206 + ./bwa mem -v 0 ref.fastq query.fastq.206 > query.fastq.206.sam 2> query.fastq.206.err + +query.fastq.207.sam query.fastq.207.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.207 + ./bwa mem -v 0 ref.fastq query.fastq.207 > query.fastq.207.sam 2> query.fastq.207.err + +query.fastq.208.sam query.fastq.208.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.208 + ./bwa mem -v 0 ref.fastq query.fastq.208 > query.fastq.208.sam 2> query.fastq.208.err + +query.fastq.209.sam query.fastq.209.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.209 + ./bwa mem -v 0 ref.fastq query.fastq.209 > query.fastq.209.sam 2> query.fastq.209.err + +query.fastq.210.sam query.fastq.210.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.210 + ./bwa mem -v 0 ref.fastq query.fastq.210 > query.fastq.210.sam 2> query.fastq.210.err + +query.fastq.211.sam query.fastq.211.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.211 + ./bwa mem -v 0 ref.fastq query.fastq.211 > query.fastq.211.sam 2> query.fastq.211.err + +query.fastq.212.sam query.fastq.212.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.212 + ./bwa mem -v 0 ref.fastq query.fastq.212 > query.fastq.212.sam 2> query.fastq.212.err + +query.fastq.213.sam query.fastq.213.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.213 + ./bwa mem -v 0 ref.fastq query.fastq.213 > query.fastq.213.sam 2> query.fastq.213.err + +query.fastq.214.sam query.fastq.214.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.214 + ./bwa mem -v 0 ref.fastq query.fastq.214 > query.fastq.214.sam 2> query.fastq.214.err + +query.fastq.215.sam query.fastq.215.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.215 + ./bwa mem -v 0 ref.fastq query.fastq.215 > query.fastq.215.sam 2> query.fastq.215.err + +query.fastq.216.sam query.fastq.216.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.216 + ./bwa mem -v 0 ref.fastq query.fastq.216 > query.fastq.216.sam 2> query.fastq.216.err + +query.fastq.217.sam query.fastq.217.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.217 + ./bwa mem -v 0 ref.fastq query.fastq.217 > query.fastq.217.sam 2> query.fastq.217.err + +query.fastq.218.sam query.fastq.218.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.218 + ./bwa mem -v 0 ref.fastq query.fastq.218 > query.fastq.218.sam 2> query.fastq.218.err + +query.fastq.219.sam query.fastq.219.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.219 + ./bwa mem -v 0 ref.fastq query.fastq.219 > query.fastq.219.sam 2> query.fastq.219.err + +query.fastq.220.sam query.fastq.220.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.220 + ./bwa mem -v 0 ref.fastq query.fastq.220 > query.fastq.220.sam 2> query.fastq.220.err + +query.fastq.221.sam query.fastq.221.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.221 + ./bwa mem -v 0 ref.fastq query.fastq.221 > query.fastq.221.sam 2> query.fastq.221.err + +query.fastq.222.sam query.fastq.222.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.222 + ./bwa mem -v 0 ref.fastq query.fastq.222 > query.fastq.222.sam 2> query.fastq.222.err + +query.fastq.223.sam query.fastq.223.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.223 + ./bwa mem -v 0 ref.fastq query.fastq.223 > query.fastq.223.sam 2> query.fastq.223.err + +query.fastq.224.sam query.fastq.224.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.224 + ./bwa mem -v 0 ref.fastq query.fastq.224 > query.fastq.224.sam 2> query.fastq.224.err + +query.fastq.225.sam query.fastq.225.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.225 + ./bwa mem -v 0 ref.fastq query.fastq.225 > query.fastq.225.sam 2> query.fastq.225.err + +query.fastq.226.sam query.fastq.226.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.226 + ./bwa mem -v 0 ref.fastq query.fastq.226 > query.fastq.226.sam 2> query.fastq.226.err + +query.fastq.227.sam query.fastq.227.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.227 + ./bwa mem -v 0 ref.fastq query.fastq.227 > query.fastq.227.sam 2> query.fastq.227.err + +query.fastq.228.sam query.fastq.228.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.228 + ./bwa mem -v 0 ref.fastq query.fastq.228 > query.fastq.228.sam 2> query.fastq.228.err + +query.fastq.229.sam query.fastq.229.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.229 + ./bwa mem -v 0 ref.fastq query.fastq.229 > query.fastq.229.sam 2> query.fastq.229.err + +query.fastq.230.sam query.fastq.230.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.230 + ./bwa mem -v 0 ref.fastq query.fastq.230 > query.fastq.230.sam 2> query.fastq.230.err + +query.fastq.231.sam query.fastq.231.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.231 + ./bwa mem -v 0 ref.fastq query.fastq.231 > query.fastq.231.sam 2> query.fastq.231.err + +query.fastq.232.sam query.fastq.232.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.232 + ./bwa mem -v 0 ref.fastq query.fastq.232 > query.fastq.232.sam 2> query.fastq.232.err + +query.fastq.233.sam query.fastq.233.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.233 + ./bwa mem -v 0 ref.fastq query.fastq.233 > query.fastq.233.sam 2> query.fastq.233.err + +query.fastq.234.sam query.fastq.234.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.234 + ./bwa mem -v 0 ref.fastq query.fastq.234 > query.fastq.234.sam 2> query.fastq.234.err + +query.fastq.235.sam query.fastq.235.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.235 + ./bwa mem -v 0 ref.fastq query.fastq.235 > query.fastq.235.sam 2> query.fastq.235.err + +query.fastq.236.sam query.fastq.236.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.236 + ./bwa mem -v 0 ref.fastq query.fastq.236 > query.fastq.236.sam 2> query.fastq.236.err + +query.fastq.237.sam query.fastq.237.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.237 + ./bwa mem -v 0 ref.fastq query.fastq.237 > query.fastq.237.sam 2> query.fastq.237.err + +query.fastq.238.sam query.fastq.238.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.238 + ./bwa mem -v 0 ref.fastq query.fastq.238 > query.fastq.238.sam 2> query.fastq.238.err + +query.fastq.239.sam query.fastq.239.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.239 + ./bwa mem -v 0 ref.fastq query.fastq.239 > query.fastq.239.sam 2> query.fastq.239.err + +query.fastq.240.sam query.fastq.240.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.240 + ./bwa mem -v 0 ref.fastq query.fastq.240 > query.fastq.240.sam 2> query.fastq.240.err + +query.fastq.241.sam query.fastq.241.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.241 + ./bwa mem -v 0 ref.fastq query.fastq.241 > query.fastq.241.sam 2> query.fastq.241.err + +query.fastq.242.sam query.fastq.242.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.242 + ./bwa mem -v 0 ref.fastq query.fastq.242 > query.fastq.242.sam 2> query.fastq.242.err + +query.fastq.243.sam query.fastq.243.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.243 + ./bwa mem -v 0 ref.fastq query.fastq.243 > query.fastq.243.sam 2> query.fastq.243.err + +query.fastq.244.sam query.fastq.244.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.244 + ./bwa mem -v 0 ref.fastq query.fastq.244 > query.fastq.244.sam 2> query.fastq.244.err + +query.fastq.245.sam query.fastq.245.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.245 + ./bwa mem -v 0 ref.fastq query.fastq.245 > query.fastq.245.sam 2> query.fastq.245.err + +query.fastq.246.sam query.fastq.246.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.246 + ./bwa mem -v 0 ref.fastq query.fastq.246 > query.fastq.246.sam 2> query.fastq.246.err + +query.fastq.247.sam query.fastq.247.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.247 + ./bwa mem -v 0 ref.fastq query.fastq.247 > query.fastq.247.sam 2> query.fastq.247.err + +query.fastq.248.sam query.fastq.248.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.248 + ./bwa mem -v 0 ref.fastq query.fastq.248 > query.fastq.248.sam 2> query.fastq.248.err + +query.fastq.249.sam query.fastq.249.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.249 + ./bwa mem -v 0 ref.fastq query.fastq.249 > query.fastq.249.sam 2> query.fastq.249.err + +query.fastq.250.sam query.fastq.250.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.250 + ./bwa mem -v 0 ref.fastq query.fastq.250 > query.fastq.250.sam 2> query.fastq.250.err + +query.fastq.251.sam query.fastq.251.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.251 + ./bwa mem -v 0 ref.fastq query.fastq.251 > query.fastq.251.sam 2> query.fastq.251.err + +query.fastq.252.sam query.fastq.252.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.252 + ./bwa mem -v 0 ref.fastq query.fastq.252 > query.fastq.252.sam 2> query.fastq.252.err + +query.fastq.253.sam query.fastq.253.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.253 + ./bwa mem -v 0 ref.fastq query.fastq.253 > query.fastq.253.sam 2> query.fastq.253.err + +query.fastq.254.sam query.fastq.254.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.254 + ./bwa mem -v 0 ref.fastq query.fastq.254 > query.fastq.254.sam 2> query.fastq.254.err + +query.fastq.255.sam query.fastq.255.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.255 + ./bwa mem -v 0 ref.fastq query.fastq.255 > query.fastq.255.sam 2> query.fastq.255.err + +query.fastq.256.sam query.fastq.256.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.256 + ./bwa mem -v 0 ref.fastq query.fastq.256 > query.fastq.256.sam 2> query.fastq.256.err + +query.fastq.257.sam query.fastq.257.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.257 + ./bwa mem -v 0 ref.fastq query.fastq.257 > query.fastq.257.sam 2> query.fastq.257.err + +query.fastq.258.sam query.fastq.258.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.258 + ./bwa mem -v 0 ref.fastq query.fastq.258 > query.fastq.258.sam 2> query.fastq.258.err + +query.fastq.259.sam query.fastq.259.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.259 + ./bwa mem -v 0 ref.fastq query.fastq.259 > query.fastq.259.sam 2> query.fastq.259.err + +query.fastq.260.sam query.fastq.260.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.260 + ./bwa mem -v 0 ref.fastq query.fastq.260 > query.fastq.260.sam 2> query.fastq.260.err + +query.fastq.261.sam query.fastq.261.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.261 + ./bwa mem -v 0 ref.fastq query.fastq.261 > query.fastq.261.sam 2> query.fastq.261.err + +query.fastq.262.sam query.fastq.262.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.262 + ./bwa mem -v 0 ref.fastq query.fastq.262 > query.fastq.262.sam 2> query.fastq.262.err + +query.fastq.263.sam query.fastq.263.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.263 + ./bwa mem -v 0 ref.fastq query.fastq.263 > query.fastq.263.sam 2> query.fastq.263.err + +query.fastq.264.sam query.fastq.264.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.264 + ./bwa mem -v 0 ref.fastq query.fastq.264 > query.fastq.264.sam 2> query.fastq.264.err + +query.fastq.265.sam query.fastq.265.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.265 + ./bwa mem -v 0 ref.fastq query.fastq.265 > query.fastq.265.sam 2> query.fastq.265.err + +query.fastq.266.sam query.fastq.266.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.266 + ./bwa mem -v 0 ref.fastq query.fastq.266 > query.fastq.266.sam 2> query.fastq.266.err + +query.fastq.267.sam query.fastq.267.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.267 + ./bwa mem -v 0 ref.fastq query.fastq.267 > query.fastq.267.sam 2> query.fastq.267.err + +query.fastq.268.sam query.fastq.268.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.268 + ./bwa mem -v 0 ref.fastq query.fastq.268 > query.fastq.268.sam 2> query.fastq.268.err + +query.fastq.269.sam query.fastq.269.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.269 + ./bwa mem -v 0 ref.fastq query.fastq.269 > query.fastq.269.sam 2> query.fastq.269.err + +query.fastq.270.sam query.fastq.270.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.270 + ./bwa mem -v 0 ref.fastq query.fastq.270 > query.fastq.270.sam 2> query.fastq.270.err + +query.fastq.271.sam query.fastq.271.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.271 + ./bwa mem -v 0 ref.fastq query.fastq.271 > query.fastq.271.sam 2> query.fastq.271.err + +query.fastq.272.sam query.fastq.272.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.272 + ./bwa mem -v 0 ref.fastq query.fastq.272 > query.fastq.272.sam 2> query.fastq.272.err + +query.fastq.273.sam query.fastq.273.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.273 + ./bwa mem -v 0 ref.fastq query.fastq.273 > query.fastq.273.sam 2> query.fastq.273.err + +query.fastq.274.sam query.fastq.274.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.274 + ./bwa mem -v 0 ref.fastq query.fastq.274 > query.fastq.274.sam 2> query.fastq.274.err + +query.fastq.275.sam query.fastq.275.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.275 + ./bwa mem -v 0 ref.fastq query.fastq.275 > query.fastq.275.sam 2> query.fastq.275.err + +query.fastq.276.sam query.fastq.276.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.276 + ./bwa mem -v 0 ref.fastq query.fastq.276 > query.fastq.276.sam 2> query.fastq.276.err + +query.fastq.277.sam query.fastq.277.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.277 + ./bwa mem -v 0 ref.fastq query.fastq.277 > query.fastq.277.sam 2> query.fastq.277.err + +query.fastq.278.sam query.fastq.278.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.278 + ./bwa mem -v 0 ref.fastq query.fastq.278 > query.fastq.278.sam 2> query.fastq.278.err + +query.fastq.279.sam query.fastq.279.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.279 + ./bwa mem -v 0 ref.fastq query.fastq.279 > query.fastq.279.sam 2> query.fastq.279.err + +query.fastq.280.sam query.fastq.280.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.280 + ./bwa mem -v 0 ref.fastq query.fastq.280 > query.fastq.280.sam 2> query.fastq.280.err + +query.fastq.281.sam query.fastq.281.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.281 + ./bwa mem -v 0 ref.fastq query.fastq.281 > query.fastq.281.sam 2> query.fastq.281.err + +query.fastq.282.sam query.fastq.282.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.282 + ./bwa mem -v 0 ref.fastq query.fastq.282 > query.fastq.282.sam 2> query.fastq.282.err + +query.fastq.283.sam query.fastq.283.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.283 + ./bwa mem -v 0 ref.fastq query.fastq.283 > query.fastq.283.sam 2> query.fastq.283.err + +query.fastq.284.sam query.fastq.284.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.284 + ./bwa mem -v 0 ref.fastq query.fastq.284 > query.fastq.284.sam 2> query.fastq.284.err + +query.fastq.285.sam query.fastq.285.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.285 + ./bwa mem -v 0 ref.fastq query.fastq.285 > query.fastq.285.sam 2> query.fastq.285.err + +query.fastq.286.sam query.fastq.286.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.286 + ./bwa mem -v 0 ref.fastq query.fastq.286 > query.fastq.286.sam 2> query.fastq.286.err + +query.fastq.287.sam query.fastq.287.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.287 + ./bwa mem -v 0 ref.fastq query.fastq.287 > query.fastq.287.sam 2> query.fastq.287.err + +query.fastq.288.sam query.fastq.288.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.288 + ./bwa mem -v 0 ref.fastq query.fastq.288 > query.fastq.288.sam 2> query.fastq.288.err + +query.fastq.289.sam query.fastq.289.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.289 + ./bwa mem -v 0 ref.fastq query.fastq.289 > query.fastq.289.sam 2> query.fastq.289.err + +query.fastq.290.sam query.fastq.290.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.290 + ./bwa mem -v 0 ref.fastq query.fastq.290 > query.fastq.290.sam 2> query.fastq.290.err + +query.fastq.291.sam query.fastq.291.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.291 + ./bwa mem -v 0 ref.fastq query.fastq.291 > query.fastq.291.sam 2> query.fastq.291.err + +query.fastq.292.sam query.fastq.292.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.292 + ./bwa mem -v 0 ref.fastq query.fastq.292 > query.fastq.292.sam 2> query.fastq.292.err + +query.fastq.293.sam query.fastq.293.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.293 + ./bwa mem -v 0 ref.fastq query.fastq.293 > query.fastq.293.sam 2> query.fastq.293.err + +query.fastq.294.sam query.fastq.294.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.294 + ./bwa mem -v 0 ref.fastq query.fastq.294 > query.fastq.294.sam 2> query.fastq.294.err + +query.fastq.295.sam query.fastq.295.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.295 + ./bwa mem -v 0 ref.fastq query.fastq.295 > query.fastq.295.sam 2> query.fastq.295.err + +query.fastq.296.sam query.fastq.296.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.296 + ./bwa mem -v 0 ref.fastq query.fastq.296 > query.fastq.296.sam 2> query.fastq.296.err + +query.fastq.297.sam query.fastq.297.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.297 + ./bwa mem -v 0 ref.fastq query.fastq.297 > query.fastq.297.sam 2> query.fastq.297.err + +query.fastq.298.sam query.fastq.298.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.298 + ./bwa mem -v 0 ref.fastq query.fastq.298 > query.fastq.298.sam 2> query.fastq.298.err + +query.fastq.299.sam query.fastq.299.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.299 + ./bwa mem -v 0 ref.fastq query.fastq.299 > query.fastq.299.sam 2> query.fastq.299.err + +query.fastq.300.sam query.fastq.300.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.300 + ./bwa mem -v 0 ref.fastq query.fastq.300 > query.fastq.300.sam 2> query.fastq.300.err + +query.fastq.301.sam query.fastq.301.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.301 + ./bwa mem -v 0 ref.fastq query.fastq.301 > query.fastq.301.sam 2> query.fastq.301.err + +query.fastq.302.sam query.fastq.302.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.302 + ./bwa mem -v 0 ref.fastq query.fastq.302 > query.fastq.302.sam 2> query.fastq.302.err + +query.fastq.303.sam query.fastq.303.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.303 + ./bwa mem -v 0 ref.fastq query.fastq.303 > query.fastq.303.sam 2> query.fastq.303.err + +query.fastq.304.sam query.fastq.304.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.304 + ./bwa mem -v 0 ref.fastq query.fastq.304 > query.fastq.304.sam 2> query.fastq.304.err + +query.fastq.305.sam query.fastq.305.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.305 + ./bwa mem -v 0 ref.fastq query.fastq.305 > query.fastq.305.sam 2> query.fastq.305.err + +query.fastq.306.sam query.fastq.306.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.306 + ./bwa mem -v 0 ref.fastq query.fastq.306 > query.fastq.306.sam 2> query.fastq.306.err + +query.fastq.307.sam query.fastq.307.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.307 + ./bwa mem -v 0 ref.fastq query.fastq.307 > query.fastq.307.sam 2> query.fastq.307.err + +query.fastq.308.sam query.fastq.308.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.308 + ./bwa mem -v 0 ref.fastq query.fastq.308 > query.fastq.308.sam 2> query.fastq.308.err + +query.fastq.309.sam query.fastq.309.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.309 + ./bwa mem -v 0 ref.fastq query.fastq.309 > query.fastq.309.sam 2> query.fastq.309.err + +query.fastq.310.sam query.fastq.310.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.310 + ./bwa mem -v 0 ref.fastq query.fastq.310 > query.fastq.310.sam 2> query.fastq.310.err + +query.fastq.311.sam query.fastq.311.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.311 + ./bwa mem -v 0 ref.fastq query.fastq.311 > query.fastq.311.sam 2> query.fastq.311.err + +query.fastq.312.sam query.fastq.312.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.312 + ./bwa mem -v 0 ref.fastq query.fastq.312 > query.fastq.312.sam 2> query.fastq.312.err + +query.fastq.313.sam query.fastq.313.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.313 + ./bwa mem -v 0 ref.fastq query.fastq.313 > query.fastq.313.sam 2> query.fastq.313.err + +query.fastq.314.sam query.fastq.314.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.314 + ./bwa mem -v 0 ref.fastq query.fastq.314 > query.fastq.314.sam 2> query.fastq.314.err + +query.fastq.315.sam query.fastq.315.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.315 + ./bwa mem -v 0 ref.fastq query.fastq.315 > query.fastq.315.sam 2> query.fastq.315.err + +query.fastq.316.sam query.fastq.316.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.316 + ./bwa mem -v 0 ref.fastq query.fastq.316 > query.fastq.316.sam 2> query.fastq.316.err + +query.fastq.317.sam query.fastq.317.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.317 + ./bwa mem -v 0 ref.fastq query.fastq.317 > query.fastq.317.sam 2> query.fastq.317.err + +query.fastq.318.sam query.fastq.318.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.318 + ./bwa mem -v 0 ref.fastq query.fastq.318 > query.fastq.318.sam 2> query.fastq.318.err + +query.fastq.319.sam query.fastq.319.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.319 + ./bwa mem -v 0 ref.fastq query.fastq.319 > query.fastq.319.sam 2> query.fastq.319.err + +query.fastq.320.sam query.fastq.320.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.320 + ./bwa mem -v 0 ref.fastq query.fastq.320 > query.fastq.320.sam 2> query.fastq.320.err + +query.fastq.321.sam query.fastq.321.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.321 + ./bwa mem -v 0 ref.fastq query.fastq.321 > query.fastq.321.sam 2> query.fastq.321.err + +query.fastq.322.sam query.fastq.322.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.322 + ./bwa mem -v 0 ref.fastq query.fastq.322 > query.fastq.322.sam 2> query.fastq.322.err + +query.fastq.323.sam query.fastq.323.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.323 + ./bwa mem -v 0 ref.fastq query.fastq.323 > query.fastq.323.sam 2> query.fastq.323.err + +query.fastq.324.sam query.fastq.324.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.324 + ./bwa mem -v 0 ref.fastq query.fastq.324 > query.fastq.324.sam 2> query.fastq.324.err + +query.fastq.325.sam query.fastq.325.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.325 + ./bwa mem -v 0 ref.fastq query.fastq.325 > query.fastq.325.sam 2> query.fastq.325.err + +query.fastq.326.sam query.fastq.326.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.326 + ./bwa mem -v 0 ref.fastq query.fastq.326 > query.fastq.326.sam 2> query.fastq.326.err + +query.fastq.327.sam query.fastq.327.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.327 + ./bwa mem -v 0 ref.fastq query.fastq.327 > query.fastq.327.sam 2> query.fastq.327.err + +query.fastq.328.sam query.fastq.328.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.328 + ./bwa mem -v 0 ref.fastq query.fastq.328 > query.fastq.328.sam 2> query.fastq.328.err + +query.fastq.329.sam query.fastq.329.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.329 + ./bwa mem -v 0 ref.fastq query.fastq.329 > query.fastq.329.sam 2> query.fastq.329.err + +query.fastq.330.sam query.fastq.330.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.330 + ./bwa mem -v 0 ref.fastq query.fastq.330 > query.fastq.330.sam 2> query.fastq.330.err + +query.fastq.331.sam query.fastq.331.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.331 + ./bwa mem -v 0 ref.fastq query.fastq.331 > query.fastq.331.sam 2> query.fastq.331.err + +query.fastq.332.sam query.fastq.332.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.332 + ./bwa mem -v 0 ref.fastq query.fastq.332 > query.fastq.332.sam 2> query.fastq.332.err + +query.fastq.333.sam query.fastq.333.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.333 + ./bwa mem -v 0 ref.fastq query.fastq.333 > query.fastq.333.sam 2> query.fastq.333.err + +query.fastq.334.sam query.fastq.334.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.334 + ./bwa mem -v 0 ref.fastq query.fastq.334 > query.fastq.334.sam 2> query.fastq.334.err + +query.fastq.335.sam query.fastq.335.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.335 + ./bwa mem -v 0 ref.fastq query.fastq.335 > query.fastq.335.sam 2> query.fastq.335.err + +query.fastq.336.sam query.fastq.336.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.336 + ./bwa mem -v 0 ref.fastq query.fastq.336 > query.fastq.336.sam 2> query.fastq.336.err + +query.fastq.337.sam query.fastq.337.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.337 + ./bwa mem -v 0 ref.fastq query.fastq.337 > query.fastq.337.sam 2> query.fastq.337.err + +query.fastq.338.sam query.fastq.338.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.338 + ./bwa mem -v 0 ref.fastq query.fastq.338 > query.fastq.338.sam 2> query.fastq.338.err + +query.fastq.339.sam query.fastq.339.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.339 + ./bwa mem -v 0 ref.fastq query.fastq.339 > query.fastq.339.sam 2> query.fastq.339.err + +query.fastq.340.sam query.fastq.340.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.340 + ./bwa mem -v 0 ref.fastq query.fastq.340 > query.fastq.340.sam 2> query.fastq.340.err + +query.fastq.341.sam query.fastq.341.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.341 + ./bwa mem -v 0 ref.fastq query.fastq.341 > query.fastq.341.sam 2> query.fastq.341.err + +query.fastq.342.sam query.fastq.342.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.342 + ./bwa mem -v 0 ref.fastq query.fastq.342 > query.fastq.342.sam 2> query.fastq.342.err + +query.fastq.343.sam query.fastq.343.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.343 + ./bwa mem -v 0 ref.fastq query.fastq.343 > query.fastq.343.sam 2> query.fastq.343.err + +query.fastq.344.sam query.fastq.344.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.344 + ./bwa mem -v 0 ref.fastq query.fastq.344 > query.fastq.344.sam 2> query.fastq.344.err + +query.fastq.345.sam query.fastq.345.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.345 + ./bwa mem -v 0 ref.fastq query.fastq.345 > query.fastq.345.sam 2> query.fastq.345.err + +query.fastq.346.sam query.fastq.346.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.346 + ./bwa mem -v 0 ref.fastq query.fastq.346 > query.fastq.346.sam 2> query.fastq.346.err + +query.fastq.347.sam query.fastq.347.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.347 + ./bwa mem -v 0 ref.fastq query.fastq.347 > query.fastq.347.sam 2> query.fastq.347.err + +query.fastq.348.sam query.fastq.348.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.348 + ./bwa mem -v 0 ref.fastq query.fastq.348 > query.fastq.348.sam 2> query.fastq.348.err + +query.fastq.349.sam query.fastq.349.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.349 + ./bwa mem -v 0 ref.fastq query.fastq.349 > query.fastq.349.sam 2> query.fastq.349.err + +query.fastq.350.sam query.fastq.350.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.350 + ./bwa mem -v 0 ref.fastq query.fastq.350 > query.fastq.350.sam 2> query.fastq.350.err + +query.fastq.351.sam query.fastq.351.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.351 + ./bwa mem -v 0 ref.fastq query.fastq.351 > query.fastq.351.sam 2> query.fastq.351.err + +query.fastq.352.sam query.fastq.352.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.352 + ./bwa mem -v 0 ref.fastq query.fastq.352 > query.fastq.352.sam 2> query.fastq.352.err + +query.fastq.353.sam query.fastq.353.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.353 + ./bwa mem -v 0 ref.fastq query.fastq.353 > query.fastq.353.sam 2> query.fastq.353.err + +query.fastq.354.sam query.fastq.354.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.354 + ./bwa mem -v 0 ref.fastq query.fastq.354 > query.fastq.354.sam 2> query.fastq.354.err + +query.fastq.355.sam query.fastq.355.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.355 + ./bwa mem -v 0 ref.fastq query.fastq.355 > query.fastq.355.sam 2> query.fastq.355.err + +query.fastq.356.sam query.fastq.356.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.356 + ./bwa mem -v 0 ref.fastq query.fastq.356 > query.fastq.356.sam 2> query.fastq.356.err + +query.fastq.357.sam query.fastq.357.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.357 + ./bwa mem -v 0 ref.fastq query.fastq.357 > query.fastq.357.sam 2> query.fastq.357.err + +query.fastq.358.sam query.fastq.358.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.358 + ./bwa mem -v 0 ref.fastq query.fastq.358 > query.fastq.358.sam 2> query.fastq.358.err + +query.fastq.359.sam query.fastq.359.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.359 + ./bwa mem -v 0 ref.fastq query.fastq.359 > query.fastq.359.sam 2> query.fastq.359.err + +query.fastq.360.sam query.fastq.360.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.360 + ./bwa mem -v 0 ref.fastq query.fastq.360 > query.fastq.360.sam 2> query.fastq.360.err + +query.fastq.361.sam query.fastq.361.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.361 + ./bwa mem -v 0 ref.fastq query.fastq.361 > query.fastq.361.sam 2> query.fastq.361.err + +query.fastq.362.sam query.fastq.362.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.362 + ./bwa mem -v 0 ref.fastq query.fastq.362 > query.fastq.362.sam 2> query.fastq.362.err + +query.fastq.363.sam query.fastq.363.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.363 + ./bwa mem -v 0 ref.fastq query.fastq.363 > query.fastq.363.sam 2> query.fastq.363.err + +query.fastq.364.sam query.fastq.364.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.364 + ./bwa mem -v 0 ref.fastq query.fastq.364 > query.fastq.364.sam 2> query.fastq.364.err + +query.fastq.365.sam query.fastq.365.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.365 + ./bwa mem -v 0 ref.fastq query.fastq.365 > query.fastq.365.sam 2> query.fastq.365.err + +query.fastq.366.sam query.fastq.366.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.366 + ./bwa mem -v 0 ref.fastq query.fastq.366 > query.fastq.366.sam 2> query.fastq.366.err + +query.fastq.367.sam query.fastq.367.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.367 + ./bwa mem -v 0 ref.fastq query.fastq.367 > query.fastq.367.sam 2> query.fastq.367.err + +query.fastq.368.sam query.fastq.368.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.368 + ./bwa mem -v 0 ref.fastq query.fastq.368 > query.fastq.368.sam 2> query.fastq.368.err + +query.fastq.369.sam query.fastq.369.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.369 + ./bwa mem -v 0 ref.fastq query.fastq.369 > query.fastq.369.sam 2> query.fastq.369.err + +query.fastq.370.sam query.fastq.370.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.370 + ./bwa mem -v 0 ref.fastq query.fastq.370 > query.fastq.370.sam 2> query.fastq.370.err + +query.fastq.371.sam query.fastq.371.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.371 + ./bwa mem -v 0 ref.fastq query.fastq.371 > query.fastq.371.sam 2> query.fastq.371.err + +query.fastq.372.sam query.fastq.372.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.372 + ./bwa mem -v 0 ref.fastq query.fastq.372 > query.fastq.372.sam 2> query.fastq.372.err + +query.fastq.373.sam query.fastq.373.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.373 + ./bwa mem -v 0 ref.fastq query.fastq.373 > query.fastq.373.sam 2> query.fastq.373.err + +query.fastq.374.sam query.fastq.374.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.374 + ./bwa mem -v 0 ref.fastq query.fastq.374 > query.fastq.374.sam 2> query.fastq.374.err + +query.fastq.375.sam query.fastq.375.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.375 + ./bwa mem -v 0 ref.fastq query.fastq.375 > query.fastq.375.sam 2> query.fastq.375.err + +query.fastq.376.sam query.fastq.376.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.376 + ./bwa mem -v 0 ref.fastq query.fastq.376 > query.fastq.376.sam 2> query.fastq.376.err + +query.fastq.377.sam query.fastq.377.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.377 + ./bwa mem -v 0 ref.fastq query.fastq.377 > query.fastq.377.sam 2> query.fastq.377.err + +query.fastq.378.sam query.fastq.378.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.378 + ./bwa mem -v 0 ref.fastq query.fastq.378 > query.fastq.378.sam 2> query.fastq.378.err + +query.fastq.379.sam query.fastq.379.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.379 + ./bwa mem -v 0 ref.fastq query.fastq.379 > query.fastq.379.sam 2> query.fastq.379.err + +query.fastq.380.sam query.fastq.380.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.380 + ./bwa mem -v 0 ref.fastq query.fastq.380 > query.fastq.380.sam 2> query.fastq.380.err + +query.fastq.381.sam query.fastq.381.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.381 + ./bwa mem -v 0 ref.fastq query.fastq.381 > query.fastq.381.sam 2> query.fastq.381.err + +query.fastq.382.sam query.fastq.382.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.382 + ./bwa mem -v 0 ref.fastq query.fastq.382 > query.fastq.382.sam 2> query.fastq.382.err + +query.fastq.383.sam query.fastq.383.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.383 + ./bwa mem -v 0 ref.fastq query.fastq.383 > query.fastq.383.sam 2> query.fastq.383.err + +query.fastq.384.sam query.fastq.384.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.384 + ./bwa mem -v 0 ref.fastq query.fastq.384 > query.fastq.384.sam 2> query.fastq.384.err + +query.fastq.385.sam query.fastq.385.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.385 + ./bwa mem -v 0 ref.fastq query.fastq.385 > query.fastq.385.sam 2> query.fastq.385.err + +query.fastq.386.sam query.fastq.386.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.386 + ./bwa mem -v 0 ref.fastq query.fastq.386 > query.fastq.386.sam 2> query.fastq.386.err + +query.fastq.387.sam query.fastq.387.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.387 + ./bwa mem -v 0 ref.fastq query.fastq.387 > query.fastq.387.sam 2> query.fastq.387.err + +query.fastq.388.sam query.fastq.388.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.388 + ./bwa mem -v 0 ref.fastq query.fastq.388 > query.fastq.388.sam 2> query.fastq.388.err + +query.fastq.389.sam query.fastq.389.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.389 + ./bwa mem -v 0 ref.fastq query.fastq.389 > query.fastq.389.sam 2> query.fastq.389.err + +query.fastq.390.sam query.fastq.390.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.390 + ./bwa mem -v 0 ref.fastq query.fastq.390 > query.fastq.390.sam 2> query.fastq.390.err + +query.fastq.391.sam query.fastq.391.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.391 + ./bwa mem -v 0 ref.fastq query.fastq.391 > query.fastq.391.sam 2> query.fastq.391.err + +query.fastq.392.sam query.fastq.392.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.392 + ./bwa mem -v 0 ref.fastq query.fastq.392 > query.fastq.392.sam 2> query.fastq.392.err + +query.fastq.393.sam query.fastq.393.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.393 + ./bwa mem -v 0 ref.fastq query.fastq.393 > query.fastq.393.sam 2> query.fastq.393.err + +query.fastq.394.sam query.fastq.394.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.394 + ./bwa mem -v 0 ref.fastq query.fastq.394 > query.fastq.394.sam 2> query.fastq.394.err + +query.fastq.395.sam query.fastq.395.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.395 + ./bwa mem -v 0 ref.fastq query.fastq.395 > query.fastq.395.sam 2> query.fastq.395.err + +query.fastq.396.sam query.fastq.396.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.396 + ./bwa mem -v 0 ref.fastq query.fastq.396 > query.fastq.396.sam 2> query.fastq.396.err + +query.fastq.397.sam query.fastq.397.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.397 + ./bwa mem -v 0 ref.fastq query.fastq.397 > query.fastq.397.sam 2> query.fastq.397.err + +query.fastq.398.sam query.fastq.398.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.398 + ./bwa mem -v 0 ref.fastq query.fastq.398 > query.fastq.398.sam 2> query.fastq.398.err + +query.fastq.399.sam query.fastq.399.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.399 + ./bwa mem -v 0 ref.fastq query.fastq.399 > query.fastq.399.sam 2> query.fastq.399.err + +query.fastq.400.sam query.fastq.400.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.400 + ./bwa mem -v 0 ref.fastq query.fastq.400 > query.fastq.400.sam 2> query.fastq.400.err + +query.fastq.401.sam query.fastq.401.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.401 + ./bwa mem -v 0 ref.fastq query.fastq.401 > query.fastq.401.sam 2> query.fastq.401.err + +query.fastq.402.sam query.fastq.402.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.402 + ./bwa mem -v 0 ref.fastq query.fastq.402 > query.fastq.402.sam 2> query.fastq.402.err + +query.fastq.403.sam query.fastq.403.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.403 + ./bwa mem -v 0 ref.fastq query.fastq.403 > query.fastq.403.sam 2> query.fastq.403.err + +query.fastq.404.sam query.fastq.404.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.404 + ./bwa mem -v 0 ref.fastq query.fastq.404 > query.fastq.404.sam 2> query.fastq.404.err + +query.fastq.405.sam query.fastq.405.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.405 + ./bwa mem -v 0 ref.fastq query.fastq.405 > query.fastq.405.sam 2> query.fastq.405.err + +query.fastq.406.sam query.fastq.406.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.406 + ./bwa mem -v 0 ref.fastq query.fastq.406 > query.fastq.406.sam 2> query.fastq.406.err + +query.fastq.407.sam query.fastq.407.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.407 + ./bwa mem -v 0 ref.fastq query.fastq.407 > query.fastq.407.sam 2> query.fastq.407.err + +query.fastq.408.sam query.fastq.408.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.408 + ./bwa mem -v 0 ref.fastq query.fastq.408 > query.fastq.408.sam 2> query.fastq.408.err + +query.fastq.409.sam query.fastq.409.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.409 + ./bwa mem -v 0 ref.fastq query.fastq.409 > query.fastq.409.sam 2> query.fastq.409.err + +query.fastq.410.sam query.fastq.410.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.410 + ./bwa mem -v 0 ref.fastq query.fastq.410 > query.fastq.410.sam 2> query.fastq.410.err + +query.fastq.411.sam query.fastq.411.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.411 + ./bwa mem -v 0 ref.fastq query.fastq.411 > query.fastq.411.sam 2> query.fastq.411.err + +query.fastq.412.sam query.fastq.412.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.412 + ./bwa mem -v 0 ref.fastq query.fastq.412 > query.fastq.412.sam 2> query.fastq.412.err + +query.fastq.413.sam query.fastq.413.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.413 + ./bwa mem -v 0 ref.fastq query.fastq.413 > query.fastq.413.sam 2> query.fastq.413.err + +query.fastq.414.sam query.fastq.414.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.414 + ./bwa mem -v 0 ref.fastq query.fastq.414 > query.fastq.414.sam 2> query.fastq.414.err + +query.fastq.415.sam query.fastq.415.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.415 + ./bwa mem -v 0 ref.fastq query.fastq.415 > query.fastq.415.sam 2> query.fastq.415.err + +query.fastq.416.sam query.fastq.416.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.416 + ./bwa mem -v 0 ref.fastq query.fastq.416 > query.fastq.416.sam 2> query.fastq.416.err + +query.fastq.417.sam query.fastq.417.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.417 + ./bwa mem -v 0 ref.fastq query.fastq.417 > query.fastq.417.sam 2> query.fastq.417.err + +query.fastq.418.sam query.fastq.418.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.418 + ./bwa mem -v 0 ref.fastq query.fastq.418 > query.fastq.418.sam 2> query.fastq.418.err + +query.fastq.419.sam query.fastq.419.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.419 + ./bwa mem -v 0 ref.fastq query.fastq.419 > query.fastq.419.sam 2> query.fastq.419.err + +query.fastq.420.sam query.fastq.420.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.420 + ./bwa mem -v 0 ref.fastq query.fastq.420 > query.fastq.420.sam 2> query.fastq.420.err + +query.fastq.421.sam query.fastq.421.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.421 + ./bwa mem -v 0 ref.fastq query.fastq.421 > query.fastq.421.sam 2> query.fastq.421.err + +query.fastq.422.sam query.fastq.422.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.422 + ./bwa mem -v 0 ref.fastq query.fastq.422 > query.fastq.422.sam 2> query.fastq.422.err + +query.fastq.423.sam query.fastq.423.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.423 + ./bwa mem -v 0 ref.fastq query.fastq.423 > query.fastq.423.sam 2> query.fastq.423.err + +query.fastq.424.sam query.fastq.424.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.424 + ./bwa mem -v 0 ref.fastq query.fastq.424 > query.fastq.424.sam 2> query.fastq.424.err + +query.fastq.425.sam query.fastq.425.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.425 + ./bwa mem -v 0 ref.fastq query.fastq.425 > query.fastq.425.sam 2> query.fastq.425.err + +query.fastq.426.sam query.fastq.426.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.426 + ./bwa mem -v 0 ref.fastq query.fastq.426 > query.fastq.426.sam 2> query.fastq.426.err + +query.fastq.427.sam query.fastq.427.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.427 + ./bwa mem -v 0 ref.fastq query.fastq.427 > query.fastq.427.sam 2> query.fastq.427.err + +query.fastq.428.sam query.fastq.428.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.428 + ./bwa mem -v 0 ref.fastq query.fastq.428 > query.fastq.428.sam 2> query.fastq.428.err + +query.fastq.429.sam query.fastq.429.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.429 + ./bwa mem -v 0 ref.fastq query.fastq.429 > query.fastq.429.sam 2> query.fastq.429.err + +query.fastq.430.sam query.fastq.430.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.430 + ./bwa mem -v 0 ref.fastq query.fastq.430 > query.fastq.430.sam 2> query.fastq.430.err + +query.fastq.431.sam query.fastq.431.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.431 + ./bwa mem -v 0 ref.fastq query.fastq.431 > query.fastq.431.sam 2> query.fastq.431.err + +query.fastq.432.sam query.fastq.432.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.432 + ./bwa mem -v 0 ref.fastq query.fastq.432 > query.fastq.432.sam 2> query.fastq.432.err + +query.fastq.433.sam query.fastq.433.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.433 + ./bwa mem -v 0 ref.fastq query.fastq.433 > query.fastq.433.sam 2> query.fastq.433.err + +query.fastq.434.sam query.fastq.434.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.434 + ./bwa mem -v 0 ref.fastq query.fastq.434 > query.fastq.434.sam 2> query.fastq.434.err + +query.fastq.435.sam query.fastq.435.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.435 + ./bwa mem -v 0 ref.fastq query.fastq.435 > query.fastq.435.sam 2> query.fastq.435.err + +query.fastq.436.sam query.fastq.436.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.436 + ./bwa mem -v 0 ref.fastq query.fastq.436 > query.fastq.436.sam 2> query.fastq.436.err + +query.fastq.437.sam query.fastq.437.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.437 + ./bwa mem -v 0 ref.fastq query.fastq.437 > query.fastq.437.sam 2> query.fastq.437.err + +query.fastq.438.sam query.fastq.438.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.438 + ./bwa mem -v 0 ref.fastq query.fastq.438 > query.fastq.438.sam 2> query.fastq.438.err + +query.fastq.439.sam query.fastq.439.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.439 + ./bwa mem -v 0 ref.fastq query.fastq.439 > query.fastq.439.sam 2> query.fastq.439.err + +query.fastq.440.sam query.fastq.440.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.440 + ./bwa mem -v 0 ref.fastq query.fastq.440 > query.fastq.440.sam 2> query.fastq.440.err + +query.fastq.441.sam query.fastq.441.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.441 + ./bwa mem -v 0 ref.fastq query.fastq.441 > query.fastq.441.sam 2> query.fastq.441.err + +query.fastq.442.sam query.fastq.442.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.442 + ./bwa mem -v 0 ref.fastq query.fastq.442 > query.fastq.442.sam 2> query.fastq.442.err + +query.fastq.443.sam query.fastq.443.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.443 + ./bwa mem -v 0 ref.fastq query.fastq.443 > query.fastq.443.sam 2> query.fastq.443.err + +query.fastq.444.sam query.fastq.444.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.444 + ./bwa mem -v 0 ref.fastq query.fastq.444 > query.fastq.444.sam 2> query.fastq.444.err + +query.fastq.445.sam query.fastq.445.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.445 + ./bwa mem -v 0 ref.fastq query.fastq.445 > query.fastq.445.sam 2> query.fastq.445.err + +query.fastq.446.sam query.fastq.446.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.446 + ./bwa mem -v 0 ref.fastq query.fastq.446 > query.fastq.446.sam 2> query.fastq.446.err + +query.fastq.447.sam query.fastq.447.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.447 + ./bwa mem -v 0 ref.fastq query.fastq.447 > query.fastq.447.sam 2> query.fastq.447.err + +query.fastq.448.sam query.fastq.448.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.448 + ./bwa mem -v 0 ref.fastq query.fastq.448 > query.fastq.448.sam 2> query.fastq.448.err + +query.fastq.449.sam query.fastq.449.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.449 + ./bwa mem -v 0 ref.fastq query.fastq.449 > query.fastq.449.sam 2> query.fastq.449.err + +query.fastq.450.sam query.fastq.450.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.450 + ./bwa mem -v 0 ref.fastq query.fastq.450 > query.fastq.450.sam 2> query.fastq.450.err + +query.fastq.451.sam query.fastq.451.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.451 + ./bwa mem -v 0 ref.fastq query.fastq.451 > query.fastq.451.sam 2> query.fastq.451.err + +query.fastq.452.sam query.fastq.452.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.452 + ./bwa mem -v 0 ref.fastq query.fastq.452 > query.fastq.452.sam 2> query.fastq.452.err + +query.fastq.453.sam query.fastq.453.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.453 + ./bwa mem -v 0 ref.fastq query.fastq.453 > query.fastq.453.sam 2> query.fastq.453.err + +query.fastq.454.sam query.fastq.454.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.454 + ./bwa mem -v 0 ref.fastq query.fastq.454 > query.fastq.454.sam 2> query.fastq.454.err + +query.fastq.455.sam query.fastq.455.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.455 + ./bwa mem -v 0 ref.fastq query.fastq.455 > query.fastq.455.sam 2> query.fastq.455.err + +query.fastq.456.sam query.fastq.456.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.456 + ./bwa mem -v 0 ref.fastq query.fastq.456 > query.fastq.456.sam 2> query.fastq.456.err + +query.fastq.457.sam query.fastq.457.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.457 + ./bwa mem -v 0 ref.fastq query.fastq.457 > query.fastq.457.sam 2> query.fastq.457.err + +query.fastq.458.sam query.fastq.458.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.458 + ./bwa mem -v 0 ref.fastq query.fastq.458 > query.fastq.458.sam 2> query.fastq.458.err + +query.fastq.459.sam query.fastq.459.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.459 + ./bwa mem -v 0 ref.fastq query.fastq.459 > query.fastq.459.sam 2> query.fastq.459.err + +query.fastq.460.sam query.fastq.460.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.460 + ./bwa mem -v 0 ref.fastq query.fastq.460 > query.fastq.460.sam 2> query.fastq.460.err + +query.fastq.461.sam query.fastq.461.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.461 + ./bwa mem -v 0 ref.fastq query.fastq.461 > query.fastq.461.sam 2> query.fastq.461.err + +query.fastq.462.sam query.fastq.462.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.462 + ./bwa mem -v 0 ref.fastq query.fastq.462 > query.fastq.462.sam 2> query.fastq.462.err + +query.fastq.463.sam query.fastq.463.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.463 + ./bwa mem -v 0 ref.fastq query.fastq.463 > query.fastq.463.sam 2> query.fastq.463.err + +query.fastq.464.sam query.fastq.464.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.464 + ./bwa mem -v 0 ref.fastq query.fastq.464 > query.fastq.464.sam 2> query.fastq.464.err + +query.fastq.465.sam query.fastq.465.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.465 + ./bwa mem -v 0 ref.fastq query.fastq.465 > query.fastq.465.sam 2> query.fastq.465.err + +query.fastq.466.sam query.fastq.466.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.466 + ./bwa mem -v 0 ref.fastq query.fastq.466 > query.fastq.466.sam 2> query.fastq.466.err + +query.fastq.467.sam query.fastq.467.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.467 + ./bwa mem -v 0 ref.fastq query.fastq.467 > query.fastq.467.sam 2> query.fastq.467.err + +query.fastq.468.sam query.fastq.468.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.468 + ./bwa mem -v 0 ref.fastq query.fastq.468 > query.fastq.468.sam 2> query.fastq.468.err + +query.fastq.469.sam query.fastq.469.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.469 + ./bwa mem -v 0 ref.fastq query.fastq.469 > query.fastq.469.sam 2> query.fastq.469.err + +query.fastq.470.sam query.fastq.470.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.470 + ./bwa mem -v 0 ref.fastq query.fastq.470 > query.fastq.470.sam 2> query.fastq.470.err + +query.fastq.471.sam query.fastq.471.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.471 + ./bwa mem -v 0 ref.fastq query.fastq.471 > query.fastq.471.sam 2> query.fastq.471.err + +query.fastq.472.sam query.fastq.472.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.472 + ./bwa mem -v 0 ref.fastq query.fastq.472 > query.fastq.472.sam 2> query.fastq.472.err + +query.fastq.473.sam query.fastq.473.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.473 + ./bwa mem -v 0 ref.fastq query.fastq.473 > query.fastq.473.sam 2> query.fastq.473.err + +query.fastq.474.sam query.fastq.474.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.474 + ./bwa mem -v 0 ref.fastq query.fastq.474 > query.fastq.474.sam 2> query.fastq.474.err + +query.fastq.475.sam query.fastq.475.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.475 + ./bwa mem -v 0 ref.fastq query.fastq.475 > query.fastq.475.sam 2> query.fastq.475.err + +query.fastq.476.sam query.fastq.476.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.476 + ./bwa mem -v 0 ref.fastq query.fastq.476 > query.fastq.476.sam 2> query.fastq.476.err + +query.fastq.477.sam query.fastq.477.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.477 + ./bwa mem -v 0 ref.fastq query.fastq.477 > query.fastq.477.sam 2> query.fastq.477.err + +query.fastq.478.sam query.fastq.478.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.478 + ./bwa mem -v 0 ref.fastq query.fastq.478 > query.fastq.478.sam 2> query.fastq.478.err + +query.fastq.479.sam query.fastq.479.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.479 + ./bwa mem -v 0 ref.fastq query.fastq.479 > query.fastq.479.sam 2> query.fastq.479.err + +query.fastq.480.sam query.fastq.480.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.480 + ./bwa mem -v 0 ref.fastq query.fastq.480 > query.fastq.480.sam 2> query.fastq.480.err + +query.fastq.481.sam query.fastq.481.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.481 + ./bwa mem -v 0 ref.fastq query.fastq.481 > query.fastq.481.sam 2> query.fastq.481.err + +query.fastq.482.sam query.fastq.482.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.482 + ./bwa mem -v 0 ref.fastq query.fastq.482 > query.fastq.482.sam 2> query.fastq.482.err + +query.fastq.483.sam query.fastq.483.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.483 + ./bwa mem -v 0 ref.fastq query.fastq.483 > query.fastq.483.sam 2> query.fastq.483.err + +query.fastq.484.sam query.fastq.484.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.484 + ./bwa mem -v 0 ref.fastq query.fastq.484 > query.fastq.484.sam 2> query.fastq.484.err + +query.fastq.485.sam query.fastq.485.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.485 + ./bwa mem -v 0 ref.fastq query.fastq.485 > query.fastq.485.sam 2> query.fastq.485.err + +query.fastq.486.sam query.fastq.486.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.486 + ./bwa mem -v 0 ref.fastq query.fastq.486 > query.fastq.486.sam 2> query.fastq.486.err + +query.fastq.487.sam query.fastq.487.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.487 + ./bwa mem -v 0 ref.fastq query.fastq.487 > query.fastq.487.sam 2> query.fastq.487.err + +query.fastq.488.sam query.fastq.488.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.488 + ./bwa mem -v 0 ref.fastq query.fastq.488 > query.fastq.488.sam 2> query.fastq.488.err + +query.fastq.489.sam query.fastq.489.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.489 + ./bwa mem -v 0 ref.fastq query.fastq.489 > query.fastq.489.sam 2> query.fastq.489.err + +query.fastq.490.sam query.fastq.490.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.490 + ./bwa mem -v 0 ref.fastq query.fastq.490 > query.fastq.490.sam 2> query.fastq.490.err + +query.fastq.491.sam query.fastq.491.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.491 + ./bwa mem -v 0 ref.fastq query.fastq.491 > query.fastq.491.sam 2> query.fastq.491.err + +query.fastq.492.sam query.fastq.492.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.492 + ./bwa mem -v 0 ref.fastq query.fastq.492 > query.fastq.492.sam 2> query.fastq.492.err + +query.fastq.493.sam query.fastq.493.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.493 + ./bwa mem -v 0 ref.fastq query.fastq.493 > query.fastq.493.sam 2> query.fastq.493.err + +query.fastq.494.sam query.fastq.494.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.494 + ./bwa mem -v 0 ref.fastq query.fastq.494 > query.fastq.494.sam 2> query.fastq.494.err + +query.fastq.495.sam query.fastq.495.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.495 + ./bwa mem -v 0 ref.fastq query.fastq.495 > query.fastq.495.sam 2> query.fastq.495.err + +query.fastq.496.sam query.fastq.496.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.496 + ./bwa mem -v 0 ref.fastq query.fastq.496 > query.fastq.496.sam 2> query.fastq.496.err + +query.fastq.497.sam query.fastq.497.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.497 + ./bwa mem -v 0 ref.fastq query.fastq.497 > query.fastq.497.sam 2> query.fastq.497.err + +query.fastq.498.sam query.fastq.498.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.498 + ./bwa mem -v 0 ref.fastq query.fastq.498 > query.fastq.498.sam 2> query.fastq.498.err + +query.fastq.499.sam query.fastq.499.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.499 + ./bwa mem -v 0 ref.fastq query.fastq.499 > query.fastq.499.sam 2> query.fastq.499.err + +query.fastq.500.sam query.fastq.500.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.500 + ./bwa mem -v 0 ref.fastq query.fastq.500 > query.fastq.500.sam 2> query.fastq.500.err + +query.fastq.501.sam query.fastq.501.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.501 + ./bwa mem -v 0 ref.fastq query.fastq.501 > query.fastq.501.sam 2> query.fastq.501.err + +query.fastq.502.sam query.fastq.502.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.502 + ./bwa mem -v 0 ref.fastq query.fastq.502 > query.fastq.502.sam 2> query.fastq.502.err + +query.fastq.503.sam query.fastq.503.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.503 + ./bwa mem -v 0 ref.fastq query.fastq.503 > query.fastq.503.sam 2> query.fastq.503.err + +query.fastq.504.sam query.fastq.504.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.504 + ./bwa mem -v 0 ref.fastq query.fastq.504 > query.fastq.504.sam 2> query.fastq.504.err + +query.fastq.505.sam query.fastq.505.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.505 + ./bwa mem -v 0 ref.fastq query.fastq.505 > query.fastq.505.sam 2> query.fastq.505.err + +query.fastq.506.sam query.fastq.506.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.506 + ./bwa mem -v 0 ref.fastq query.fastq.506 > query.fastq.506.sam 2> query.fastq.506.err + +query.fastq.507.sam query.fastq.507.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.507 + ./bwa mem -v 0 ref.fastq query.fastq.507 > query.fastq.507.sam 2> query.fastq.507.err + +query.fastq.508.sam query.fastq.508.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.508 + ./bwa mem -v 0 ref.fastq query.fastq.508 > query.fastq.508.sam 2> query.fastq.508.err + +query.fastq.509.sam query.fastq.509.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.509 + ./bwa mem -v 0 ref.fastq query.fastq.509 > query.fastq.509.sam 2> query.fastq.509.err + +query.fastq.510.sam query.fastq.510.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.510 + ./bwa mem -v 0 ref.fastq query.fastq.510 > query.fastq.510.sam 2> query.fastq.510.err + +query.fastq.511.sam query.fastq.511.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.511 + ./bwa mem -v 0 ref.fastq query.fastq.511 > query.fastq.511.sam 2> query.fastq.511.err + +query.fastq.512.sam query.fastq.512.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.512 + ./bwa mem -v 0 ref.fastq query.fastq.512 > query.fastq.512.sam 2> query.fastq.512.err + +query.fastq.513.sam query.fastq.513.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.513 + ./bwa mem -v 0 ref.fastq query.fastq.513 > query.fastq.513.sam 2> query.fastq.513.err + +query.fastq.514.sam query.fastq.514.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.514 + ./bwa mem -v 0 ref.fastq query.fastq.514 > query.fastq.514.sam 2> query.fastq.514.err + +query.fastq.515.sam query.fastq.515.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.515 + ./bwa mem -v 0 ref.fastq query.fastq.515 > query.fastq.515.sam 2> query.fastq.515.err + +query.fastq.516.sam query.fastq.516.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.516 + ./bwa mem -v 0 ref.fastq query.fastq.516 > query.fastq.516.sam 2> query.fastq.516.err + +query.fastq.517.sam query.fastq.517.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.517 + ./bwa mem -v 0 ref.fastq query.fastq.517 > query.fastq.517.sam 2> query.fastq.517.err + +query.fastq.518.sam query.fastq.518.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.518 + ./bwa mem -v 0 ref.fastq query.fastq.518 > query.fastq.518.sam 2> query.fastq.518.err + +query.fastq.519.sam query.fastq.519.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.519 + ./bwa mem -v 0 ref.fastq query.fastq.519 > query.fastq.519.sam 2> query.fastq.519.err + +query.fastq.520.sam query.fastq.520.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.520 + ./bwa mem -v 0 ref.fastq query.fastq.520 > query.fastq.520.sam 2> query.fastq.520.err + +query.fastq.521.sam query.fastq.521.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.521 + ./bwa mem -v 0 ref.fastq query.fastq.521 > query.fastq.521.sam 2> query.fastq.521.err + +query.fastq.522.sam query.fastq.522.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.522 + ./bwa mem -v 0 ref.fastq query.fastq.522 > query.fastq.522.sam 2> query.fastq.522.err + +query.fastq.523.sam query.fastq.523.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.523 + ./bwa mem -v 0 ref.fastq query.fastq.523 > query.fastq.523.sam 2> query.fastq.523.err + +query.fastq.524.sam query.fastq.524.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.524 + ./bwa mem -v 0 ref.fastq query.fastq.524 > query.fastq.524.sam 2> query.fastq.524.err + +query.fastq.525.sam query.fastq.525.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.525 + ./bwa mem -v 0 ref.fastq query.fastq.525 > query.fastq.525.sam 2> query.fastq.525.err + +query.fastq.526.sam query.fastq.526.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.526 + ./bwa mem -v 0 ref.fastq query.fastq.526 > query.fastq.526.sam 2> query.fastq.526.err + +query.fastq.527.sam query.fastq.527.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.527 + ./bwa mem -v 0 ref.fastq query.fastq.527 > query.fastq.527.sam 2> query.fastq.527.err + +query.fastq.528.sam query.fastq.528.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.528 + ./bwa mem -v 0 ref.fastq query.fastq.528 > query.fastq.528.sam 2> query.fastq.528.err + +query.fastq.529.sam query.fastq.529.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.529 + ./bwa mem -v 0 ref.fastq query.fastq.529 > query.fastq.529.sam 2> query.fastq.529.err + +query.fastq.530.sam query.fastq.530.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.530 + ./bwa mem -v 0 ref.fastq query.fastq.530 > query.fastq.530.sam 2> query.fastq.530.err + +query.fastq.531.sam query.fastq.531.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.531 + ./bwa mem -v 0 ref.fastq query.fastq.531 > query.fastq.531.sam 2> query.fastq.531.err + +query.fastq.532.sam query.fastq.532.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.532 + ./bwa mem -v 0 ref.fastq query.fastq.532 > query.fastq.532.sam 2> query.fastq.532.err + +query.fastq.533.sam query.fastq.533.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.533 + ./bwa mem -v 0 ref.fastq query.fastq.533 > query.fastq.533.sam 2> query.fastq.533.err + +query.fastq.534.sam query.fastq.534.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.534 + ./bwa mem -v 0 ref.fastq query.fastq.534 > query.fastq.534.sam 2> query.fastq.534.err + +query.fastq.535.sam query.fastq.535.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.535 + ./bwa mem -v 0 ref.fastq query.fastq.535 > query.fastq.535.sam 2> query.fastq.535.err + +query.fastq.536.sam query.fastq.536.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.536 + ./bwa mem -v 0 ref.fastq query.fastq.536 > query.fastq.536.sam 2> query.fastq.536.err + +query.fastq.537.sam query.fastq.537.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.537 + ./bwa mem -v 0 ref.fastq query.fastq.537 > query.fastq.537.sam 2> query.fastq.537.err + +query.fastq.538.sam query.fastq.538.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.538 + ./bwa mem -v 0 ref.fastq query.fastq.538 > query.fastq.538.sam 2> query.fastq.538.err + +query.fastq.539.sam query.fastq.539.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.539 + ./bwa mem -v 0 ref.fastq query.fastq.539 > query.fastq.539.sam 2> query.fastq.539.err + +query.fastq.540.sam query.fastq.540.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.540 + ./bwa mem -v 0 ref.fastq query.fastq.540 > query.fastq.540.sam 2> query.fastq.540.err + +query.fastq.541.sam query.fastq.541.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.541 + ./bwa mem -v 0 ref.fastq query.fastq.541 > query.fastq.541.sam 2> query.fastq.541.err + +query.fastq.542.sam query.fastq.542.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.542 + ./bwa mem -v 0 ref.fastq query.fastq.542 > query.fastq.542.sam 2> query.fastq.542.err + +query.fastq.543.sam query.fastq.543.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.543 + ./bwa mem -v 0 ref.fastq query.fastq.543 > query.fastq.543.sam 2> query.fastq.543.err + +query.fastq.544.sam query.fastq.544.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.544 + ./bwa mem -v 0 ref.fastq query.fastq.544 > query.fastq.544.sam 2> query.fastq.544.err + +query.fastq.545.sam query.fastq.545.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.545 + ./bwa mem -v 0 ref.fastq query.fastq.545 > query.fastq.545.sam 2> query.fastq.545.err + +query.fastq.546.sam query.fastq.546.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.546 + ./bwa mem -v 0 ref.fastq query.fastq.546 > query.fastq.546.sam 2> query.fastq.546.err + +query.fastq.547.sam query.fastq.547.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.547 + ./bwa mem -v 0 ref.fastq query.fastq.547 > query.fastq.547.sam 2> query.fastq.547.err + +query.fastq.548.sam query.fastq.548.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.548 + ./bwa mem -v 0 ref.fastq query.fastq.548 > query.fastq.548.sam 2> query.fastq.548.err + +query.fastq.549.sam query.fastq.549.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.549 + ./bwa mem -v 0 ref.fastq query.fastq.549 > query.fastq.549.sam 2> query.fastq.549.err + +query.fastq.550.sam query.fastq.550.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.550 + ./bwa mem -v 0 ref.fastq query.fastq.550 > query.fastq.550.sam 2> query.fastq.550.err + +query.fastq.551.sam query.fastq.551.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.551 + ./bwa mem -v 0 ref.fastq query.fastq.551 > query.fastq.551.sam 2> query.fastq.551.err + +query.fastq.552.sam query.fastq.552.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.552 + ./bwa mem -v 0 ref.fastq query.fastq.552 > query.fastq.552.sam 2> query.fastq.552.err + +query.fastq.553.sam query.fastq.553.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.553 + ./bwa mem -v 0 ref.fastq query.fastq.553 > query.fastq.553.sam 2> query.fastq.553.err + +query.fastq.554.sam query.fastq.554.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.554 + ./bwa mem -v 0 ref.fastq query.fastq.554 > query.fastq.554.sam 2> query.fastq.554.err + +query.fastq.555.sam query.fastq.555.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.555 + ./bwa mem -v 0 ref.fastq query.fastq.555 > query.fastq.555.sam 2> query.fastq.555.err + +query.fastq.556.sam query.fastq.556.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.556 + ./bwa mem -v 0 ref.fastq query.fastq.556 > query.fastq.556.sam 2> query.fastq.556.err + +query.fastq.557.sam query.fastq.557.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.557 + ./bwa mem -v 0 ref.fastq query.fastq.557 > query.fastq.557.sam 2> query.fastq.557.err + +query.fastq.558.sam query.fastq.558.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.558 + ./bwa mem -v 0 ref.fastq query.fastq.558 > query.fastq.558.sam 2> query.fastq.558.err + +query.fastq.559.sam query.fastq.559.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.559 + ./bwa mem -v 0 ref.fastq query.fastq.559 > query.fastq.559.sam 2> query.fastq.559.err + +query.fastq.560.sam query.fastq.560.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.560 + ./bwa mem -v 0 ref.fastq query.fastq.560 > query.fastq.560.sam 2> query.fastq.560.err + +query.fastq.561.sam query.fastq.561.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.561 + ./bwa mem -v 0 ref.fastq query.fastq.561 > query.fastq.561.sam 2> query.fastq.561.err + +query.fastq.562.sam query.fastq.562.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.562 + ./bwa mem -v 0 ref.fastq query.fastq.562 > query.fastq.562.sam 2> query.fastq.562.err + +query.fastq.563.sam query.fastq.563.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.563 + ./bwa mem -v 0 ref.fastq query.fastq.563 > query.fastq.563.sam 2> query.fastq.563.err + +query.fastq.564.sam query.fastq.564.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.564 + ./bwa mem -v 0 ref.fastq query.fastq.564 > query.fastq.564.sam 2> query.fastq.564.err + +query.fastq.565.sam query.fastq.565.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.565 + ./bwa mem -v 0 ref.fastq query.fastq.565 > query.fastq.565.sam 2> query.fastq.565.err + +query.fastq.566.sam query.fastq.566.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.566 + ./bwa mem -v 0 ref.fastq query.fastq.566 > query.fastq.566.sam 2> query.fastq.566.err + +query.fastq.567.sam query.fastq.567.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.567 + ./bwa mem -v 0 ref.fastq query.fastq.567 > query.fastq.567.sam 2> query.fastq.567.err + +query.fastq.568.sam query.fastq.568.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.568 + ./bwa mem -v 0 ref.fastq query.fastq.568 > query.fastq.568.sam 2> query.fastq.568.err + +query.fastq.569.sam query.fastq.569.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.569 + ./bwa mem -v 0 ref.fastq query.fastq.569 > query.fastq.569.sam 2> query.fastq.569.err + +query.fastq.570.sam query.fastq.570.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.570 + ./bwa mem -v 0 ref.fastq query.fastq.570 > query.fastq.570.sam 2> query.fastq.570.err + +query.fastq.571.sam query.fastq.571.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.571 + ./bwa mem -v 0 ref.fastq query.fastq.571 > query.fastq.571.sam 2> query.fastq.571.err + +query.fastq.572.sam query.fastq.572.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.572 + ./bwa mem -v 0 ref.fastq query.fastq.572 > query.fastq.572.sam 2> query.fastq.572.err + +query.fastq.573.sam query.fastq.573.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.573 + ./bwa mem -v 0 ref.fastq query.fastq.573 > query.fastq.573.sam 2> query.fastq.573.err + +query.fastq.574.sam query.fastq.574.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.574 + ./bwa mem -v 0 ref.fastq query.fastq.574 > query.fastq.574.sam 2> query.fastq.574.err + +query.fastq.575.sam query.fastq.575.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.575 + ./bwa mem -v 0 ref.fastq query.fastq.575 > query.fastq.575.sam 2> query.fastq.575.err + +query.fastq.576.sam query.fastq.576.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.576 + ./bwa mem -v 0 ref.fastq query.fastq.576 > query.fastq.576.sam 2> query.fastq.576.err + +query.fastq.577.sam query.fastq.577.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.577 + ./bwa mem -v 0 ref.fastq query.fastq.577 > query.fastq.577.sam 2> query.fastq.577.err + +query.fastq.578.sam query.fastq.578.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.578 + ./bwa mem -v 0 ref.fastq query.fastq.578 > query.fastq.578.sam 2> query.fastq.578.err + +query.fastq.579.sam query.fastq.579.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.579 + ./bwa mem -v 0 ref.fastq query.fastq.579 > query.fastq.579.sam 2> query.fastq.579.err + +query.fastq.580.sam query.fastq.580.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.580 + ./bwa mem -v 0 ref.fastq query.fastq.580 > query.fastq.580.sam 2> query.fastq.580.err + +query.fastq.581.sam query.fastq.581.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.581 + ./bwa mem -v 0 ref.fastq query.fastq.581 > query.fastq.581.sam 2> query.fastq.581.err + +query.fastq.582.sam query.fastq.582.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.582 + ./bwa mem -v 0 ref.fastq query.fastq.582 > query.fastq.582.sam 2> query.fastq.582.err + +query.fastq.583.sam query.fastq.583.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.583 + ./bwa mem -v 0 ref.fastq query.fastq.583 > query.fastq.583.sam 2> query.fastq.583.err + +query.fastq.584.sam query.fastq.584.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.584 + ./bwa mem -v 0 ref.fastq query.fastq.584 > query.fastq.584.sam 2> query.fastq.584.err + +query.fastq.585.sam query.fastq.585.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.585 + ./bwa mem -v 0 ref.fastq query.fastq.585 > query.fastq.585.sam 2> query.fastq.585.err + +query.fastq.586.sam query.fastq.586.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.586 + ./bwa mem -v 0 ref.fastq query.fastq.586 > query.fastq.586.sam 2> query.fastq.586.err + +query.fastq.587.sam query.fastq.587.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.587 + ./bwa mem -v 0 ref.fastq query.fastq.587 > query.fastq.587.sam 2> query.fastq.587.err + +query.fastq.588.sam query.fastq.588.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.588 + ./bwa mem -v 0 ref.fastq query.fastq.588 > query.fastq.588.sam 2> query.fastq.588.err + +query.fastq.589.sam query.fastq.589.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.589 + ./bwa mem -v 0 ref.fastq query.fastq.589 > query.fastq.589.sam 2> query.fastq.589.err + +query.fastq.590.sam query.fastq.590.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.590 + ./bwa mem -v 0 ref.fastq query.fastq.590 > query.fastq.590.sam 2> query.fastq.590.err + +query.fastq.591.sam query.fastq.591.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.591 + ./bwa mem -v 0 ref.fastq query.fastq.591 > query.fastq.591.sam 2> query.fastq.591.err + +query.fastq.592.sam query.fastq.592.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.592 + ./bwa mem -v 0 ref.fastq query.fastq.592 > query.fastq.592.sam 2> query.fastq.592.err + +query.fastq.593.sam query.fastq.593.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.593 + ./bwa mem -v 0 ref.fastq query.fastq.593 > query.fastq.593.sam 2> query.fastq.593.err + +query.fastq.594.sam query.fastq.594.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.594 + ./bwa mem -v 0 ref.fastq query.fastq.594 > query.fastq.594.sam 2> query.fastq.594.err + +query.fastq.595.sam query.fastq.595.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.595 + ./bwa mem -v 0 ref.fastq query.fastq.595 > query.fastq.595.sam 2> query.fastq.595.err + +query.fastq.596.sam query.fastq.596.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.596 + ./bwa mem -v 0 ref.fastq query.fastq.596 > query.fastq.596.sam 2> query.fastq.596.err + +query.fastq.597.sam query.fastq.597.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.597 + ./bwa mem -v 0 ref.fastq query.fastq.597 > query.fastq.597.sam 2> query.fastq.597.err + +query.fastq.598.sam query.fastq.598.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.598 + ./bwa mem -v 0 ref.fastq query.fastq.598 > query.fastq.598.sam 2> query.fastq.598.err + +query.fastq.599.sam query.fastq.599.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.599 + ./bwa mem -v 0 ref.fastq query.fastq.599 > query.fastq.599.sam 2> query.fastq.599.err + +query.fastq.600.sam query.fastq.600.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.600 + ./bwa mem -v 0 ref.fastq query.fastq.600 > query.fastq.600.sam 2> query.fastq.600.err + +query.fastq.601.sam query.fastq.601.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.601 + ./bwa mem -v 0 ref.fastq query.fastq.601 > query.fastq.601.sam 2> query.fastq.601.err + +query.fastq.602.sam query.fastq.602.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.602 + ./bwa mem -v 0 ref.fastq query.fastq.602 > query.fastq.602.sam 2> query.fastq.602.err + +query.fastq.603.sam query.fastq.603.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.603 + ./bwa mem -v 0 ref.fastq query.fastq.603 > query.fastq.603.sam 2> query.fastq.603.err + +query.fastq.604.sam query.fastq.604.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.604 + ./bwa mem -v 0 ref.fastq query.fastq.604 > query.fastq.604.sam 2> query.fastq.604.err + +query.fastq.605.sam query.fastq.605.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.605 + ./bwa mem -v 0 ref.fastq query.fastq.605 > query.fastq.605.sam 2> query.fastq.605.err + +query.fastq.606.sam query.fastq.606.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.606 + ./bwa mem -v 0 ref.fastq query.fastq.606 > query.fastq.606.sam 2> query.fastq.606.err + +query.fastq.607.sam query.fastq.607.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.607 + ./bwa mem -v 0 ref.fastq query.fastq.607 > query.fastq.607.sam 2> query.fastq.607.err + +query.fastq.608.sam query.fastq.608.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.608 + ./bwa mem -v 0 ref.fastq query.fastq.608 > query.fastq.608.sam 2> query.fastq.608.err + +query.fastq.609.sam query.fastq.609.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.609 + ./bwa mem -v 0 ref.fastq query.fastq.609 > query.fastq.609.sam 2> query.fastq.609.err + +query.fastq.610.sam query.fastq.610.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.610 + ./bwa mem -v 0 ref.fastq query.fastq.610 > query.fastq.610.sam 2> query.fastq.610.err + +query.fastq.611.sam query.fastq.611.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.611 + ./bwa mem -v 0 ref.fastq query.fastq.611 > query.fastq.611.sam 2> query.fastq.611.err + +query.fastq.612.sam query.fastq.612.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.612 + ./bwa mem -v 0 ref.fastq query.fastq.612 > query.fastq.612.sam 2> query.fastq.612.err + +query.fastq.613.sam query.fastq.613.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.613 + ./bwa mem -v 0 ref.fastq query.fastq.613 > query.fastq.613.sam 2> query.fastq.613.err + +query.fastq.614.sam query.fastq.614.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.614 + ./bwa mem -v 0 ref.fastq query.fastq.614 > query.fastq.614.sam 2> query.fastq.614.err + +query.fastq.615.sam query.fastq.615.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.615 + ./bwa mem -v 0 ref.fastq query.fastq.615 > query.fastq.615.sam 2> query.fastq.615.err + +query.fastq.616.sam query.fastq.616.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.616 + ./bwa mem -v 0 ref.fastq query.fastq.616 > query.fastq.616.sam 2> query.fastq.616.err + +query.fastq.617.sam query.fastq.617.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.617 + ./bwa mem -v 0 ref.fastq query.fastq.617 > query.fastq.617.sam 2> query.fastq.617.err + +query.fastq.618.sam query.fastq.618.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.618 + ./bwa mem -v 0 ref.fastq query.fastq.618 > query.fastq.618.sam 2> query.fastq.618.err + +query.fastq.619.sam query.fastq.619.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.619 + ./bwa mem -v 0 ref.fastq query.fastq.619 > query.fastq.619.sam 2> query.fastq.619.err + +query.fastq.620.sam query.fastq.620.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.620 + ./bwa mem -v 0 ref.fastq query.fastq.620 > query.fastq.620.sam 2> query.fastq.620.err + +query.fastq.621.sam query.fastq.621.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.621 + ./bwa mem -v 0 ref.fastq query.fastq.621 > query.fastq.621.sam 2> query.fastq.621.err + +query.fastq.622.sam query.fastq.622.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.622 + ./bwa mem -v 0 ref.fastq query.fastq.622 > query.fastq.622.sam 2> query.fastq.622.err + +query.fastq.623.sam query.fastq.623.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.623 + ./bwa mem -v 0 ref.fastq query.fastq.623 > query.fastq.623.sam 2> query.fastq.623.err + +query.fastq.624.sam query.fastq.624.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.624 + ./bwa mem -v 0 ref.fastq query.fastq.624 > query.fastq.624.sam 2> query.fastq.624.err + +query.fastq.625.sam query.fastq.625.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.625 + ./bwa mem -v 0 ref.fastq query.fastq.625 > query.fastq.625.sam 2> query.fastq.625.err + +query.fastq.626.sam query.fastq.626.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.626 + ./bwa mem -v 0 ref.fastq query.fastq.626 > query.fastq.626.sam 2> query.fastq.626.err + +query.fastq.627.sam query.fastq.627.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.627 + ./bwa mem -v 0 ref.fastq query.fastq.627 > query.fastq.627.sam 2> query.fastq.627.err + +query.fastq.628.sam query.fastq.628.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.628 + ./bwa mem -v 0 ref.fastq query.fastq.628 > query.fastq.628.sam 2> query.fastq.628.err + +query.fastq.629.sam query.fastq.629.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.629 + ./bwa mem -v 0 ref.fastq query.fastq.629 > query.fastq.629.sam 2> query.fastq.629.err + +query.fastq.630.sam query.fastq.630.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.630 + ./bwa mem -v 0 ref.fastq query.fastq.630 > query.fastq.630.sam 2> query.fastq.630.err + +query.fastq.631.sam query.fastq.631.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.631 + ./bwa mem -v 0 ref.fastq query.fastq.631 > query.fastq.631.sam 2> query.fastq.631.err + +query.fastq.632.sam query.fastq.632.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.632 + ./bwa mem -v 0 ref.fastq query.fastq.632 > query.fastq.632.sam 2> query.fastq.632.err + +query.fastq.633.sam query.fastq.633.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.633 + ./bwa mem -v 0 ref.fastq query.fastq.633 > query.fastq.633.sam 2> query.fastq.633.err + +query.fastq.634.sam query.fastq.634.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.634 + ./bwa mem -v 0 ref.fastq query.fastq.634 > query.fastq.634.sam 2> query.fastq.634.err + +query.fastq.635.sam query.fastq.635.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.635 + ./bwa mem -v 0 ref.fastq query.fastq.635 > query.fastq.635.sam 2> query.fastq.635.err + +query.fastq.636.sam query.fastq.636.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.636 + ./bwa mem -v 0 ref.fastq query.fastq.636 > query.fastq.636.sam 2> query.fastq.636.err + +query.fastq.637.sam query.fastq.637.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.637 + ./bwa mem -v 0 ref.fastq query.fastq.637 > query.fastq.637.sam 2> query.fastq.637.err + +query.fastq.638.sam query.fastq.638.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.638 + ./bwa mem -v 0 ref.fastq query.fastq.638 > query.fastq.638.sam 2> query.fastq.638.err + +query.fastq.639.sam query.fastq.639.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.639 + ./bwa mem -v 0 ref.fastq query.fastq.639 > query.fastq.639.sam 2> query.fastq.639.err + +query.fastq.640.sam query.fastq.640.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.640 + ./bwa mem -v 0 ref.fastq query.fastq.640 > query.fastq.640.sam 2> query.fastq.640.err + +query.fastq.641.sam query.fastq.641.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.641 + ./bwa mem -v 0 ref.fastq query.fastq.641 > query.fastq.641.sam 2> query.fastq.641.err + +query.fastq.642.sam query.fastq.642.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.642 + ./bwa mem -v 0 ref.fastq query.fastq.642 > query.fastq.642.sam 2> query.fastq.642.err + +query.fastq.643.sam query.fastq.643.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.643 + ./bwa mem -v 0 ref.fastq query.fastq.643 > query.fastq.643.sam 2> query.fastq.643.err + +query.fastq.644.sam query.fastq.644.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.644 + ./bwa mem -v 0 ref.fastq query.fastq.644 > query.fastq.644.sam 2> query.fastq.644.err + +query.fastq.645.sam query.fastq.645.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.645 + ./bwa mem -v 0 ref.fastq query.fastq.645 > query.fastq.645.sam 2> query.fastq.645.err + +query.fastq.646.sam query.fastq.646.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.646 + ./bwa mem -v 0 ref.fastq query.fastq.646 > query.fastq.646.sam 2> query.fastq.646.err + +query.fastq.647.sam query.fastq.647.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.647 + ./bwa mem -v 0 ref.fastq query.fastq.647 > query.fastq.647.sam 2> query.fastq.647.err + +query.fastq.648.sam query.fastq.648.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.648 + ./bwa mem -v 0 ref.fastq query.fastq.648 > query.fastq.648.sam 2> query.fastq.648.err + +query.fastq.649.sam query.fastq.649.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.649 + ./bwa mem -v 0 ref.fastq query.fastq.649 > query.fastq.649.sam 2> query.fastq.649.err + +query.fastq.650.sam query.fastq.650.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.650 + ./bwa mem -v 0 ref.fastq query.fastq.650 > query.fastq.650.sam 2> query.fastq.650.err + +query.fastq.651.sam query.fastq.651.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.651 + ./bwa mem -v 0 ref.fastq query.fastq.651 > query.fastq.651.sam 2> query.fastq.651.err + +query.fastq.652.sam query.fastq.652.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.652 + ./bwa mem -v 0 ref.fastq query.fastq.652 > query.fastq.652.sam 2> query.fastq.652.err + +query.fastq.653.sam query.fastq.653.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.653 + ./bwa mem -v 0 ref.fastq query.fastq.653 > query.fastq.653.sam 2> query.fastq.653.err + +query.fastq.654.sam query.fastq.654.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.654 + ./bwa mem -v 0 ref.fastq query.fastq.654 > query.fastq.654.sam 2> query.fastq.654.err + +query.fastq.655.sam query.fastq.655.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.655 + ./bwa mem -v 0 ref.fastq query.fastq.655 > query.fastq.655.sam 2> query.fastq.655.err + +query.fastq.656.sam query.fastq.656.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.656 + ./bwa mem -v 0 ref.fastq query.fastq.656 > query.fastq.656.sam 2> query.fastq.656.err + +query.fastq.657.sam query.fastq.657.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.657 + ./bwa mem -v 0 ref.fastq query.fastq.657 > query.fastq.657.sam 2> query.fastq.657.err + +query.fastq.658.sam query.fastq.658.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.658 + ./bwa mem -v 0 ref.fastq query.fastq.658 > query.fastq.658.sam 2> query.fastq.658.err + +query.fastq.659.sam query.fastq.659.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.659 + ./bwa mem -v 0 ref.fastq query.fastq.659 > query.fastq.659.sam 2> query.fastq.659.err + +query.fastq.660.sam query.fastq.660.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.660 + ./bwa mem -v 0 ref.fastq query.fastq.660 > query.fastq.660.sam 2> query.fastq.660.err + +query.fastq.661.sam query.fastq.661.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.661 + ./bwa mem -v 0 ref.fastq query.fastq.661 > query.fastq.661.sam 2> query.fastq.661.err + +query.fastq.662.sam query.fastq.662.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.662 + ./bwa mem -v 0 ref.fastq query.fastq.662 > query.fastq.662.sam 2> query.fastq.662.err + +query.fastq.663.sam query.fastq.663.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.663 + ./bwa mem -v 0 ref.fastq query.fastq.663 > query.fastq.663.sam 2> query.fastq.663.err + +query.fastq.664.sam query.fastq.664.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.664 + ./bwa mem -v 0 ref.fastq query.fastq.664 > query.fastq.664.sam 2> query.fastq.664.err + +query.fastq.665.sam query.fastq.665.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.665 + ./bwa mem -v 0 ref.fastq query.fastq.665 > query.fastq.665.sam 2> query.fastq.665.err + +query.fastq.666.sam query.fastq.666.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.666 + ./bwa mem -v 0 ref.fastq query.fastq.666 > query.fastq.666.sam 2> query.fastq.666.err + +query.fastq.667.sam query.fastq.667.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.667 + ./bwa mem -v 0 ref.fastq query.fastq.667 > query.fastq.667.sam 2> query.fastq.667.err + +query.fastq.668.sam query.fastq.668.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.668 + ./bwa mem -v 0 ref.fastq query.fastq.668 > query.fastq.668.sam 2> query.fastq.668.err + +query.fastq.669.sam query.fastq.669.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.669 + ./bwa mem -v 0 ref.fastq query.fastq.669 > query.fastq.669.sam 2> query.fastq.669.err + +query.fastq.670.sam query.fastq.670.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.670 + ./bwa mem -v 0 ref.fastq query.fastq.670 > query.fastq.670.sam 2> query.fastq.670.err + +query.fastq.671.sam query.fastq.671.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.671 + ./bwa mem -v 0 ref.fastq query.fastq.671 > query.fastq.671.sam 2> query.fastq.671.err + +query.fastq.672.sam query.fastq.672.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.672 + ./bwa mem -v 0 ref.fastq query.fastq.672 > query.fastq.672.sam 2> query.fastq.672.err + +query.fastq.673.sam query.fastq.673.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.673 + ./bwa mem -v 0 ref.fastq query.fastq.673 > query.fastq.673.sam 2> query.fastq.673.err + +query.fastq.674.sam query.fastq.674.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.674 + ./bwa mem -v 0 ref.fastq query.fastq.674 > query.fastq.674.sam 2> query.fastq.674.err + +query.fastq.675.sam query.fastq.675.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.675 + ./bwa mem -v 0 ref.fastq query.fastq.675 > query.fastq.675.sam 2> query.fastq.675.err + +query.fastq.676.sam query.fastq.676.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.676 + ./bwa mem -v 0 ref.fastq query.fastq.676 > query.fastq.676.sam 2> query.fastq.676.err + +query.fastq.677.sam query.fastq.677.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.677 + ./bwa mem -v 0 ref.fastq query.fastq.677 > query.fastq.677.sam 2> query.fastq.677.err + +query.fastq.678.sam query.fastq.678.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.678 + ./bwa mem -v 0 ref.fastq query.fastq.678 > query.fastq.678.sam 2> query.fastq.678.err + +query.fastq.679.sam query.fastq.679.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.679 + ./bwa mem -v 0 ref.fastq query.fastq.679 > query.fastq.679.sam 2> query.fastq.679.err + +query.fastq.680.sam query.fastq.680.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.680 + ./bwa mem -v 0 ref.fastq query.fastq.680 > query.fastq.680.sam 2> query.fastq.680.err + +query.fastq.681.sam query.fastq.681.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.681 + ./bwa mem -v 0 ref.fastq query.fastq.681 > query.fastq.681.sam 2> query.fastq.681.err + +query.fastq.682.sam query.fastq.682.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.682 + ./bwa mem -v 0 ref.fastq query.fastq.682 > query.fastq.682.sam 2> query.fastq.682.err + +query.fastq.683.sam query.fastq.683.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.683 + ./bwa mem -v 0 ref.fastq query.fastq.683 > query.fastq.683.sam 2> query.fastq.683.err + +query.fastq.684.sam query.fastq.684.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.684 + ./bwa mem -v 0 ref.fastq query.fastq.684 > query.fastq.684.sam 2> query.fastq.684.err + +query.fastq.685.sam query.fastq.685.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.685 + ./bwa mem -v 0 ref.fastq query.fastq.685 > query.fastq.685.sam 2> query.fastq.685.err + +query.fastq.686.sam query.fastq.686.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.686 + ./bwa mem -v 0 ref.fastq query.fastq.686 > query.fastq.686.sam 2> query.fastq.686.err + +query.fastq.687.sam query.fastq.687.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.687 + ./bwa mem -v 0 ref.fastq query.fastq.687 > query.fastq.687.sam 2> query.fastq.687.err + +query.fastq.688.sam query.fastq.688.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.688 + ./bwa mem -v 0 ref.fastq query.fastq.688 > query.fastq.688.sam 2> query.fastq.688.err + +query.fastq.689.sam query.fastq.689.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.689 + ./bwa mem -v 0 ref.fastq query.fastq.689 > query.fastq.689.sam 2> query.fastq.689.err + +query.fastq.690.sam query.fastq.690.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.690 + ./bwa mem -v 0 ref.fastq query.fastq.690 > query.fastq.690.sam 2> query.fastq.690.err + +query.fastq.691.sam query.fastq.691.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.691 + ./bwa mem -v 0 ref.fastq query.fastq.691 > query.fastq.691.sam 2> query.fastq.691.err + +query.fastq.692.sam query.fastq.692.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.692 + ./bwa mem -v 0 ref.fastq query.fastq.692 > query.fastq.692.sam 2> query.fastq.692.err + +query.fastq.693.sam query.fastq.693.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.693 + ./bwa mem -v 0 ref.fastq query.fastq.693 > query.fastq.693.sam 2> query.fastq.693.err + +query.fastq.694.sam query.fastq.694.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.694 + ./bwa mem -v 0 ref.fastq query.fastq.694 > query.fastq.694.sam 2> query.fastq.694.err + +query.fastq.695.sam query.fastq.695.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.695 + ./bwa mem -v 0 ref.fastq query.fastq.695 > query.fastq.695.sam 2> query.fastq.695.err + +query.fastq.696.sam query.fastq.696.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.696 + ./bwa mem -v 0 ref.fastq query.fastq.696 > query.fastq.696.sam 2> query.fastq.696.err + +query.fastq.697.sam query.fastq.697.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.697 + ./bwa mem -v 0 ref.fastq query.fastq.697 > query.fastq.697.sam 2> query.fastq.697.err + +query.fastq.698.sam query.fastq.698.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.698 + ./bwa mem -v 0 ref.fastq query.fastq.698 > query.fastq.698.sam 2> query.fastq.698.err + +query.fastq.699.sam query.fastq.699.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.699 + ./bwa mem -v 0 ref.fastq query.fastq.699 > query.fastq.699.sam 2> query.fastq.699.err + +query.fastq.700.sam query.fastq.700.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.700 + ./bwa mem -v 0 ref.fastq query.fastq.700 > query.fastq.700.sam 2> query.fastq.700.err + +query.fastq.701.sam query.fastq.701.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.701 + ./bwa mem -v 0 ref.fastq query.fastq.701 > query.fastq.701.sam 2> query.fastq.701.err + +query.fastq.702.sam query.fastq.702.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.702 + ./bwa mem -v 0 ref.fastq query.fastq.702 > query.fastq.702.sam 2> query.fastq.702.err + +query.fastq.703.sam query.fastq.703.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.703 + ./bwa mem -v 0 ref.fastq query.fastq.703 > query.fastq.703.sam 2> query.fastq.703.err + +query.fastq.704.sam query.fastq.704.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.704 + ./bwa mem -v 0 ref.fastq query.fastq.704 > query.fastq.704.sam 2> query.fastq.704.err + +query.fastq.705.sam query.fastq.705.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.705 + ./bwa mem -v 0 ref.fastq query.fastq.705 > query.fastq.705.sam 2> query.fastq.705.err + +query.fastq.706.sam query.fastq.706.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.706 + ./bwa mem -v 0 ref.fastq query.fastq.706 > query.fastq.706.sam 2> query.fastq.706.err + +query.fastq.707.sam query.fastq.707.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.707 + ./bwa mem -v 0 ref.fastq query.fastq.707 > query.fastq.707.sam 2> query.fastq.707.err + +query.fastq.708.sam query.fastq.708.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.708 + ./bwa mem -v 0 ref.fastq query.fastq.708 > query.fastq.708.sam 2> query.fastq.708.err + +query.fastq.709.sam query.fastq.709.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.709 + ./bwa mem -v 0 ref.fastq query.fastq.709 > query.fastq.709.sam 2> query.fastq.709.err + +query.fastq.710.sam query.fastq.710.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.710 + ./bwa mem -v 0 ref.fastq query.fastq.710 > query.fastq.710.sam 2> query.fastq.710.err + +query.fastq.711.sam query.fastq.711.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.711 + ./bwa mem -v 0 ref.fastq query.fastq.711 > query.fastq.711.sam 2> query.fastq.711.err + +query.fastq.712.sam query.fastq.712.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.712 + ./bwa mem -v 0 ref.fastq query.fastq.712 > query.fastq.712.sam 2> query.fastq.712.err + +query.fastq.713.sam query.fastq.713.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.713 + ./bwa mem -v 0 ref.fastq query.fastq.713 > query.fastq.713.sam 2> query.fastq.713.err + +query.fastq.714.sam query.fastq.714.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.714 + ./bwa mem -v 0 ref.fastq query.fastq.714 > query.fastq.714.sam 2> query.fastq.714.err + +query.fastq.715.sam query.fastq.715.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.715 + ./bwa mem -v 0 ref.fastq query.fastq.715 > query.fastq.715.sam 2> query.fastq.715.err + +query.fastq.716.sam query.fastq.716.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.716 + ./bwa mem -v 0 ref.fastq query.fastq.716 > query.fastq.716.sam 2> query.fastq.716.err + +query.fastq.717.sam query.fastq.717.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.717 + ./bwa mem -v 0 ref.fastq query.fastq.717 > query.fastq.717.sam 2> query.fastq.717.err + +query.fastq.718.sam query.fastq.718.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.718 + ./bwa mem -v 0 ref.fastq query.fastq.718 > query.fastq.718.sam 2> query.fastq.718.err + +query.fastq.719.sam query.fastq.719.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.719 + ./bwa mem -v 0 ref.fastq query.fastq.719 > query.fastq.719.sam 2> query.fastq.719.err + +query.fastq.720.sam query.fastq.720.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.720 + ./bwa mem -v 0 ref.fastq query.fastq.720 > query.fastq.720.sam 2> query.fastq.720.err + +query.fastq.721.sam query.fastq.721.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.721 + ./bwa mem -v 0 ref.fastq query.fastq.721 > query.fastq.721.sam 2> query.fastq.721.err + +query.fastq.722.sam query.fastq.722.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.722 + ./bwa mem -v 0 ref.fastq query.fastq.722 > query.fastq.722.sam 2> query.fastq.722.err + +query.fastq.723.sam query.fastq.723.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.723 + ./bwa mem -v 0 ref.fastq query.fastq.723 > query.fastq.723.sam 2> query.fastq.723.err + +query.fastq.724.sam query.fastq.724.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.724 + ./bwa mem -v 0 ref.fastq query.fastq.724 > query.fastq.724.sam 2> query.fastq.724.err + +query.fastq.725.sam query.fastq.725.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.725 + ./bwa mem -v 0 ref.fastq query.fastq.725 > query.fastq.725.sam 2> query.fastq.725.err + +query.fastq.726.sam query.fastq.726.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.726 + ./bwa mem -v 0 ref.fastq query.fastq.726 > query.fastq.726.sam 2> query.fastq.726.err + +query.fastq.727.sam query.fastq.727.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.727 + ./bwa mem -v 0 ref.fastq query.fastq.727 > query.fastq.727.sam 2> query.fastq.727.err + +query.fastq.728.sam query.fastq.728.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.728 + ./bwa mem -v 0 ref.fastq query.fastq.728 > query.fastq.728.sam 2> query.fastq.728.err + +query.fastq.729.sam query.fastq.729.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.729 + ./bwa mem -v 0 ref.fastq query.fastq.729 > query.fastq.729.sam 2> query.fastq.729.err + +query.fastq.730.sam query.fastq.730.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.730 + ./bwa mem -v 0 ref.fastq query.fastq.730 > query.fastq.730.sam 2> query.fastq.730.err + +query.fastq.731.sam query.fastq.731.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.731 + ./bwa mem -v 0 ref.fastq query.fastq.731 > query.fastq.731.sam 2> query.fastq.731.err + +query.fastq.732.sam query.fastq.732.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.732 + ./bwa mem -v 0 ref.fastq query.fastq.732 > query.fastq.732.sam 2> query.fastq.732.err + +query.fastq.733.sam query.fastq.733.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.733 + ./bwa mem -v 0 ref.fastq query.fastq.733 > query.fastq.733.sam 2> query.fastq.733.err + +query.fastq.734.sam query.fastq.734.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.734 + ./bwa mem -v 0 ref.fastq query.fastq.734 > query.fastq.734.sam 2> query.fastq.734.err + +query.fastq.735.sam query.fastq.735.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.735 + ./bwa mem -v 0 ref.fastq query.fastq.735 > query.fastq.735.sam 2> query.fastq.735.err + +query.fastq.736.sam query.fastq.736.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.736 + ./bwa mem -v 0 ref.fastq query.fastq.736 > query.fastq.736.sam 2> query.fastq.736.err + +query.fastq.737.sam query.fastq.737.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.737 + ./bwa mem -v 0 ref.fastq query.fastq.737 > query.fastq.737.sam 2> query.fastq.737.err + +query.fastq.738.sam query.fastq.738.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.738 + ./bwa mem -v 0 ref.fastq query.fastq.738 > query.fastq.738.sam 2> query.fastq.738.err + +query.fastq.739.sam query.fastq.739.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.739 + ./bwa mem -v 0 ref.fastq query.fastq.739 > query.fastq.739.sam 2> query.fastq.739.err + +query.fastq.740.sam query.fastq.740.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.740 + ./bwa mem -v 0 ref.fastq query.fastq.740 > query.fastq.740.sam 2> query.fastq.740.err + +query.fastq.741.sam query.fastq.741.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.741 + ./bwa mem -v 0 ref.fastq query.fastq.741 > query.fastq.741.sam 2> query.fastq.741.err + +query.fastq.742.sam query.fastq.742.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.742 + ./bwa mem -v 0 ref.fastq query.fastq.742 > query.fastq.742.sam 2> query.fastq.742.err + +query.fastq.743.sam query.fastq.743.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.743 + ./bwa mem -v 0 ref.fastq query.fastq.743 > query.fastq.743.sam 2> query.fastq.743.err + +query.fastq.744.sam query.fastq.744.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.744 + ./bwa mem -v 0 ref.fastq query.fastq.744 > query.fastq.744.sam 2> query.fastq.744.err + +query.fastq.745.sam query.fastq.745.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.745 + ./bwa mem -v 0 ref.fastq query.fastq.745 > query.fastq.745.sam 2> query.fastq.745.err + +query.fastq.746.sam query.fastq.746.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.746 + ./bwa mem -v 0 ref.fastq query.fastq.746 > query.fastq.746.sam 2> query.fastq.746.err + +query.fastq.747.sam query.fastq.747.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.747 + ./bwa mem -v 0 ref.fastq query.fastq.747 > query.fastq.747.sam 2> query.fastq.747.err + +query.fastq.748.sam query.fastq.748.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.748 + ./bwa mem -v 0 ref.fastq query.fastq.748 > query.fastq.748.sam 2> query.fastq.748.err + +query.fastq.749.sam query.fastq.749.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.749 + ./bwa mem -v 0 ref.fastq query.fastq.749 > query.fastq.749.sam 2> query.fastq.749.err + +query.fastq.750.sam query.fastq.750.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.750 + ./bwa mem -v 0 ref.fastq query.fastq.750 > query.fastq.750.sam 2> query.fastq.750.err + +query.fastq.751.sam query.fastq.751.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.751 + ./bwa mem -v 0 ref.fastq query.fastq.751 > query.fastq.751.sam 2> query.fastq.751.err + +query.fastq.752.sam query.fastq.752.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.752 + ./bwa mem -v 0 ref.fastq query.fastq.752 > query.fastq.752.sam 2> query.fastq.752.err + +query.fastq.753.sam query.fastq.753.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.753 + ./bwa mem -v 0 ref.fastq query.fastq.753 > query.fastq.753.sam 2> query.fastq.753.err + +query.fastq.754.sam query.fastq.754.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.754 + ./bwa mem -v 0 ref.fastq query.fastq.754 > query.fastq.754.sam 2> query.fastq.754.err + +query.fastq.755.sam query.fastq.755.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.755 + ./bwa mem -v 0 ref.fastq query.fastq.755 > query.fastq.755.sam 2> query.fastq.755.err + +query.fastq.756.sam query.fastq.756.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.756 + ./bwa mem -v 0 ref.fastq query.fastq.756 > query.fastq.756.sam 2> query.fastq.756.err + +query.fastq.757.sam query.fastq.757.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.757 + ./bwa mem -v 0 ref.fastq query.fastq.757 > query.fastq.757.sam 2> query.fastq.757.err + +query.fastq.758.sam query.fastq.758.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.758 + ./bwa mem -v 0 ref.fastq query.fastq.758 > query.fastq.758.sam 2> query.fastq.758.err + +query.fastq.759.sam query.fastq.759.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.759 + ./bwa mem -v 0 ref.fastq query.fastq.759 > query.fastq.759.sam 2> query.fastq.759.err + +query.fastq.760.sam query.fastq.760.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.760 + ./bwa mem -v 0 ref.fastq query.fastq.760 > query.fastq.760.sam 2> query.fastq.760.err + +query.fastq.761.sam query.fastq.761.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.761 + ./bwa mem -v 0 ref.fastq query.fastq.761 > query.fastq.761.sam 2> query.fastq.761.err + +query.fastq.762.sam query.fastq.762.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.762 + ./bwa mem -v 0 ref.fastq query.fastq.762 > query.fastq.762.sam 2> query.fastq.762.err + +query.fastq.763.sam query.fastq.763.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.763 + ./bwa mem -v 0 ref.fastq query.fastq.763 > query.fastq.763.sam 2> query.fastq.763.err + +query.fastq.764.sam query.fastq.764.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.764 + ./bwa mem -v 0 ref.fastq query.fastq.764 > query.fastq.764.sam 2> query.fastq.764.err + +query.fastq.765.sam query.fastq.765.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.765 + ./bwa mem -v 0 ref.fastq query.fastq.765 > query.fastq.765.sam 2> query.fastq.765.err + +query.fastq.766.sam query.fastq.766.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.766 + ./bwa mem -v 0 ref.fastq query.fastq.766 > query.fastq.766.sam 2> query.fastq.766.err + +query.fastq.767.sam query.fastq.767.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.767 + ./bwa mem -v 0 ref.fastq query.fastq.767 > query.fastq.767.sam 2> query.fastq.767.err + +query.fastq.768.sam query.fastq.768.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.768 + ./bwa mem -v 0 ref.fastq query.fastq.768 > query.fastq.768.sam 2> query.fastq.768.err + +query.fastq.769.sam query.fastq.769.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.769 + ./bwa mem -v 0 ref.fastq query.fastq.769 > query.fastq.769.sam 2> query.fastq.769.err + +query.fastq.770.sam query.fastq.770.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.770 + ./bwa mem -v 0 ref.fastq query.fastq.770 > query.fastq.770.sam 2> query.fastq.770.err + +query.fastq.771.sam query.fastq.771.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.771 + ./bwa mem -v 0 ref.fastq query.fastq.771 > query.fastq.771.sam 2> query.fastq.771.err + +query.fastq.772.sam query.fastq.772.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.772 + ./bwa mem -v 0 ref.fastq query.fastq.772 > query.fastq.772.sam 2> query.fastq.772.err + +query.fastq.773.sam query.fastq.773.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.773 + ./bwa mem -v 0 ref.fastq query.fastq.773 > query.fastq.773.sam 2> query.fastq.773.err + +query.fastq.774.sam query.fastq.774.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.774 + ./bwa mem -v 0 ref.fastq query.fastq.774 > query.fastq.774.sam 2> query.fastq.774.err + +query.fastq.775.sam query.fastq.775.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.775 + ./bwa mem -v 0 ref.fastq query.fastq.775 > query.fastq.775.sam 2> query.fastq.775.err + +query.fastq.776.sam query.fastq.776.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.776 + ./bwa mem -v 0 ref.fastq query.fastq.776 > query.fastq.776.sam 2> query.fastq.776.err + +query.fastq.777.sam query.fastq.777.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.777 + ./bwa mem -v 0 ref.fastq query.fastq.777 > query.fastq.777.sam 2> query.fastq.777.err + +query.fastq.778.sam query.fastq.778.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.778 + ./bwa mem -v 0 ref.fastq query.fastq.778 > query.fastq.778.sam 2> query.fastq.778.err + +query.fastq.779.sam query.fastq.779.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.779 + ./bwa mem -v 0 ref.fastq query.fastq.779 > query.fastq.779.sam 2> query.fastq.779.err + +query.fastq.780.sam query.fastq.780.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.780 + ./bwa mem -v 0 ref.fastq query.fastq.780 > query.fastq.780.sam 2> query.fastq.780.err + +query.fastq.781.sam query.fastq.781.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.781 + ./bwa mem -v 0 ref.fastq query.fastq.781 > query.fastq.781.sam 2> query.fastq.781.err + +query.fastq.782.sam query.fastq.782.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.782 + ./bwa mem -v 0 ref.fastq query.fastq.782 > query.fastq.782.sam 2> query.fastq.782.err + +query.fastq.783.sam query.fastq.783.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.783 + ./bwa mem -v 0 ref.fastq query.fastq.783 > query.fastq.783.sam 2> query.fastq.783.err + +query.fastq.784.sam query.fastq.784.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.784 + ./bwa mem -v 0 ref.fastq query.fastq.784 > query.fastq.784.sam 2> query.fastq.784.err + +query.fastq.785.sam query.fastq.785.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.785 + ./bwa mem -v 0 ref.fastq query.fastq.785 > query.fastq.785.sam 2> query.fastq.785.err + +query.fastq.786.sam query.fastq.786.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.786 + ./bwa mem -v 0 ref.fastq query.fastq.786 > query.fastq.786.sam 2> query.fastq.786.err + +query.fastq.787.sam query.fastq.787.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.787 + ./bwa mem -v 0 ref.fastq query.fastq.787 > query.fastq.787.sam 2> query.fastq.787.err + +query.fastq.788.sam query.fastq.788.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.788 + ./bwa mem -v 0 ref.fastq query.fastq.788 > query.fastq.788.sam 2> query.fastq.788.err + +query.fastq.789.sam query.fastq.789.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.789 + ./bwa mem -v 0 ref.fastq query.fastq.789 > query.fastq.789.sam 2> query.fastq.789.err + +query.fastq.790.sam query.fastq.790.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.790 + ./bwa mem -v 0 ref.fastq query.fastq.790 > query.fastq.790.sam 2> query.fastq.790.err + +query.fastq.791.sam query.fastq.791.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.791 + ./bwa mem -v 0 ref.fastq query.fastq.791 > query.fastq.791.sam 2> query.fastq.791.err + +query.fastq.792.sam query.fastq.792.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.792 + ./bwa mem -v 0 ref.fastq query.fastq.792 > query.fastq.792.sam 2> query.fastq.792.err + +query.fastq.793.sam query.fastq.793.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.793 + ./bwa mem -v 0 ref.fastq query.fastq.793 > query.fastq.793.sam 2> query.fastq.793.err + +query.fastq.794.sam query.fastq.794.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.794 + ./bwa mem -v 0 ref.fastq query.fastq.794 > query.fastq.794.sam 2> query.fastq.794.err + +query.fastq.795.sam query.fastq.795.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.795 + ./bwa mem -v 0 ref.fastq query.fastq.795 > query.fastq.795.sam 2> query.fastq.795.err + +query.fastq.796.sam query.fastq.796.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.796 + ./bwa mem -v 0 ref.fastq query.fastq.796 > query.fastq.796.sam 2> query.fastq.796.err + +query.fastq.797.sam query.fastq.797.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.797 + ./bwa mem -v 0 ref.fastq query.fastq.797 > query.fastq.797.sam 2> query.fastq.797.err + +query.fastq.798.sam query.fastq.798.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.798 + ./bwa mem -v 0 ref.fastq query.fastq.798 > query.fastq.798.sam 2> query.fastq.798.err + +query.fastq.799.sam query.fastq.799.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.799 + ./bwa mem -v 0 ref.fastq query.fastq.799 > query.fastq.799.sam 2> query.fastq.799.err + +query.fastq.800.sam query.fastq.800.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.800 + ./bwa mem -v 0 ref.fastq query.fastq.800 > query.fastq.800.sam 2> query.fastq.800.err + +query.fastq.801.sam query.fastq.801.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.801 + ./bwa mem -v 0 ref.fastq query.fastq.801 > query.fastq.801.sam 2> query.fastq.801.err + +query.fastq.802.sam query.fastq.802.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.802 + ./bwa mem -v 0 ref.fastq query.fastq.802 > query.fastq.802.sam 2> query.fastq.802.err + +query.fastq.803.sam query.fastq.803.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.803 + ./bwa mem -v 0 ref.fastq query.fastq.803 > query.fastq.803.sam 2> query.fastq.803.err + +query.fastq.804.sam query.fastq.804.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.804 + ./bwa mem -v 0 ref.fastq query.fastq.804 > query.fastq.804.sam 2> query.fastq.804.err + +query.fastq.805.sam query.fastq.805.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.805 + ./bwa mem -v 0 ref.fastq query.fastq.805 > query.fastq.805.sam 2> query.fastq.805.err + +query.fastq.806.sam query.fastq.806.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.806 + ./bwa mem -v 0 ref.fastq query.fastq.806 > query.fastq.806.sam 2> query.fastq.806.err + +query.fastq.807.sam query.fastq.807.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.807 + ./bwa mem -v 0 ref.fastq query.fastq.807 > query.fastq.807.sam 2> query.fastq.807.err + +query.fastq.808.sam query.fastq.808.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.808 + ./bwa mem -v 0 ref.fastq query.fastq.808 > query.fastq.808.sam 2> query.fastq.808.err + +query.fastq.809.sam query.fastq.809.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.809 + ./bwa mem -v 0 ref.fastq query.fastq.809 > query.fastq.809.sam 2> query.fastq.809.err + +query.fastq.810.sam query.fastq.810.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.810 + ./bwa mem -v 0 ref.fastq query.fastq.810 > query.fastq.810.sam 2> query.fastq.810.err + +query.fastq.811.sam query.fastq.811.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.811 + ./bwa mem -v 0 ref.fastq query.fastq.811 > query.fastq.811.sam 2> query.fastq.811.err + +query.fastq.812.sam query.fastq.812.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.812 + ./bwa mem -v 0 ref.fastq query.fastq.812 > query.fastq.812.sam 2> query.fastq.812.err + +query.fastq.813.sam query.fastq.813.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.813 + ./bwa mem -v 0 ref.fastq query.fastq.813 > query.fastq.813.sam 2> query.fastq.813.err + +query.fastq.814.sam query.fastq.814.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.814 + ./bwa mem -v 0 ref.fastq query.fastq.814 > query.fastq.814.sam 2> query.fastq.814.err + +query.fastq.815.sam query.fastq.815.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.815 + ./bwa mem -v 0 ref.fastq query.fastq.815 > query.fastq.815.sam 2> query.fastq.815.err + +query.fastq.816.sam query.fastq.816.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.816 + ./bwa mem -v 0 ref.fastq query.fastq.816 > query.fastq.816.sam 2> query.fastq.816.err + +query.fastq.817.sam query.fastq.817.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.817 + ./bwa mem -v 0 ref.fastq query.fastq.817 > query.fastq.817.sam 2> query.fastq.817.err + +query.fastq.818.sam query.fastq.818.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.818 + ./bwa mem -v 0 ref.fastq query.fastq.818 > query.fastq.818.sam 2> query.fastq.818.err + +query.fastq.819.sam query.fastq.819.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.819 + ./bwa mem -v 0 ref.fastq query.fastq.819 > query.fastq.819.sam 2> query.fastq.819.err + +query.fastq.820.sam query.fastq.820.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.820 + ./bwa mem -v 0 ref.fastq query.fastq.820 > query.fastq.820.sam 2> query.fastq.820.err + +query.fastq.821.sam query.fastq.821.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.821 + ./bwa mem -v 0 ref.fastq query.fastq.821 > query.fastq.821.sam 2> query.fastq.821.err + +query.fastq.822.sam query.fastq.822.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.822 + ./bwa mem -v 0 ref.fastq query.fastq.822 > query.fastq.822.sam 2> query.fastq.822.err + +query.fastq.823.sam query.fastq.823.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.823 + ./bwa mem -v 0 ref.fastq query.fastq.823 > query.fastq.823.sam 2> query.fastq.823.err + +query.fastq.824.sam query.fastq.824.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.824 + ./bwa mem -v 0 ref.fastq query.fastq.824 > query.fastq.824.sam 2> query.fastq.824.err + +query.fastq.825.sam query.fastq.825.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.825 + ./bwa mem -v 0 ref.fastq query.fastq.825 > query.fastq.825.sam 2> query.fastq.825.err + +query.fastq.826.sam query.fastq.826.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.826 + ./bwa mem -v 0 ref.fastq query.fastq.826 > query.fastq.826.sam 2> query.fastq.826.err + +query.fastq.827.sam query.fastq.827.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.827 + ./bwa mem -v 0 ref.fastq query.fastq.827 > query.fastq.827.sam 2> query.fastq.827.err + +query.fastq.828.sam query.fastq.828.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.828 + ./bwa mem -v 0 ref.fastq query.fastq.828 > query.fastq.828.sam 2> query.fastq.828.err + +query.fastq.829.sam query.fastq.829.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.829 + ./bwa mem -v 0 ref.fastq query.fastq.829 > query.fastq.829.sam 2> query.fastq.829.err + +query.fastq.830.sam query.fastq.830.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.830 + ./bwa mem -v 0 ref.fastq query.fastq.830 > query.fastq.830.sam 2> query.fastq.830.err + +query.fastq.831.sam query.fastq.831.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.831 + ./bwa mem -v 0 ref.fastq query.fastq.831 > query.fastq.831.sam 2> query.fastq.831.err + +query.fastq.832.sam query.fastq.832.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.832 + ./bwa mem -v 0 ref.fastq query.fastq.832 > query.fastq.832.sam 2> query.fastq.832.err + +query.fastq.833.sam query.fastq.833.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.833 + ./bwa mem -v 0 ref.fastq query.fastq.833 > query.fastq.833.sam 2> query.fastq.833.err + +query.fastq.834.sam query.fastq.834.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.834 + ./bwa mem -v 0 ref.fastq query.fastq.834 > query.fastq.834.sam 2> query.fastq.834.err + +query.fastq.835.sam query.fastq.835.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.835 + ./bwa mem -v 0 ref.fastq query.fastq.835 > query.fastq.835.sam 2> query.fastq.835.err + +query.fastq.836.sam query.fastq.836.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.836 + ./bwa mem -v 0 ref.fastq query.fastq.836 > query.fastq.836.sam 2> query.fastq.836.err + +query.fastq.837.sam query.fastq.837.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.837 + ./bwa mem -v 0 ref.fastq query.fastq.837 > query.fastq.837.sam 2> query.fastq.837.err + +query.fastq.838.sam query.fastq.838.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.838 + ./bwa mem -v 0 ref.fastq query.fastq.838 > query.fastq.838.sam 2> query.fastq.838.err + +query.fastq.839.sam query.fastq.839.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.839 + ./bwa mem -v 0 ref.fastq query.fastq.839 > query.fastq.839.sam 2> query.fastq.839.err + +query.fastq.840.sam query.fastq.840.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.840 + ./bwa mem -v 0 ref.fastq query.fastq.840 > query.fastq.840.sam 2> query.fastq.840.err + +query.fastq.841.sam query.fastq.841.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.841 + ./bwa mem -v 0 ref.fastq query.fastq.841 > query.fastq.841.sam 2> query.fastq.841.err + +query.fastq.842.sam query.fastq.842.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.842 + ./bwa mem -v 0 ref.fastq query.fastq.842 > query.fastq.842.sam 2> query.fastq.842.err + +query.fastq.843.sam query.fastq.843.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.843 + ./bwa mem -v 0 ref.fastq query.fastq.843 > query.fastq.843.sam 2> query.fastq.843.err + +query.fastq.844.sam query.fastq.844.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.844 + ./bwa mem -v 0 ref.fastq query.fastq.844 > query.fastq.844.sam 2> query.fastq.844.err + +query.fastq.845.sam query.fastq.845.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.845 + ./bwa mem -v 0 ref.fastq query.fastq.845 > query.fastq.845.sam 2> query.fastq.845.err + +query.fastq.846.sam query.fastq.846.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.846 + ./bwa mem -v 0 ref.fastq query.fastq.846 > query.fastq.846.sam 2> query.fastq.846.err + +query.fastq.847.sam query.fastq.847.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.847 + ./bwa mem -v 0 ref.fastq query.fastq.847 > query.fastq.847.sam 2> query.fastq.847.err + +query.fastq.848.sam query.fastq.848.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.848 + ./bwa mem -v 0 ref.fastq query.fastq.848 > query.fastq.848.sam 2> query.fastq.848.err + +query.fastq.849.sam query.fastq.849.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.849 + ./bwa mem -v 0 ref.fastq query.fastq.849 > query.fastq.849.sam 2> query.fastq.849.err + +query.fastq.850.sam query.fastq.850.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.850 + ./bwa mem -v 0 ref.fastq query.fastq.850 > query.fastq.850.sam 2> query.fastq.850.err + +query.fastq.851.sam query.fastq.851.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.851 + ./bwa mem -v 0 ref.fastq query.fastq.851 > query.fastq.851.sam 2> query.fastq.851.err + +query.fastq.852.sam query.fastq.852.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.852 + ./bwa mem -v 0 ref.fastq query.fastq.852 > query.fastq.852.sam 2> query.fastq.852.err + +query.fastq.853.sam query.fastq.853.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.853 + ./bwa mem -v 0 ref.fastq query.fastq.853 > query.fastq.853.sam 2> query.fastq.853.err + +query.fastq.854.sam query.fastq.854.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.854 + ./bwa mem -v 0 ref.fastq query.fastq.854 > query.fastq.854.sam 2> query.fastq.854.err + +query.fastq.855.sam query.fastq.855.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.855 + ./bwa mem -v 0 ref.fastq query.fastq.855 > query.fastq.855.sam 2> query.fastq.855.err + +query.fastq.856.sam query.fastq.856.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.856 + ./bwa mem -v 0 ref.fastq query.fastq.856 > query.fastq.856.sam 2> query.fastq.856.err + +query.fastq.857.sam query.fastq.857.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.857 + ./bwa mem -v 0 ref.fastq query.fastq.857 > query.fastq.857.sam 2> query.fastq.857.err + +query.fastq.858.sam query.fastq.858.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.858 + ./bwa mem -v 0 ref.fastq query.fastq.858 > query.fastq.858.sam 2> query.fastq.858.err + +query.fastq.859.sam query.fastq.859.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.859 + ./bwa mem -v 0 ref.fastq query.fastq.859 > query.fastq.859.sam 2> query.fastq.859.err + +query.fastq.860.sam query.fastq.860.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.860 + ./bwa mem -v 0 ref.fastq query.fastq.860 > query.fastq.860.sam 2> query.fastq.860.err + +query.fastq.861.sam query.fastq.861.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.861 + ./bwa mem -v 0 ref.fastq query.fastq.861 > query.fastq.861.sam 2> query.fastq.861.err + +query.fastq.862.sam query.fastq.862.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.862 + ./bwa mem -v 0 ref.fastq query.fastq.862 > query.fastq.862.sam 2> query.fastq.862.err + +query.fastq.863.sam query.fastq.863.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.863 + ./bwa mem -v 0 ref.fastq query.fastq.863 > query.fastq.863.sam 2> query.fastq.863.err + +query.fastq.864.sam query.fastq.864.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.864 + ./bwa mem -v 0 ref.fastq query.fastq.864 > query.fastq.864.sam 2> query.fastq.864.err + +query.fastq.865.sam query.fastq.865.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.865 + ./bwa mem -v 0 ref.fastq query.fastq.865 > query.fastq.865.sam 2> query.fastq.865.err + +query.fastq.866.sam query.fastq.866.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.866 + ./bwa mem -v 0 ref.fastq query.fastq.866 > query.fastq.866.sam 2> query.fastq.866.err + +query.fastq.867.sam query.fastq.867.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.867 + ./bwa mem -v 0 ref.fastq query.fastq.867 > query.fastq.867.sam 2> query.fastq.867.err + +query.fastq.868.sam query.fastq.868.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.868 + ./bwa mem -v 0 ref.fastq query.fastq.868 > query.fastq.868.sam 2> query.fastq.868.err + +query.fastq.869.sam query.fastq.869.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.869 + ./bwa mem -v 0 ref.fastq query.fastq.869 > query.fastq.869.sam 2> query.fastq.869.err + +query.fastq.870.sam query.fastq.870.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.870 + ./bwa mem -v 0 ref.fastq query.fastq.870 > query.fastq.870.sam 2> query.fastq.870.err + +query.fastq.871.sam query.fastq.871.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.871 + ./bwa mem -v 0 ref.fastq query.fastq.871 > query.fastq.871.sam 2> query.fastq.871.err + +query.fastq.872.sam query.fastq.872.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.872 + ./bwa mem -v 0 ref.fastq query.fastq.872 > query.fastq.872.sam 2> query.fastq.872.err + +query.fastq.873.sam query.fastq.873.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.873 + ./bwa mem -v 0 ref.fastq query.fastq.873 > query.fastq.873.sam 2> query.fastq.873.err + +query.fastq.874.sam query.fastq.874.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.874 + ./bwa mem -v 0 ref.fastq query.fastq.874 > query.fastq.874.sam 2> query.fastq.874.err + +query.fastq.875.sam query.fastq.875.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.875 + ./bwa mem -v 0 ref.fastq query.fastq.875 > query.fastq.875.sam 2> query.fastq.875.err + +query.fastq.876.sam query.fastq.876.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.876 + ./bwa mem -v 0 ref.fastq query.fastq.876 > query.fastq.876.sam 2> query.fastq.876.err + +query.fastq.877.sam query.fastq.877.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.877 + ./bwa mem -v 0 ref.fastq query.fastq.877 > query.fastq.877.sam 2> query.fastq.877.err + +query.fastq.878.sam query.fastq.878.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.878 + ./bwa mem -v 0 ref.fastq query.fastq.878 > query.fastq.878.sam 2> query.fastq.878.err + +query.fastq.879.sam query.fastq.879.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.879 + ./bwa mem -v 0 ref.fastq query.fastq.879 > query.fastq.879.sam 2> query.fastq.879.err + +query.fastq.880.sam query.fastq.880.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.880 + ./bwa mem -v 0 ref.fastq query.fastq.880 > query.fastq.880.sam 2> query.fastq.880.err + +query.fastq.881.sam query.fastq.881.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.881 + ./bwa mem -v 0 ref.fastq query.fastq.881 > query.fastq.881.sam 2> query.fastq.881.err + +query.fastq.882.sam query.fastq.882.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.882 + ./bwa mem -v 0 ref.fastq query.fastq.882 > query.fastq.882.sam 2> query.fastq.882.err + +query.fastq.883.sam query.fastq.883.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.883 + ./bwa mem -v 0 ref.fastq query.fastq.883 > query.fastq.883.sam 2> query.fastq.883.err + +query.fastq.884.sam query.fastq.884.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.884 + ./bwa mem -v 0 ref.fastq query.fastq.884 > query.fastq.884.sam 2> query.fastq.884.err + +query.fastq.885.sam query.fastq.885.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.885 + ./bwa mem -v 0 ref.fastq query.fastq.885 > query.fastq.885.sam 2> query.fastq.885.err + +query.fastq.886.sam query.fastq.886.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.886 + ./bwa mem -v 0 ref.fastq query.fastq.886 > query.fastq.886.sam 2> query.fastq.886.err + +query.fastq.887.sam query.fastq.887.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.887 + ./bwa mem -v 0 ref.fastq query.fastq.887 > query.fastq.887.sam 2> query.fastq.887.err + +query.fastq.888.sam query.fastq.888.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.888 + ./bwa mem -v 0 ref.fastq query.fastq.888 > query.fastq.888.sam 2> query.fastq.888.err + +query.fastq.889.sam query.fastq.889.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.889 + ./bwa mem -v 0 ref.fastq query.fastq.889 > query.fastq.889.sam 2> query.fastq.889.err + +query.fastq.890.sam query.fastq.890.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.890 + ./bwa mem -v 0 ref.fastq query.fastq.890 > query.fastq.890.sam 2> query.fastq.890.err + +query.fastq.891.sam query.fastq.891.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.891 + ./bwa mem -v 0 ref.fastq query.fastq.891 > query.fastq.891.sam 2> query.fastq.891.err + +query.fastq.892.sam query.fastq.892.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.892 + ./bwa mem -v 0 ref.fastq query.fastq.892 > query.fastq.892.sam 2> query.fastq.892.err + +query.fastq.893.sam query.fastq.893.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.893 + ./bwa mem -v 0 ref.fastq query.fastq.893 > query.fastq.893.sam 2> query.fastq.893.err + +query.fastq.894.sam query.fastq.894.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.894 + ./bwa mem -v 0 ref.fastq query.fastq.894 > query.fastq.894.sam 2> query.fastq.894.err + +query.fastq.895.sam query.fastq.895.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.895 + ./bwa mem -v 0 ref.fastq query.fastq.895 > query.fastq.895.sam 2> query.fastq.895.err + +query.fastq.896.sam query.fastq.896.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.896 + ./bwa mem -v 0 ref.fastq query.fastq.896 > query.fastq.896.sam 2> query.fastq.896.err + +query.fastq.897.sam query.fastq.897.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.897 + ./bwa mem -v 0 ref.fastq query.fastq.897 > query.fastq.897.sam 2> query.fastq.897.err + +query.fastq.898.sam query.fastq.898.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.898 + ./bwa mem -v 0 ref.fastq query.fastq.898 > query.fastq.898.sam 2> query.fastq.898.err + +query.fastq.899.sam query.fastq.899.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.899 + ./bwa mem -v 0 ref.fastq query.fastq.899 > query.fastq.899.sam 2> query.fastq.899.err + +query.fastq.900.sam query.fastq.900.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.900 + ./bwa mem -v 0 ref.fastq query.fastq.900 > query.fastq.900.sam 2> query.fastq.900.err + +query.fastq.901.sam query.fastq.901.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.901 + ./bwa mem -v 0 ref.fastq query.fastq.901 > query.fastq.901.sam 2> query.fastq.901.err + +query.fastq.902.sam query.fastq.902.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.902 + ./bwa mem -v 0 ref.fastq query.fastq.902 > query.fastq.902.sam 2> query.fastq.902.err + +query.fastq.903.sam query.fastq.903.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.903 + ./bwa mem -v 0 ref.fastq query.fastq.903 > query.fastq.903.sam 2> query.fastq.903.err + +query.fastq.904.sam query.fastq.904.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.904 + ./bwa mem -v 0 ref.fastq query.fastq.904 > query.fastq.904.sam 2> query.fastq.904.err + +query.fastq.905.sam query.fastq.905.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.905 + ./bwa mem -v 0 ref.fastq query.fastq.905 > query.fastq.905.sam 2> query.fastq.905.err + +query.fastq.906.sam query.fastq.906.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.906 + ./bwa mem -v 0 ref.fastq query.fastq.906 > query.fastq.906.sam 2> query.fastq.906.err + +query.fastq.907.sam query.fastq.907.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.907 + ./bwa mem -v 0 ref.fastq query.fastq.907 > query.fastq.907.sam 2> query.fastq.907.err + +query.fastq.908.sam query.fastq.908.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.908 + ./bwa mem -v 0 ref.fastq query.fastq.908 > query.fastq.908.sam 2> query.fastq.908.err + +query.fastq.909.sam query.fastq.909.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.909 + ./bwa mem -v 0 ref.fastq query.fastq.909 > query.fastq.909.sam 2> query.fastq.909.err + +query.fastq.910.sam query.fastq.910.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.910 + ./bwa mem -v 0 ref.fastq query.fastq.910 > query.fastq.910.sam 2> query.fastq.910.err + +query.fastq.911.sam query.fastq.911.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.911 + ./bwa mem -v 0 ref.fastq query.fastq.911 > query.fastq.911.sam 2> query.fastq.911.err + +query.fastq.912.sam query.fastq.912.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.912 + ./bwa mem -v 0 ref.fastq query.fastq.912 > query.fastq.912.sam 2> query.fastq.912.err + +query.fastq.913.sam query.fastq.913.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.913 + ./bwa mem -v 0 ref.fastq query.fastq.913 > query.fastq.913.sam 2> query.fastq.913.err + +query.fastq.914.sam query.fastq.914.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.914 + ./bwa mem -v 0 ref.fastq query.fastq.914 > query.fastq.914.sam 2> query.fastq.914.err + +query.fastq.915.sam query.fastq.915.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.915 + ./bwa mem -v 0 ref.fastq query.fastq.915 > query.fastq.915.sam 2> query.fastq.915.err + +query.fastq.916.sam query.fastq.916.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.916 + ./bwa mem -v 0 ref.fastq query.fastq.916 > query.fastq.916.sam 2> query.fastq.916.err + +query.fastq.917.sam query.fastq.917.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.917 + ./bwa mem -v 0 ref.fastq query.fastq.917 > query.fastq.917.sam 2> query.fastq.917.err + +query.fastq.918.sam query.fastq.918.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.918 + ./bwa mem -v 0 ref.fastq query.fastq.918 > query.fastq.918.sam 2> query.fastq.918.err + +query.fastq.919.sam query.fastq.919.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.919 + ./bwa mem -v 0 ref.fastq query.fastq.919 > query.fastq.919.sam 2> query.fastq.919.err + +query.fastq.920.sam query.fastq.920.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.920 + ./bwa mem -v 0 ref.fastq query.fastq.920 > query.fastq.920.sam 2> query.fastq.920.err + +query.fastq.921.sam query.fastq.921.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.921 + ./bwa mem -v 0 ref.fastq query.fastq.921 > query.fastq.921.sam 2> query.fastq.921.err + +query.fastq.922.sam query.fastq.922.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.922 + ./bwa mem -v 0 ref.fastq query.fastq.922 > query.fastq.922.sam 2> query.fastq.922.err + +query.fastq.923.sam query.fastq.923.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.923 + ./bwa mem -v 0 ref.fastq query.fastq.923 > query.fastq.923.sam 2> query.fastq.923.err + +query.fastq.924.sam query.fastq.924.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.924 + ./bwa mem -v 0 ref.fastq query.fastq.924 > query.fastq.924.sam 2> query.fastq.924.err + +query.fastq.925.sam query.fastq.925.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.925 + ./bwa mem -v 0 ref.fastq query.fastq.925 > query.fastq.925.sam 2> query.fastq.925.err + +query.fastq.926.sam query.fastq.926.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.926 + ./bwa mem -v 0 ref.fastq query.fastq.926 > query.fastq.926.sam 2> query.fastq.926.err + +query.fastq.927.sam query.fastq.927.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.927 + ./bwa mem -v 0 ref.fastq query.fastq.927 > query.fastq.927.sam 2> query.fastq.927.err + +query.fastq.928.sam query.fastq.928.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.928 + ./bwa mem -v 0 ref.fastq query.fastq.928 > query.fastq.928.sam 2> query.fastq.928.err + +query.fastq.929.sam query.fastq.929.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.929 + ./bwa mem -v 0 ref.fastq query.fastq.929 > query.fastq.929.sam 2> query.fastq.929.err + +query.fastq.930.sam query.fastq.930.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.930 + ./bwa mem -v 0 ref.fastq query.fastq.930 > query.fastq.930.sam 2> query.fastq.930.err + +query.fastq.931.sam query.fastq.931.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.931 + ./bwa mem -v 0 ref.fastq query.fastq.931 > query.fastq.931.sam 2> query.fastq.931.err + +query.fastq.932.sam query.fastq.932.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.932 + ./bwa mem -v 0 ref.fastq query.fastq.932 > query.fastq.932.sam 2> query.fastq.932.err + +query.fastq.933.sam query.fastq.933.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.933 + ./bwa mem -v 0 ref.fastq query.fastq.933 > query.fastq.933.sam 2> query.fastq.933.err + +query.fastq.934.sam query.fastq.934.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.934 + ./bwa mem -v 0 ref.fastq query.fastq.934 > query.fastq.934.sam 2> query.fastq.934.err + +query.fastq.935.sam query.fastq.935.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.935 + ./bwa mem -v 0 ref.fastq query.fastq.935 > query.fastq.935.sam 2> query.fastq.935.err + +query.fastq.936.sam query.fastq.936.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.936 + ./bwa mem -v 0 ref.fastq query.fastq.936 > query.fastq.936.sam 2> query.fastq.936.err + +query.fastq.937.sam query.fastq.937.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.937 + ./bwa mem -v 0 ref.fastq query.fastq.937 > query.fastq.937.sam 2> query.fastq.937.err + +query.fastq.938.sam query.fastq.938.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.938 + ./bwa mem -v 0 ref.fastq query.fastq.938 > query.fastq.938.sam 2> query.fastq.938.err + +query.fastq.939.sam query.fastq.939.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.939 + ./bwa mem -v 0 ref.fastq query.fastq.939 > query.fastq.939.sam 2> query.fastq.939.err + +query.fastq.940.sam query.fastq.940.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.940 + ./bwa mem -v 0 ref.fastq query.fastq.940 > query.fastq.940.sam 2> query.fastq.940.err + +query.fastq.941.sam query.fastq.941.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.941 + ./bwa mem -v 0 ref.fastq query.fastq.941 > query.fastq.941.sam 2> query.fastq.941.err + +query.fastq.942.sam query.fastq.942.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.942 + ./bwa mem -v 0 ref.fastq query.fastq.942 > query.fastq.942.sam 2> query.fastq.942.err + +query.fastq.943.sam query.fastq.943.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.943 + ./bwa mem -v 0 ref.fastq query.fastq.943 > query.fastq.943.sam 2> query.fastq.943.err + +query.fastq.944.sam query.fastq.944.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.944 + ./bwa mem -v 0 ref.fastq query.fastq.944 > query.fastq.944.sam 2> query.fastq.944.err + +query.fastq.945.sam query.fastq.945.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.945 + ./bwa mem -v 0 ref.fastq query.fastq.945 > query.fastq.945.sam 2> query.fastq.945.err + +query.fastq.946.sam query.fastq.946.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.946 + ./bwa mem -v 0 ref.fastq query.fastq.946 > query.fastq.946.sam 2> query.fastq.946.err + +query.fastq.947.sam query.fastq.947.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.947 + ./bwa mem -v 0 ref.fastq query.fastq.947 > query.fastq.947.sam 2> query.fastq.947.err + +query.fastq.948.sam query.fastq.948.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.948 + ./bwa mem -v 0 ref.fastq query.fastq.948 > query.fastq.948.sam 2> query.fastq.948.err + +query.fastq.949.sam query.fastq.949.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.949 + ./bwa mem -v 0 ref.fastq query.fastq.949 > query.fastq.949.sam 2> query.fastq.949.err + +query.fastq.950.sam query.fastq.950.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.950 + ./bwa mem -v 0 ref.fastq query.fastq.950 > query.fastq.950.sam 2> query.fastq.950.err + +query.fastq.951.sam query.fastq.951.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.951 + ./bwa mem -v 0 ref.fastq query.fastq.951 > query.fastq.951.sam 2> query.fastq.951.err + +query.fastq.952.sam query.fastq.952.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.952 + ./bwa mem -v 0 ref.fastq query.fastq.952 > query.fastq.952.sam 2> query.fastq.952.err + +query.fastq.953.sam query.fastq.953.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.953 + ./bwa mem -v 0 ref.fastq query.fastq.953 > query.fastq.953.sam 2> query.fastq.953.err + +query.fastq.954.sam query.fastq.954.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.954 + ./bwa mem -v 0 ref.fastq query.fastq.954 > query.fastq.954.sam 2> query.fastq.954.err + +query.fastq.955.sam query.fastq.955.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.955 + ./bwa mem -v 0 ref.fastq query.fastq.955 > query.fastq.955.sam 2> query.fastq.955.err + +query.fastq.956.sam query.fastq.956.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.956 + ./bwa mem -v 0 ref.fastq query.fastq.956 > query.fastq.956.sam 2> query.fastq.956.err + +query.fastq.957.sam query.fastq.957.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.957 + ./bwa mem -v 0 ref.fastq query.fastq.957 > query.fastq.957.sam 2> query.fastq.957.err + +query.fastq.958.sam query.fastq.958.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.958 + ./bwa mem -v 0 ref.fastq query.fastq.958 > query.fastq.958.sam 2> query.fastq.958.err + +query.fastq.959.sam query.fastq.959.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.959 + ./bwa mem -v 0 ref.fastq query.fastq.959 > query.fastq.959.sam 2> query.fastq.959.err + +query.fastq.960.sam query.fastq.960.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.960 + ./bwa mem -v 0 ref.fastq query.fastq.960 > query.fastq.960.sam 2> query.fastq.960.err + +query.fastq.961.sam query.fastq.961.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.961 + ./bwa mem -v 0 ref.fastq query.fastq.961 > query.fastq.961.sam 2> query.fastq.961.err + +query.fastq.962.sam query.fastq.962.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.962 + ./bwa mem -v 0 ref.fastq query.fastq.962 > query.fastq.962.sam 2> query.fastq.962.err + +query.fastq.963.sam query.fastq.963.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.963 + ./bwa mem -v 0 ref.fastq query.fastq.963 > query.fastq.963.sam 2> query.fastq.963.err + +query.fastq.964.sam query.fastq.964.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.964 + ./bwa mem -v 0 ref.fastq query.fastq.964 > query.fastq.964.sam 2> query.fastq.964.err + +query.fastq.965.sam query.fastq.965.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.965 + ./bwa mem -v 0 ref.fastq query.fastq.965 > query.fastq.965.sam 2> query.fastq.965.err + +query.fastq.966.sam query.fastq.966.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.966 + ./bwa mem -v 0 ref.fastq query.fastq.966 > query.fastq.966.sam 2> query.fastq.966.err + +query.fastq.967.sam query.fastq.967.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.967 + ./bwa mem -v 0 ref.fastq query.fastq.967 > query.fastq.967.sam 2> query.fastq.967.err + +query.fastq.968.sam query.fastq.968.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.968 + ./bwa mem -v 0 ref.fastq query.fastq.968 > query.fastq.968.sam 2> query.fastq.968.err + +query.fastq.969.sam query.fastq.969.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.969 + ./bwa mem -v 0 ref.fastq query.fastq.969 > query.fastq.969.sam 2> query.fastq.969.err + +query.fastq.970.sam query.fastq.970.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.970 + ./bwa mem -v 0 ref.fastq query.fastq.970 > query.fastq.970.sam 2> query.fastq.970.err + +query.fastq.971.sam query.fastq.971.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.971 + ./bwa mem -v 0 ref.fastq query.fastq.971 > query.fastq.971.sam 2> query.fastq.971.err + +query.fastq.972.sam query.fastq.972.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.972 + ./bwa mem -v 0 ref.fastq query.fastq.972 > query.fastq.972.sam 2> query.fastq.972.err + +query.fastq.973.sam query.fastq.973.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.973 + ./bwa mem -v 0 ref.fastq query.fastq.973 > query.fastq.973.sam 2> query.fastq.973.err + +query.fastq.974.sam query.fastq.974.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.974 + ./bwa mem -v 0 ref.fastq query.fastq.974 > query.fastq.974.sam 2> query.fastq.974.err + +query.fastq.975.sam query.fastq.975.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.975 + ./bwa mem -v 0 ref.fastq query.fastq.975 > query.fastq.975.sam 2> query.fastq.975.err + +query.fastq.976.sam query.fastq.976.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.976 + ./bwa mem -v 0 ref.fastq query.fastq.976 > query.fastq.976.sam 2> query.fastq.976.err + +query.fastq.977.sam query.fastq.977.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.977 + ./bwa mem -v 0 ref.fastq query.fastq.977 > query.fastq.977.sam 2> query.fastq.977.err + +query.fastq.978.sam query.fastq.978.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.978 + ./bwa mem -v 0 ref.fastq query.fastq.978 > query.fastq.978.sam 2> query.fastq.978.err + +query.fastq.979.sam query.fastq.979.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.979 + ./bwa mem -v 0 ref.fastq query.fastq.979 > query.fastq.979.sam 2> query.fastq.979.err + +query.fastq.980.sam query.fastq.980.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.980 + ./bwa mem -v 0 ref.fastq query.fastq.980 > query.fastq.980.sam 2> query.fastq.980.err + +query.fastq.981.sam query.fastq.981.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.981 + ./bwa mem -v 0 ref.fastq query.fastq.981 > query.fastq.981.sam 2> query.fastq.981.err + +query.fastq.982.sam query.fastq.982.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.982 + ./bwa mem -v 0 ref.fastq query.fastq.982 > query.fastq.982.sam 2> query.fastq.982.err + +query.fastq.983.sam query.fastq.983.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.983 + ./bwa mem -v 0 ref.fastq query.fastq.983 > query.fastq.983.sam 2> query.fastq.983.err + +query.fastq.984.sam query.fastq.984.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.984 + ./bwa mem -v 0 ref.fastq query.fastq.984 > query.fastq.984.sam 2> query.fastq.984.err + +query.fastq.985.sam query.fastq.985.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.985 + ./bwa mem -v 0 ref.fastq query.fastq.985 > query.fastq.985.sam 2> query.fastq.985.err + +query.fastq.986.sam query.fastq.986.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.986 + ./bwa mem -v 0 ref.fastq query.fastq.986 > query.fastq.986.sam 2> query.fastq.986.err + +query.fastq.987.sam query.fastq.987.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.987 + ./bwa mem -v 0 ref.fastq query.fastq.987 > query.fastq.987.sam 2> query.fastq.987.err + +query.fastq.988.sam query.fastq.988.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.988 + ./bwa mem -v 0 ref.fastq query.fastq.988 > query.fastq.988.sam 2> query.fastq.988.err + +query.fastq.989.sam query.fastq.989.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.989 + ./bwa mem -v 0 ref.fastq query.fastq.989 > query.fastq.989.sam 2> query.fastq.989.err + +query.fastq.990.sam query.fastq.990.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.990 + ./bwa mem -v 0 ref.fastq query.fastq.990 > query.fastq.990.sam 2> query.fastq.990.err + +query.fastq.991.sam query.fastq.991.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.991 + ./bwa mem -v 0 ref.fastq query.fastq.991 > query.fastq.991.sam 2> query.fastq.991.err + +query.fastq.992.sam query.fastq.992.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.992 + ./bwa mem -v 0 ref.fastq query.fastq.992 > query.fastq.992.sam 2> query.fastq.992.err + +query.fastq.993.sam query.fastq.993.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.993 + ./bwa mem -v 0 ref.fastq query.fastq.993 > query.fastq.993.sam 2> query.fastq.993.err + +query.fastq.994.sam query.fastq.994.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.994 + ./bwa mem -v 0 ref.fastq query.fastq.994 > query.fastq.994.sam 2> query.fastq.994.err + +query.fastq.995.sam query.fastq.995.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.995 + ./bwa mem -v 0 ref.fastq query.fastq.995 > query.fastq.995.sam 2> query.fastq.995.err + +query.fastq.996.sam query.fastq.996.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.996 + ./bwa mem -v 0 ref.fastq query.fastq.996 > query.fastq.996.sam 2> query.fastq.996.err + +query.fastq.997.sam query.fastq.997.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.997 + ./bwa mem -v 0 ref.fastq query.fastq.997 > query.fastq.997.sam 2> query.fastq.997.err + +query.fastq.998.sam query.fastq.998.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.998 + ./bwa mem -v 0 ref.fastq query.fastq.998 > query.fastq.998.sam 2> query.fastq.998.err + +query.fastq.999.sam query.fastq.999.err : bwa ref.fastq ref.fastq.bwt ref.fastq.pac ref.fastq.amb ref.fastq.ann ref.fastq.sa query.fastq.999 + ./bwa mem -v 0 ref.fastq query.fastq.999 > query.fastq.999.sam 2> query.fastq.999.err + +CATEGORY=analysis + +query.sam : cat_bwa query.fastq.0.sam query.fastq.1.sam query.fastq.2.sam query.fastq.3.sam query.fastq.4.sam query.fastq.5.sam query.fastq.6.sam query.fastq.7.sam query.fastq.8.sam query.fastq.9.sam query.fastq.10.sam query.fastq.11.sam query.fastq.12.sam query.fastq.13.sam query.fastq.14.sam query.fastq.15.sam query.fastq.16.sam query.fastq.17.sam query.fastq.18.sam query.fastq.19.sam query.fastq.20.sam query.fastq.21.sam query.fastq.22.sam query.fastq.23.sam query.fastq.24.sam query.fastq.25.sam query.fastq.26.sam query.fastq.27.sam query.fastq.28.sam query.fastq.29.sam query.fastq.30.sam query.fastq.31.sam query.fastq.32.sam query.fastq.33.sam query.fastq.34.sam query.fastq.35.sam query.fastq.36.sam query.fastq.37.sam query.fastq.38.sam query.fastq.39.sam query.fastq.40.sam query.fastq.41.sam query.fastq.42.sam query.fastq.43.sam query.fastq.44.sam query.fastq.45.sam query.fastq.46.sam query.fastq.47.sam query.fastq.48.sam query.fastq.49.sam query.fastq.50.sam query.fastq.51.sam query.fastq.52.sam query.fastq.53.sam query.fastq.54.sam query.fastq.55.sam query.fastq.56.sam query.fastq.57.sam query.fastq.58.sam query.fastq.59.sam query.fastq.60.sam query.fastq.61.sam query.fastq.62.sam query.fastq.63.sam query.fastq.64.sam query.fastq.65.sam query.fastq.66.sam query.fastq.67.sam query.fastq.68.sam query.fastq.69.sam query.fastq.70.sam query.fastq.71.sam query.fastq.72.sam query.fastq.73.sam query.fastq.74.sam query.fastq.75.sam query.fastq.76.sam query.fastq.77.sam query.fastq.78.sam query.fastq.79.sam query.fastq.80.sam query.fastq.81.sam query.fastq.82.sam query.fastq.83.sam query.fastq.84.sam query.fastq.85.sam 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query.fastq.678.err query.fastq.679.err query.fastq.680.err query.fastq.681.err query.fastq.682.err query.fastq.683.err query.fastq.684.err query.fastq.685.err query.fastq.686.err query.fastq.687.err query.fastq.688.err query.fastq.689.err query.fastq.690.err query.fastq.691.err query.fastq.692.err query.fastq.693.err query.fastq.694.err query.fastq.695.err query.fastq.696.err query.fastq.697.err query.fastq.698.err query.fastq.699.err query.fastq.700.err query.fastq.701.err query.fastq.702.err query.fastq.703.err query.fastq.704.err query.fastq.705.err query.fastq.706.err query.fastq.707.err query.fastq.708.err query.fastq.709.err query.fastq.710.err query.fastq.711.err query.fastq.712.err query.fastq.713.err query.fastq.714.err query.fastq.715.err query.fastq.716.err query.fastq.717.err query.fastq.718.err query.fastq.719.err query.fastq.720.err query.fastq.721.err query.fastq.722.err query.fastq.723.err query.fastq.724.err query.fastq.725.err query.fastq.726.err query.fastq.727.err query.fastq.728.err query.fastq.729.err query.fastq.730.err query.fastq.731.err query.fastq.732.err query.fastq.733.err query.fastq.734.err query.fastq.735.err query.fastq.736.err query.fastq.737.err query.fastq.738.err query.fastq.739.err query.fastq.740.err query.fastq.741.err query.fastq.742.err query.fastq.743.err query.fastq.744.err query.fastq.745.err query.fastq.746.err query.fastq.747.err query.fastq.748.err query.fastq.749.err query.fastq.750.err query.fastq.751.err query.fastq.752.err query.fastq.753.err query.fastq.754.err query.fastq.755.err query.fastq.756.err query.fastq.757.err query.fastq.758.err query.fastq.759.err query.fastq.760.err query.fastq.761.err query.fastq.762.err query.fastq.763.err query.fastq.764.err query.fastq.765.err query.fastq.766.err query.fastq.767.err query.fastq.768.err query.fastq.769.err query.fastq.770.err query.fastq.771.err query.fastq.772.err query.fastq.773.err query.fastq.774.err query.fastq.775.err query.fastq.776.err query.fastq.777.err query.fastq.778.err query.fastq.779.err query.fastq.780.err query.fastq.781.err query.fastq.782.err query.fastq.783.err query.fastq.784.err query.fastq.785.err query.fastq.786.err query.fastq.787.err query.fastq.788.err query.fastq.789.err query.fastq.790.err query.fastq.791.err query.fastq.792.err query.fastq.793.err query.fastq.794.err query.fastq.795.err query.fastq.796.err query.fastq.797.err query.fastq.798.err query.fastq.799.err query.fastq.800.err query.fastq.801.err query.fastq.802.err query.fastq.803.err query.fastq.804.err query.fastq.805.err query.fastq.806.err query.fastq.807.err query.fastq.808.err query.fastq.809.err query.fastq.810.err query.fastq.811.err query.fastq.812.err query.fastq.813.err query.fastq.814.err query.fastq.815.err query.fastq.816.err query.fastq.817.err query.fastq.818.err query.fastq.819.err query.fastq.820.err query.fastq.821.err query.fastq.822.err query.fastq.823.err query.fastq.824.err query.fastq.825.err query.fastq.826.err query.fastq.827.err query.fastq.828.err query.fastq.829.err query.fastq.830.err query.fastq.831.err query.fastq.832.err query.fastq.833.err query.fastq.834.err query.fastq.835.err query.fastq.836.err query.fastq.837.err query.fastq.838.err query.fastq.839.err query.fastq.840.err query.fastq.841.err query.fastq.842.err query.fastq.843.err query.fastq.844.err query.fastq.845.err query.fastq.846.err query.fastq.847.err query.fastq.848.err query.fastq.849.err query.fastq.850.err query.fastq.851.err query.fastq.852.err query.fastq.853.err query.fastq.854.err query.fastq.855.err query.fastq.856.err query.fastq.857.err query.fastq.858.err query.fastq.859.err query.fastq.860.err query.fastq.861.err query.fastq.862.err query.fastq.863.err query.fastq.864.err query.fastq.865.err query.fastq.866.err query.fastq.867.err query.fastq.868.err query.fastq.869.err query.fastq.870.err query.fastq.871.err query.fastq.872.err query.fastq.873.err query.fastq.874.err query.fastq.875.err query.fastq.876.err query.fastq.877.err query.fastq.878.err query.fastq.879.err query.fastq.880.err query.fastq.881.err query.fastq.882.err query.fastq.883.err query.fastq.884.err query.fastq.885.err query.fastq.886.err query.fastq.887.err query.fastq.888.err query.fastq.889.err query.fastq.890.err query.fastq.891.err query.fastq.892.err query.fastq.893.err query.fastq.894.err query.fastq.895.err query.fastq.896.err query.fastq.897.err query.fastq.898.err query.fastq.899.err query.fastq.900.err query.fastq.901.err query.fastq.902.err query.fastq.903.err query.fastq.904.err query.fastq.905.err query.fastq.906.err query.fastq.907.err query.fastq.908.err query.fastq.909.err query.fastq.910.err query.fastq.911.err query.fastq.912.err query.fastq.913.err query.fastq.914.err query.fastq.915.err query.fastq.916.err query.fastq.917.err query.fastq.918.err query.fastq.919.err query.fastq.920.err query.fastq.921.err query.fastq.922.err query.fastq.923.err query.fastq.924.err query.fastq.925.err query.fastq.926.err query.fastq.927.err query.fastq.928.err query.fastq.929.err query.fastq.930.err query.fastq.931.err query.fastq.932.err query.fastq.933.err query.fastq.934.err query.fastq.935.err query.fastq.936.err query.fastq.937.err query.fastq.938.err query.fastq.939.err query.fastq.940.err query.fastq.941.err query.fastq.942.err query.fastq.943.err query.fastq.944.err query.fastq.945.err query.fastq.946.err query.fastq.947.err query.fastq.948.err query.fastq.949.err query.fastq.950.err query.fastq.951.err query.fastq.952.err query.fastq.953.err query.fastq.954.err query.fastq.955.err query.fastq.956.err query.fastq.957.err query.fastq.958.err query.fastq.959.err query.fastq.960.err query.fastq.961.err query.fastq.962.err query.fastq.963.err query.fastq.964.err query.fastq.965.err query.fastq.966.err query.fastq.967.err query.fastq.968.err query.fastq.969.err query.fastq.970.err query.fastq.971.err query.fastq.972.err query.fastq.973.err query.fastq.974.err query.fastq.975.err query.fastq.976.err query.fastq.977.err query.fastq.978.err query.fastq.979.err query.fastq.980.err query.fastq.981.err query.fastq.982.err query.fastq.983.err query.fastq.984.err query.fastq.985.err query.fastq.986.err query.fastq.987.err query.fastq.988.err query.fastq.989.err query.fastq.990.err query.fastq.991.err query.fastq.992.err query.fastq.993.err query.fastq.994.err query.fastq.995.err query.fastq.996.err query.fastq.997.err query.fastq.998.err query.fastq.999.err LOCAL cat query.fastq.*.err > query.err diff --git a/hecil/hecil.json b/hecil/hecil.json index 3ee7c3d..61fe532 100644 --- a/hecil/hecil.json +++ b/hecil/hecil.json @@ -28,7 +28,7 @@ }, "rules": [ - + { "command":"./bwa index ref.fasta 2> index.err", "inputs": @@ -45,9 +45,10 @@ "ref.fasta.pac", "ref.fasta.sa" ], - "local_job":true + "local_job":true, + "category":"bwa_preprocessing" }, - + { "command":"./fastq_reduce query.fastq 100", "inputs": @@ -68,9 +69,10 @@ "query.fastq.8", "query.fastq.9" ], - "local_job":true + "local_job":true, + "category":"bwa_preprocessing" }, - + { "command":"./bwa mem ref.fasta query.fastq.0 > Out.0.sam 2> mem.0.err", "inputs": @@ -87,9 +89,16 @@ [ "Out.0.sam", "mem.0.err" - ] + ], + "resources" : { + "cores":1, + "memory":100, + "disk":1100, + "wall-time":10 + }, + "category": "bwa_simulation" }, - + { "command":"./bwa mem ref.fasta query.fastq.1 > Out.1.sam 2> mem.1.err", "inputs": @@ -106,9 +115,16 @@ [ "Out.1.sam", "mem.1.err" - ] + ], + "resources" : { + "cores":1, + "memory":100, + "disk":1100, + "wall-time":10 + }, + "category": "bwa_simulation" }, - + { "command":"./bwa mem ref.fasta query.fastq.2 > Out.2.sam 2> mem.2.err", "inputs": @@ -125,9 +141,16 @@ [ "Out.2.sam", "mem.2.err" - ] + ], + "resources" : { + "cores":1, + "memory":100, + "disk":1100, + "wall-time":10 + }, + "category": "bwa_simulation" }, - + { "command":"./bwa mem ref.fasta query.fastq.3 > Out.3.sam 2> mem.3.err", "inputs": @@ -144,9 +167,16 @@ [ "Out.3.sam", "mem.3.err" - ] + ], + "resources" : { + "cores":1, + "memory":100, + "disk":1100, + "wall-time":10 + }, + "category": "bwa_simulation" }, - + { "command":"./bwa mem ref.fasta query.fastq.4 > Out.4.sam 2> mem.4.err", "inputs": @@ -163,9 +193,16 @@ [ "Out.4.sam", "mem.4.err" - ] + ], + "resources" : { + "cores":1, + "memory":100, + "disk":1100, + "wall-time":10 + }, + "category": "bwa_simulation" }, - + { "command":"./bwa mem ref.fasta query.fastq.5 > Out.5.sam 2> mem.5.err", "inputs": @@ -182,9 +219,16 @@ [ "Out.5.sam", "mem.5.err" - ] + ], + "resources" : { + "cores":1, + "memory":100, + "disk":1100, + "wall-time":10 + }, + "category": "bwa_simulation" }, - + { "command":"./bwa mem ref.fasta query.fastq.6 > Out.6.sam 2> mem.6.err", "inputs": @@ -201,9 +245,16 @@ [ "Out.6.sam", "mem.6.err" - ] + ], + "resources" : { + "cores":1, + "memory":100, + "disk":1100, + "wall-time":10 + }, + "category": "bwa_simulation" }, - + { "command":"./bwa mem ref.fasta query.fastq.7 > Out.7.sam 2> mem.7.err", "inputs": @@ -220,9 +271,16 @@ [ "Out.7.sam", "mem.7.err" - ] + ], + "resources" : { + "cores":1, + "memory":100, + "disk":1100, + "wall-time":10 + }, + "category": "bwa_simulation" }, - + { "command":"./bwa mem ref.fasta query.fastq.8 > Out.8.sam 2> mem.8.err", "inputs": @@ -239,9 +297,16 @@ [ "Out.8.sam", "mem.8.err" - ] + ], + "resources" : { + "cores":1, + "memory":100, + "disk":1100, + "wall-time":10 + }, + "category": "bwa_simulation" }, - + { "command":"./bwa mem ref.fasta query.fastq.9 > Out.9.sam 2> mem.9.err", "inputs": @@ -258,9 +323,16 @@ [ "Out.9.sam", "mem.9.err" - ] + ], + "resources" : { + "cores":1, + "memory":100, + "disk":1100, + "wall-time":10 + }, + "category": "bwa_simulation" }, - + { "command":"./sam_cat.sh Out.0.sam Out.1.sam Out.2.sam Out.3.sam Out.4.sam Out.5.sam Out.6.sam Out.7.sam Out.8.sam Out.9.sam > Out.sam", "inputs": @@ -281,9 +353,10 @@ [ "Out.sam" ], - "local_job":true + "local_job":true, + "category": "bwa_output" }, - + { "command":"cat mem.*.err > mem.err", "inputs": @@ -303,9 +376,10 @@ [ "mem.err" ], - "local_job":true + "local_job":true, + "category": "bwa_output" }, - + { "command":"./samtools view -bS Out.sam | ./samtools sort - Out 2> sort.err", "inputs": @@ -317,9 +391,10 @@ [ "Out.bam", "sort.err" - ] + ], + "category": "pileup" }, - + { "command":"./samtools mpileup -s -f ref.fasta Out.bam > pileup.txt 2> pileup.err", "inputs": @@ -333,9 +408,10 @@ "pileup.txt", "ref.fasta.fai", "pileup.err" - ] + ], + "category": "pileup" }, - + { "command":"./Split_Pileup.sh pileup.txt 2 2> Split_Pileup.err", "inputs": @@ -350,9 +426,10 @@ "Pileup_Set2.txt", "List_RefHeader.txt" ], - "local_job":true + "local_job":true, + "category": "hecil_preprocessing" }, - + { "command":"python Correction.py Pileup_Set0.txt ref.fasta lc.0.out Out.sam 10 > corr.0.out 2> corr.0.err ; echo \"\" >> lc.0.out ; echo \"\" >> corr.0.out", "inputs": @@ -368,9 +445,10 @@ "lc.0.out", "corr.0.err" ], - "local_job":true + "local_job":true, + "category": "hecil_preprocessing" }, - + { "command":"python Correction.py Pileup_Set1.txt ref.fasta lc.1.out Out.sam 10 > corr.1.out 2> corr.1.err ; echo \"\" >> lc.1.out ; echo \"\" >> corr.1.out", "inputs": @@ -386,9 +464,10 @@ "lc.1.out", "corr.1.err" ], - "local_job":true + "local_job":true, + "category": "hecil_preprocessing" }, - + { "command":"cat corr.0.out corr.1.out > corr.out", "inputs": @@ -400,9 +479,10 @@ [ "corr.out" ], - "local_job":true + "local_job":true, + "category": "hecil_preprocessing" }, - + { "command":"cat corr.0.err corr.1.err > corr.err", "inputs": @@ -414,9 +494,10 @@ [ "corr.err" ], - "local_job":true + "local_job":true, + "category": "hecil_preprocessing" }, - + { "command":"cat lc.0.out lc.1.out > LowConf.txt", "inputs": @@ -428,9 +509,10 @@ [ "LowConf.txt" ], - "local_job":true + "local_job":true, + "category": "hecil_preprocessing" }, - + { "command":"./fasta_reduce ref.fasta 1000", "inputs": @@ -451,9 +533,10 @@ "ref.fasta.8", "ref.fasta.9" ], - "local_job":true + "local_job":true, + "category": "hecil_preprocessing" }, - + { "command":"python Create_Corrected_AllLRReads.py ref.fasta.0 corr.out 2> create.err.0", "inputs": @@ -465,9 +548,16 @@ "outputs": [ "Corrected_ref.fasta.0" - ] + ], + "resources" : { + "cores":1, + "memory":100, + "disk":1300, + "wall-time":10 + }, + "category": "hecil_simulation" }, - + { "command":"python Create_Corrected_AllLRReads.py ref.fasta.1 corr.out 2> create.err.1", "inputs": @@ -479,9 +569,16 @@ "outputs": [ "Corrected_ref.fasta.1" - ] + ], + "resources" : { + "cores":1, + "memory":100, + "disk":1300, + "wall-time":10 + }, + "category": "hecil_simulation" }, - + { "command":"python Create_Corrected_AllLRReads.py ref.fasta.2 corr.out 2> create.err.2", "inputs": @@ -493,9 +590,16 @@ "outputs": [ "Corrected_ref.fasta.2" - ] + ], + "resources" : { + "cores":1, + "memory":100, + "disk":1300, + "wall-time":10 + }, + "category": "hecil_simulation" }, - + { "command":"python Create_Corrected_AllLRReads.py ref.fasta.3 corr.out 2> create.err.3", "inputs": @@ -507,9 +611,16 @@ "outputs": [ "Corrected_ref.fasta.3" - ] + ], + "resources" : { + "cores":1, + "memory":100, + "disk":1300, + "wall-time":10 + }, + "category": "hecil_simulation" }, - + { "command":"python Create_Corrected_AllLRReads.py ref.fasta.4 corr.out 2> create.err.4", "inputs": @@ -521,9 +632,16 @@ "outputs": [ "Corrected_ref.fasta.4" - ] + ], + "resources" : { + "cores":1, + "memory":100, + "disk":1300, + "wall-time":10 + }, + "category": "hecil_simulation" }, - + { "command":"python Create_Corrected_AllLRReads.py ref.fasta.5 corr.out 2> create.err.5", "inputs": @@ -535,9 +653,16 @@ "outputs": [ "Corrected_ref.fasta.5" - ] + ], + "resources" : { + "cores":1, + "memory":100, + "disk":1300, + "wall-time":10 + }, + "category": "hecil_simulation" }, - + { "command":"python Create_Corrected_AllLRReads.py ref.fasta.6 corr.out 2> create.err.6", "inputs": @@ -549,9 +674,16 @@ "outputs": [ "Corrected_ref.fasta.6" - ] + ], + "resources" : { + "cores":1, + "memory":100, + "disk":1300, + "wall-time":10 + }, + "category": "hecil_simulation" }, - + { "command":"python Create_Corrected_AllLRReads.py ref.fasta.7 corr.out 2> create.err.7", "inputs": @@ -563,9 +695,16 @@ "outputs": [ "Corrected_ref.fasta.7" - ] + ], + "resources" : { + "cores":1, + "memory":100, + "disk":1300, + "wall-time":10 + }, + "category": "hecil_simulation" }, - + { "command":"python Create_Corrected_AllLRReads.py ref.fasta.8 corr.out 2> create.err.8", "inputs": @@ -577,9 +716,16 @@ "outputs": [ "Corrected_ref.fasta.8" - ] + ], + "resources" : { + "cores":1, + "memory":100, + "disk":1300, + "wall-time":10 + }, + "category": "hecil_simulation" }, - + { "command":"python Create_Corrected_AllLRReads.py ref.fasta.9 corr.out 2> create.err.9", "inputs": @@ -591,9 +737,16 @@ "outputs": [ "Corrected_ref.fasta.9" - ] + ], + "resources" : { + "cores":1, + "memory":100, + "disk":1300, + "wall-time":10 + }, + "category": "hecil_simulation" }, - + { "command":"cat Corrected_ref.fasta.0 Corrected_ref.fasta.1 Corrected_ref.fasta.2 Corrected_ref.fasta.3 Corrected_ref.fasta.4 Corrected_ref.fasta.5 Corrected_ref.fasta.6 Corrected_ref.fasta.7 Corrected_ref.fasta.8 Corrected_ref.fasta.9 > Corrected_ref.fasta", "inputs": @@ -613,7 +766,8 @@ [ "Corrected_ref.fasta" ], - "local_job":true + "local_job":true, + "category": "hecil_analysis" } ] } diff --git a/hecil/hecil.jx b/hecil/hecil.jx index 6d61251..9c9753e 100644 --- a/hecil/hecil.jx +++ b/hecil/hecil.jx @@ -24,7 +24,7 @@ }, "rules": [ - + { "command":format("%s index %s 2> index.err",BWA,REF), "inputs": @@ -37,9 +37,10 @@ "index.err", x for x in REF_INDEX ], - "local_job":true + "local_job":true, + "category":"bwa_preprocessing" }, - + { "command":format("%s %s %d",SPLIT,INPUT_PRE,SEQ_PER_SPLIT), "inputs": @@ -51,9 +52,10 @@ [ format("%s.%d",INPUT_PRE,x) for x in range(ceil(TOTAL_SEQ/SEQ_PER_SPLIT)) ], - "local_job":true + "local_job":true, + "category":"bwa_preprocessing" }, - + { "command":format("%s %s %s %s.%d > Out.%d.sam 2> mem.%d.err",BWA,ARGS,REF,INPUT_PRE,i,i,i), "inputs": @@ -66,9 +68,16 @@ [ format("Out.%d.sam",i), format("mem.%d.err",i) - ] + ], + "resources" : { + "cores":1, + "memory":100, + "disk":1100, + "wall-time":10 + }, + "category": "bwa_simulation" } for i in range(ceil(TOTAL_SEQ/SEQ_PER_SPLIT)), - + { "command":format("%s %s > Out.sam",CONCAT,join([format("Out.%d.sam",x) for x in range(ceil(TOTAL_SEQ/SEQ_PER_SPLIT))])), "inputs": @@ -80,9 +89,10 @@ [ "Out.sam" ], - "local_job":true + "local_job":true, + "category": "bwa_output" }, - + { "command":format("cat mem.*.err > mem.err"), "inputs": @@ -93,9 +103,10 @@ [ "mem.err" ], - "local_job":true + "local_job":true, + "category": "bwa_output" }, - + { "command":format("%s view -bS Out.sam | %s sort - Out 2> sort.err",TOOLS,TOOLS), "inputs": @@ -107,9 +118,10 @@ [ "Out.bam", "sort.err" - ] + ], + "category": "pileup" }, - + { "command":format("%s mpileup -s -f %s Out.bam > pileup.txt 2> pileup.err",TOOLS,REF), "inputs": @@ -123,9 +135,10 @@ "pileup.txt", "ref.fasta.fai", "pileup.err" - ] + ], + "category": "pileup" }, - + { "command":format("%s pileup.txt 2 2> Split_Pileup.err",PILEUP), "inputs": @@ -139,9 +152,9 @@ format("Pileup_Set%d.txt",x) for x in range(1,3), "List_RefHeader.txt" ], - "local_job":true + "category": "hecil_preprocessing" }, - + { "command":format("%s %s Pileup_Set%d.txt %s lc.%d.out Out.sam %d > corr.%d.out 2> corr.%d.err ; echo \"\" >> lc.%d.out ; echo \"\" >> corr.%d.out",PYTHON,CORRECTION,x,REF,x,ceil(TOTAL_SEQ/SEQ_PER_SPLIT),x,x,x,x), "inputs": @@ -157,9 +170,10 @@ format("lc.%d.out",x), format("corr.%d.err",x) ], - "local_job":true + "local_job":true, + "category": "hecil_preprocessing" } for x in range(2), - + { "command":format("cat %s > corr.out",join([format("corr.%d.out",x) for x in range(2)])), "inputs": @@ -170,9 +184,10 @@ [ "corr.out" ], - "local_job":true + "local_job":true, + "category": "hecil_preprocessing" }, - + { "command":format("cat %s > corr.err",join([format("corr.%d.err",x) for x in range(2)])), "inputs": @@ -183,9 +198,10 @@ [ "corr.err" ], - "local_job":true + "local_job":true, + "category": "hecil_preprocessing" }, - + { "command":format("cat %s > LowConf.txt",join([format("lc.%d.out",x) for x in range(2)])), "inputs": @@ -196,9 +212,10 @@ [ "LowConf.txt" ], - "local_job":true + "local_job":true, + "category": "hecil_preprocessing" }, - + { "command":format("%s %s 1000",SPLITA,REF), "inputs": @@ -210,9 +227,10 @@ [ format("%s.%d",REF,x) for x in range(ceil(TOTAL_SEQ/SEQ_PER_SPLIT)) ], - "local_job":true + "local_job":true, + "category": "hecil_preprocessing" }, - + { "command":format("%s %s %s.%d corr.out 2> create.err.%d",PYTHON,CORRECT_ALLLR,REF,x,x), "inputs": @@ -224,9 +242,16 @@ "outputs": [ format("Corrected_ref.fasta.%d",x) - ] + ], + "resources" : { + "cores":1, + "memory":100, + "disk":1300, + "wall-time":10 + }, + "category": "hecil_simulation" } for x in range(ceil(TOTAL_SEQ/SEQ_PER_SPLIT)), - + { "command":format("cat %s > Corrected_ref.fasta",join([format("Corrected_ref.fasta.%d",x) for x in range(ceil(TOTAL_SEQ/SEQ_PER_SPLIT))])), "inputs": @@ -237,7 +262,8 @@ [ "Corrected_ref.fasta" ], - "local_job":true + "local_job":true, + "category": "hecil_analysis" } ] } diff --git a/hecil/hecil.mf b/hecil/hecil.mf index 6260869..f8a2f47 100644 --- a/hecil/hecil.mf +++ b/hecil/hecil.mf @@ -1,13 +1,19 @@ MAKEFLOW_INPUTS=bwa Correction.py Create_Corrected_AllLRReads.py fastq_reduce ref.fasta sam_cat.sh samtools query.fastq MAKEFLOW_OUTPUTS=corr.out corr.err Corrected_ref.fasta index.err LowConf.txt ref.fasta.fai mem.err pileup.err sort.err create.err - +CATEGORY = bwa_preprocessing index.err ref.fasta.sa ref.fasta.pac ref.fasta.bwt ref.fasta.ann ref.fasta.amb : bwa ref.fasta LOCAL ./bwa index ref.fasta 2> index.err query.fastq.0 query.fastq.1 query.fastq.2 query.fastq.3 query.fastq.4 query.fastq.5 query.fastq.6 query.fastq.7 query.fastq.8 query.fastq.9 query.fastq.10 query.fastq.11 query.fastq.12 query.fastq.13 query.fastq.14 query.fastq.15 query.fastq.16 query.fastq.17 query.fastq.18 query.fastq.19 query.fastq.20 query.fastq.21 query.fastq.22 query.fastq.23 query.fastq.24 query.fastq.25 query.fastq.26 query.fastq.27 query.fastq.28 query.fastq.29 query.fastq.30 query.fastq.31 query.fastq.32 query.fastq.33 query.fastq.34 query.fastq.35 query.fastq.36 query.fastq.37 query.fastq.38 query.fastq.39 query.fastq.40 query.fastq.41 query.fastq.42 query.fastq.43 query.fastq.44 query.fastq.45 query.fastq.46 query.fastq.47 query.fastq.48 query.fastq.49 query.fastq.50 query.fastq.51 query.fastq.52 query.fastq.53 query.fastq.54 query.fastq.55 query.fastq.56 query.fastq.57 query.fastq.58 query.fastq.59 query.fastq.60 query.fastq.61 query.fastq.62 query.fastq.63 query.fastq.64 query.fastq.65 query.fastq.66 query.fastq.67 query.fastq.68 query.fastq.69 query.fastq.70 query.fastq.71 query.fastq.72 query.fastq.73 query.fastq.74 query.fastq.75 query.fastq.76 query.fastq.77 query.fastq.78 query.fastq.79 query.fastq.80 query.fastq.81 query.fastq.82 query.fastq.83 query.fastq.84 query.fastq.85 query.fastq.86 query.fastq.87 query.fastq.88 query.fastq.89 query.fastq.90 query.fastq.91 query.fastq.92 query.fastq.93 query.fastq.94 query.fastq.95 query.fastq.96 query.fastq.97 query.fastq.98 query.fastq.99 : fastq_reduce query.fastq LOCAL perl fastq_reduce query.fastq 100 +CATEGORY = bwa_simulation +CORES=1 +MEMORY=100 +DISK=1100 +WALLTIME=10 + Out.0.sam mem.0.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.0 ./bwa mem ref.fasta query.fastq.0 > Out.0.sam 2> mem.0.err @@ -308,18 +314,24 @@ Out.98.sam mem.98.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb Out.99.sam mem.99.err : bwa ref.fasta ref.fasta.bwt ref.fasta.pac ref.fasta.amb ref.fasta.ann ref.fasta.sa query.fastq.99 ./bwa mem ref.fasta query.fastq.99 > Out.99.sam 2> mem.99.err +CATEGORY=bwa_output + Out.sam : sam_cat.sh Out.0.sam Out.1.sam Out.2.sam Out.3.sam Out.4.sam Out.5.sam Out.6.sam Out.7.sam Out.8.sam Out.9.sam Out.10.sam Out.11.sam Out.12.sam Out.13.sam Out.14.sam Out.15.sam Out.16.sam Out.17.sam Out.18.sam Out.19.sam Out.20.sam Out.21.sam Out.22.sam Out.23.sam Out.24.sam Out.25.sam Out.26.sam Out.27.sam Out.28.sam Out.29.sam Out.30.sam Out.31.sam Out.32.sam Out.33.sam Out.34.sam Out.35.sam Out.36.sam Out.37.sam Out.38.sam Out.39.sam Out.40.sam Out.41.sam Out.42.sam Out.43.sam Out.44.sam Out.45.sam Out.46.sam Out.47.sam Out.48.sam Out.49.sam Out.50.sam Out.51.sam Out.52.sam Out.53.sam Out.54.sam Out.55.sam Out.56.sam Out.57.sam Out.58.sam Out.59.sam Out.60.sam Out.61.sam Out.62.sam Out.63.sam Out.64.sam Out.65.sam Out.66.sam Out.67.sam Out.68.sam Out.69.sam Out.70.sam Out.71.sam Out.72.sam Out.73.sam Out.74.sam Out.75.sam Out.76.sam Out.77.sam Out.78.sam Out.79.sam Out.80.sam Out.81.sam Out.82.sam Out.83.sam Out.84.sam Out.85.sam Out.86.sam Out.87.sam Out.88.sam Out.89.sam Out.90.sam Out.91.sam Out.92.sam Out.93.sam Out.94.sam Out.95.sam Out.96.sam Out.97.sam Out.98.sam Out.99.sam LOCAL ./sam_cat.sh Out.*.sam > Out.sam mem.err : mem.0.err mem.1.err mem.2.err mem.3.err mem.4.err mem.5.err mem.6.err mem.7.err mem.8.err mem.9.err mem.10.err mem.11.err mem.12.err mem.13.err mem.14.err mem.15.err mem.16.err mem.17.err mem.18.err mem.19.err mem.20.err mem.21.err mem.22.err mem.23.err mem.24.err mem.25.err mem.26.err mem.27.err mem.28.err mem.29.err mem.30.err mem.31.err mem.32.err mem.33.err mem.34.err mem.35.err mem.36.err mem.37.err mem.38.err mem.39.err mem.40.err mem.41.err mem.42.err mem.43.err mem.44.err mem.45.err mem.46.err mem.47.err mem.48.err mem.49.err mem.50.err mem.51.err mem.52.err mem.53.err mem.54.err mem.55.err mem.56.err mem.57.err mem.58.err mem.59.err mem.60.err mem.61.err mem.62.err mem.63.err mem.64.err mem.65.err mem.66.err mem.67.err mem.68.err mem.69.err mem.70.err mem.71.err mem.72.err mem.73.err mem.74.err mem.75.err mem.76.err mem.77.err mem.78.err mem.79.err mem.80.err mem.81.err mem.82.err mem.83.err mem.84.err mem.85.err mem.86.err mem.87.err mem.88.err mem.89.err mem.90.err mem.91.err mem.92.err mem.93.err mem.94.err mem.95.err mem.96.err mem.97.err mem.98.err mem.99.err LOCAL cat mem.*.err > mem.err +CATEGORY=pileup + Out.bam sort.err : samtools Out.sam ./samtools view -bS Out.sam | ./samtools sort - Out 2> sort.err pileup.txt ref.fasta.fai pileup.err : samtools ref.fasta Out.bam ./samtools mpileup -s -f ref.fasta Out.bam > pileup.txt 2> pileup.err +CATEGORY=hecil_preprocessing + List_RefHeader.txt Pileup_Set1.txt Pileup_Set2.txt : Split_Pileup.sh Create_SubsetPileup.sh pileup.txt LOCAL ./Split_Pileup.sh pileup.txt 2 2> Split_Pileup.err @@ -341,6 +353,12 @@ LowConf.txt : lc.0.out lc.1.out ref.fasta.0 ref.fasta.1 ref.fasta.2 ref.fasta.3 ref.fasta.4 ref.fasta.5 ref.fasta.6 ref.fasta.7 ref.fasta.8 ref.fasta.9 ref.fasta.10 ref.fasta.11 ref.fasta.12 ref.fasta.13 ref.fasta.14 ref.fasta.15 ref.fasta.16 ref.fasta.17 ref.fasta.18 ref.fasta.19 ref.fasta.20 ref.fasta.21 ref.fasta.22 ref.fasta.23 ref.fasta.24 ref.fasta.25 ref.fasta.26 ref.fasta.27 ref.fasta.28 ref.fasta.29 ref.fasta.30 ref.fasta.31 ref.fasta.32 ref.fasta.33 ref.fasta.34 ref.fasta.35 ref.fasta.36 ref.fasta.37 ref.fasta.38 ref.fasta.39 ref.fasta.40 ref.fasta.41 ref.fasta.42 ref.fasta.43 ref.fasta.44 ref.fasta.45 ref.fasta.46 ref.fasta.47 ref.fasta.48 ref.fasta.49 ref.fasta.50 ref.fasta.51 ref.fasta.52 ref.fasta.53 ref.fasta.54 ref.fasta.55 ref.fasta.56 ref.fasta.57 ref.fasta.58 ref.fasta.59 ref.fasta.60 ref.fasta.61 ref.fasta.62 ref.fasta.63 ref.fasta.64 ref.fasta.65 ref.fasta.66 ref.fasta.67 ref.fasta.68 ref.fasta.69 ref.fasta.70 ref.fasta.71 ref.fasta.72 ref.fasta.73 ref.fasta.74 ref.fasta.75 ref.fasta.76 ref.fasta.77 ref.fasta.78 ref.fasta.79 ref.fasta.80 ref.fasta.81 ref.fasta.82 ref.fasta.83 ref.fasta.84 ref.fasta.85 ref.fasta.86 ref.fasta.87 ref.fasta.88 ref.fasta.89 ref.fasta.90 ref.fasta.91 ref.fasta.92 ref.fasta.93 ref.fasta.94 ref.fasta.95 ref.fasta.96 ref.fasta.97 ref.fasta.98 ref.fasta.99 : fasta_reduce ref.fasta LOCAL ./fasta_reduce ref.fasta 1000 +CATEGORY=hecil_simulation +CORES=1 +MEMORY=100 +DISK=1300 +WALLTIME=10 + Corrected_ref.fasta.0 create.err.0 : Create_Corrected_AllLRReads.py ref.fasta.0 corr.out python Create_Corrected_AllLRReads.py ref.fasta.0 corr.out 2> create.err.0 @@ -641,6 +659,7 @@ Corrected_ref.fasta.98 create.err.98 : Create_Corrected_AllLRReads.py ref.fasta. Corrected_ref.fasta.99 create.err.99 : Create_Corrected_AllLRReads.py ref.fasta.99 corr.out python Create_Corrected_AllLRReads.py ref.fasta.99 corr.out 2> create.err.99 +CATEGORY=hecil_analysis + Corrected_ref.fasta : Corrected_ref.fasta.0 Corrected_ref.fasta.1 Corrected_ref.fasta.2 Corrected_ref.fasta.3 Corrected_ref.fasta.4 Corrected_ref.fasta.5 Corrected_ref.fasta.6 Corrected_ref.fasta.7 Corrected_ref.fasta.8 Corrected_ref.fasta.9 Corrected_ref.fasta.10 Corrected_ref.fasta.11 Corrected_ref.fasta.12 Corrected_ref.fasta.13 Corrected_ref.fasta.14 Corrected_ref.fasta.15 Corrected_ref.fasta.16 Corrected_ref.fasta.17 Corrected_ref.fasta.18 Corrected_ref.fasta.19 Corrected_ref.fasta.20 Corrected_ref.fasta.21 Corrected_ref.fasta.22 Corrected_ref.fasta.23 Corrected_ref.fasta.24 Corrected_ref.fasta.25 Corrected_ref.fasta.26 Corrected_ref.fasta.27 Corrected_ref.fasta.28 Corrected_ref.fasta.29 Corrected_ref.fasta.30 Corrected_ref.fasta.31 Corrected_ref.fasta.32 Corrected_ref.fasta.33 Corrected_ref.fasta.34 Corrected_ref.fasta.35 Corrected_ref.fasta.36 Corrected_ref.fasta.37 Corrected_ref.fasta.38 Corrected_ref.fasta.39 Corrected_ref.fasta.40 Corrected_ref.fasta.41 Corrected_ref.fasta.42 Corrected_ref.fasta.43 Corrected_ref.fasta.44 Corrected_ref.fasta.45 Corrected_ref.fasta.46 Corrected_ref.fasta.47 Corrected_ref.fasta.48 Corrected_ref.fasta.49 Corrected_ref.fasta.50 Corrected_ref.fasta.51 Corrected_ref.fasta.52 Corrected_ref.fasta.53 Corrected_ref.fasta.54 Corrected_ref.fasta.55 Corrected_ref.fasta.56 Corrected_ref.fasta.57 Corrected_ref.fasta.58 Corrected_ref.fasta.59 Corrected_ref.fasta.60 Corrected_ref.fasta.61 Corrected_ref.fasta.62 Corrected_ref.fasta.63 Corrected_ref.fasta.64 Corrected_ref.fasta.65 Corrected_ref.fasta.66 Corrected_ref.fasta.67 Corrected_ref.fasta.68 Corrected_ref.fasta.69 Corrected_ref.fasta.70 Corrected_ref.fasta.71 Corrected_ref.fasta.72 Corrected_ref.fasta.73 Corrected_ref.fasta.74 Corrected_ref.fasta.75 Corrected_ref.fasta.76 Corrected_ref.fasta.77 Corrected_ref.fasta.78 Corrected_ref.fasta.79 Corrected_ref.fasta.80 Corrected_ref.fasta.81 Corrected_ref.fasta.82 Corrected_ref.fasta.83 Corrected_ref.fasta.84 Corrected_ref.fasta.85 Corrected_ref.fasta.86 Corrected_ref.fasta.87 Corrected_ref.fasta.88 Corrected_ref.fasta.89 Corrected_ref.fasta.90 Corrected_ref.fasta.91 Corrected_ref.fasta.92 Corrected_ref.fasta.93 Corrected_ref.fasta.94 Corrected_ref.fasta.95 Corrected_ref.fasta.96 Corrected_ref.fasta.97 Corrected_ref.fasta.98 Corrected_ref.fasta.99 LOCAL cat Corrected_ref.fasta.* > Corrected_ref.fasta - diff --git a/shrimp/shrimp.json b/shrimp/shrimp.json index fd098f1..0e59872 100644 --- a/shrimp/shrimp.json +++ b/shrimp/shrimp.json @@ -1,12233 +1,15274 @@ - { - "define": - { - "QUERY":"query.csfasta", - "GENOME":"genome.fasta", - "MAPPER":"./rmapper-cs", - "MOPTIONS":"-M fast -M 50bp", - "SPLIT":"./split_fasta", - "SEQ_PER_SPLIT":10000, - "TOTAL_SEQ":7620000 - }, - "rules": - [ - - { - "command":"./split_fasta 10000 query.csfasta", - "inputs": - [ - "query.csfasta", - "./split_fasta" - ], - "outputs": - [ - "query.csfasta.0", - "query.csfasta.1", - "query.csfasta.2", - "query.csfasta.3", - "query.csfasta.4", - "query.csfasta.5", - "query.csfasta.6", - "query.csfasta.7", - "query.csfasta.8", - "query.csfasta.9", - "query.csfasta.10", - "query.csfasta.11", - "query.csfasta.12", - "query.csfasta.13", - "query.csfasta.14", - "query.csfasta.15", - "query.csfasta.16", - "query.csfasta.17", - "query.csfasta.18", - "query.csfasta.19", - "query.csfasta.20", - "query.csfasta.21", - "query.csfasta.22", - "query.csfasta.23", - "query.csfasta.24", - "query.csfasta.25", - "query.csfasta.26", - "query.csfasta.27", - "query.csfasta.28", - "query.csfasta.29", - "query.csfasta.30", - "query.csfasta.31", - "query.csfasta.32", - "query.csfasta.33", - "query.csfasta.34", - "query.csfasta.35", - "query.csfasta.36", - "query.csfasta.37", - "query.csfasta.38", - "query.csfasta.39", - 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query.csfasta.1 genome.fasta > output.1", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.1" - ], - "outputs": - [ - "output.1" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.2 genome.fasta > output.2", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.2" - ], - "outputs": - [ - "output.2" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.3 genome.fasta > output.3", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.3" - ], - "outputs": - [ - "output.3" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.4 genome.fasta > output.4", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.4" - ], - "outputs": - [ - "output.4" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.5 genome.fasta > output.5", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.5" - ], - "outputs": - [ - "output.5" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.6 genome.fasta > output.6", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.6" - ], - "outputs": - [ - "output.6" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.7 genome.fasta > output.7", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.7" - ], - "outputs": - [ - "output.7" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.8 genome.fasta > output.8", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.8" - ], - "outputs": - [ - "output.8" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.9 genome.fasta > output.9", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.9" - ], - "outputs": - [ - "output.9" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.10 genome.fasta > output.10", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.10" - ], - "outputs": - [ - "output.10" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.11 genome.fasta > output.11", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.11" - ], - "outputs": - [ - "output.11" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.12 genome.fasta > output.12", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.12" - ], - "outputs": - [ - "output.12" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.13 genome.fasta > output.13", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.13" - ], - "outputs": - [ - "output.13" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.14 genome.fasta > output.14", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.14" - ], - "outputs": - [ - "output.14" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.15 genome.fasta > output.15", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.15" - ], - "outputs": - [ - "output.15" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.16 genome.fasta > output.16", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.16" - ], - "outputs": - [ - "output.16" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.17 genome.fasta > output.17", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.17" - ], - "outputs": - [ - "output.17" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.18 genome.fasta > output.18", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.18" - ], - "outputs": - [ - "output.18" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.19 genome.fasta > output.19", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.19" - ], - "outputs": - [ - "output.19" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.20 genome.fasta > output.20", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.20" - ], - "outputs": - [ - "output.20" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.21 genome.fasta > output.21", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.21" - ], - "outputs": - [ - "output.21" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.22 genome.fasta > output.22", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.22" - ], - "outputs": - [ - "output.22" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.23 genome.fasta > output.23", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.23" - ], - "outputs": - [ - "output.23" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.24 genome.fasta > output.24", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.24" - ], - "outputs": - [ - "output.24" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.25 genome.fasta > output.25", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.25" - ], - "outputs": - [ - "output.25" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.26 genome.fasta > output.26", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.26" - ], - "outputs": - [ - "output.26" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.27 genome.fasta > output.27", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.27" - ], - "outputs": - [ - "output.27" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.28 genome.fasta > output.28", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.28" - ], - "outputs": - [ - "output.28" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.29 genome.fasta > output.29", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.29" - ], - "outputs": - [ - "output.29" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.30 genome.fasta > output.30", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.30" - ], - "outputs": - [ - "output.30" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.31 genome.fasta > output.31", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.31" - ], - "outputs": - [ - "output.31" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.32 genome.fasta > output.32", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.32" - ], - "outputs": - [ - "output.32" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.33 genome.fasta > output.33", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.33" - ], - "outputs": - [ - "output.33" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.34 genome.fasta > output.34", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.34" - ], - "outputs": - [ - "output.34" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.35 genome.fasta > output.35", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.35" - ], - "outputs": - [ - "output.35" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.36 genome.fasta > output.36", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.36" - ], - "outputs": - [ - "output.36" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.37 genome.fasta > output.37", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.37" - ], - "outputs": - [ - "output.37" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.38 genome.fasta > output.38", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.38" - ], - "outputs": - [ - "output.38" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.39 genome.fasta > output.39", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.39" - ], - "outputs": - [ - "output.39" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.40 genome.fasta > output.40", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.40" - ], - "outputs": - [ - "output.40" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.41 genome.fasta > output.41", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.41" - ], - "outputs": - [ - "output.41" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.42 genome.fasta > output.42", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.42" - ], - "outputs": - [ - "output.42" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.43 genome.fasta > output.43", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.43" - ], - "outputs": - [ - "output.43" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.44 genome.fasta > output.44", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.44" - ], - "outputs": - [ - "output.44" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.45 genome.fasta > output.45", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.45" - ], - "outputs": - [ - "output.45" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.46 genome.fasta > output.46", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.46" - ], - "outputs": - [ - "output.46" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.47 genome.fasta > output.47", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.47" - ], - "outputs": - [ - "output.47" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.48 genome.fasta > output.48", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.48" - ], - "outputs": - [ - "output.48" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.49 genome.fasta > output.49", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.49" - ], - "outputs": - [ - "output.49" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.50 genome.fasta > output.50", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.50" - ], - "outputs": - [ - "output.50" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.51 genome.fasta > output.51", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.51" - ], - "outputs": - [ - "output.51" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.52 genome.fasta > output.52", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.52" - ], - "outputs": - [ - "output.52" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.53 genome.fasta > output.53", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.53" - ], - "outputs": - [ - "output.53" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.54 genome.fasta > output.54", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.54" - ], - "outputs": - [ - "output.54" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.55 genome.fasta > output.55", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.55" - ], - "outputs": - [ - "output.55" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.56 genome.fasta > output.56", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.56" - ], - "outputs": - [ - "output.56" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.57 genome.fasta > output.57", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.57" - ], - "outputs": - [ - "output.57" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.58 genome.fasta > output.58", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.58" - ], - "outputs": - [ - "output.58" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.59 genome.fasta > output.59", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.59" - ], - "outputs": - [ - "output.59" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.60 genome.fasta > output.60", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.60" - ], - "outputs": - [ - "output.60" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.61 genome.fasta > output.61", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.61" - ], - "outputs": - [ - "output.61" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.62 genome.fasta > output.62", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.62" - ], - "outputs": - [ - "output.62" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.63 genome.fasta > output.63", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.63" - ], - "outputs": - [ - "output.63" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.64 genome.fasta > output.64", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.64" - ], - "outputs": - [ - "output.64" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.65 genome.fasta > output.65", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.65" - ], - "outputs": - [ - "output.65" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.66 genome.fasta > output.66", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.66" - ], - "outputs": - [ - "output.66" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.67 genome.fasta > output.67", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.67" - ], - "outputs": - [ - "output.67" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.68 genome.fasta > output.68", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.68" - ], - "outputs": - [ - "output.68" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.69 genome.fasta > output.69", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.69" - ], - "outputs": - [ - "output.69" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.70 genome.fasta > output.70", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.70" - ], - "outputs": - [ - "output.70" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.71 genome.fasta > output.71", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.71" - ], - "outputs": - [ - "output.71" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.72 genome.fasta > output.72", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.72" - ], - "outputs": - [ - "output.72" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.73 genome.fasta > output.73", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.73" - ], - "outputs": - [ - "output.73" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.74 genome.fasta > output.74", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.74" - ], - "outputs": - [ - "output.74" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.75 genome.fasta > output.75", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.75" - ], - "outputs": - [ - "output.75" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.76 genome.fasta > output.76", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.76" - ], - "outputs": - [ - "output.76" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.77 genome.fasta > output.77", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.77" - ], - "outputs": - [ - "output.77" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.78 genome.fasta > output.78", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.78" - ], - "outputs": - [ - "output.78" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.79 genome.fasta > output.79", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.79" - ], - "outputs": - [ - "output.79" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.80 genome.fasta > output.80", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.80" - ], - "outputs": - [ - "output.80" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.81 genome.fasta > output.81", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.81" - ], - "outputs": - [ - "output.81" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.82 genome.fasta > output.82", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.82" - ], - "outputs": - [ - "output.82" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.83 genome.fasta > output.83", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.83" - ], - "outputs": - [ - "output.83" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.84 genome.fasta > output.84", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.84" - ], - "outputs": - [ - "output.84" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.85 genome.fasta > output.85", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.85" - ], - "outputs": - [ - "output.85" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.86 genome.fasta > output.86", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.86" - ], - "outputs": - [ - "output.86" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.87 genome.fasta > output.87", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.87" - ], - "outputs": - [ - "output.87" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.88 genome.fasta > output.88", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.88" - ], - "outputs": - [ - "output.88" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.89 genome.fasta > output.89", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.89" - ], - "outputs": - [ - "output.89" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.90 genome.fasta > output.90", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.90" - ], - "outputs": - [ - "output.90" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.91 genome.fasta > output.91", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.91" - ], - "outputs": - [ - "output.91" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.92 genome.fasta > output.92", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.92" - ], - "outputs": - [ - "output.92" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.93 genome.fasta > output.93", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.93" - ], - "outputs": - [ - "output.93" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.94 genome.fasta > output.94", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.94" - ], - "outputs": - [ - "output.94" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.95 genome.fasta > output.95", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.95" - ], - "outputs": - [ - "output.95" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.96 genome.fasta > output.96", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.96" - ], - "outputs": - [ - "output.96" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.97 genome.fasta > output.97", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.97" - ], - "outputs": - [ - "output.97" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.98 genome.fasta > output.98", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.98" - ], - "outputs": - [ - "output.98" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.99 genome.fasta > output.99", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.99" - ], - "outputs": - [ - "output.99" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.100 genome.fasta > output.100", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.100" - ], - "outputs": - [ - "output.100" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.101 genome.fasta > output.101", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.101" - ], - "outputs": - [ - "output.101" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.102 genome.fasta > output.102", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.102" - ], - "outputs": - [ - "output.102" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.103 genome.fasta > output.103", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.103" - ], - "outputs": - [ - "output.103" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.104 genome.fasta > output.104", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.104" - ], - "outputs": - [ - "output.104" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.105 genome.fasta > output.105", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.105" - ], - "outputs": - [ - "output.105" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.106 genome.fasta > output.106", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.106" - ], - "outputs": - [ - "output.106" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.107 genome.fasta > output.107", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.107" - ], - "outputs": - [ - "output.107" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.108 genome.fasta > output.108", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.108" - ], - "outputs": - [ - "output.108" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.109 genome.fasta > output.109", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.109" - ], - "outputs": - [ - "output.109" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.110 genome.fasta > output.110", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.110" - ], - "outputs": - [ - "output.110" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.111 genome.fasta > output.111", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.111" - ], - "outputs": - [ - "output.111" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.112 genome.fasta > output.112", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.112" - ], - "outputs": - [ - "output.112" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.113 genome.fasta > output.113", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.113" - ], - "outputs": - [ - "output.113" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.114 genome.fasta > output.114", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.114" - ], - "outputs": - [ - "output.114" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.115 genome.fasta > output.115", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.115" - ], - "outputs": - [ - "output.115" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.116 genome.fasta > output.116", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.116" - ], - "outputs": - [ - "output.116" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.117 genome.fasta > output.117", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.117" - ], - "outputs": - [ - "output.117" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.118 genome.fasta > output.118", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.118" - ], - "outputs": - [ - "output.118" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.119 genome.fasta > output.119", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.119" - ], - "outputs": - [ - "output.119" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.120 genome.fasta > output.120", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.120" - ], - "outputs": - [ - "output.120" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.121 genome.fasta > output.121", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.121" - ], - "outputs": - [ - "output.121" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.122 genome.fasta > output.122", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.122" - ], - "outputs": - [ - "output.122" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.123 genome.fasta > output.123", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.123" - ], - "outputs": - [ - "output.123" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.124 genome.fasta > output.124", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.124" - ], - "outputs": - [ - "output.124" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.125 genome.fasta > output.125", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.125" - ], - "outputs": - [ - "output.125" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.126 genome.fasta > output.126", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.126" - ], - "outputs": - [ - "output.126" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.127 genome.fasta > output.127", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.127" - ], - "outputs": - [ - "output.127" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.128 genome.fasta > output.128", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.128" - ], - "outputs": - [ - "output.128" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.129 genome.fasta > output.129", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.129" - ], - "outputs": - [ - "output.129" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.130 genome.fasta > output.130", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.130" - ], - "outputs": - [ - "output.130" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.131 genome.fasta > output.131", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.131" - ], - "outputs": - [ - "output.131" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.132 genome.fasta > output.132", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.132" - ], - "outputs": - [ - "output.132" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.133 genome.fasta > output.133", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.133" - ], - "outputs": - [ - "output.133" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.134 genome.fasta > output.134", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.134" - ], - "outputs": - [ - "output.134" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.135 genome.fasta > output.135", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.135" - ], - "outputs": - [ - "output.135" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.136 genome.fasta > output.136", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.136" - ], - "outputs": - [ - "output.136" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.137 genome.fasta > output.137", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.137" - ], - "outputs": - [ - "output.137" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.138 genome.fasta > output.138", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.138" - ], - "outputs": - [ - "output.138" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.139 genome.fasta > output.139", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.139" - ], - "outputs": - [ - "output.139" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.140 genome.fasta > output.140", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.140" - ], - "outputs": - [ - "output.140" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.141 genome.fasta > output.141", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.141" - ], - "outputs": - [ - "output.141" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.142 genome.fasta > output.142", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.142" - ], - "outputs": - [ - "output.142" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.143 genome.fasta > output.143", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.143" - ], - "outputs": - [ - "output.143" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.144 genome.fasta > output.144", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.144" - ], - "outputs": - [ - "output.144" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.145 genome.fasta > output.145", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.145" - ], - "outputs": - [ - "output.145" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.146 genome.fasta > output.146", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.146" - ], - "outputs": - [ - "output.146" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.147 genome.fasta > output.147", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.147" - ], - "outputs": - [ - "output.147" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.148 genome.fasta > output.148", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.148" - ], - "outputs": - [ - "output.148" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.149 genome.fasta > output.149", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.149" - ], - "outputs": - [ - "output.149" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.150 genome.fasta > output.150", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.150" - ], - "outputs": - [ - "output.150" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.151 genome.fasta > output.151", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.151" - ], - "outputs": - [ - "output.151" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.152 genome.fasta > output.152", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.152" - ], - "outputs": - [ - "output.152" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.153 genome.fasta > output.153", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.153" - ], - "outputs": - [ - "output.153" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.154 genome.fasta > output.154", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.154" - ], - "outputs": - [ - "output.154" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.155 genome.fasta > output.155", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.155" - ], - "outputs": - [ - "output.155" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.156 genome.fasta > output.156", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.156" - ], - "outputs": - [ - "output.156" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.157 genome.fasta > output.157", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.157" - ], - "outputs": - [ - "output.157" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.158 genome.fasta > output.158", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.158" - ], - "outputs": - [ - "output.158" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.159 genome.fasta > output.159", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.159" - ], - "outputs": - [ - "output.159" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.160 genome.fasta > output.160", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.160" - ], - "outputs": - [ - "output.160" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.161 genome.fasta > output.161", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.161" - ], - "outputs": - [ - "output.161" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.162 genome.fasta > output.162", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.162" - ], - "outputs": - [ - "output.162" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.163 genome.fasta > output.163", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.163" - ], - "outputs": - [ - "output.163" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.164 genome.fasta > output.164", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.164" - ], - "outputs": - [ - "output.164" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.165 genome.fasta > output.165", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.165" - ], - "outputs": - [ - "output.165" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.166 genome.fasta > output.166", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.166" - ], - "outputs": - [ - "output.166" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.167 genome.fasta > output.167", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.167" - ], - "outputs": - [ - "output.167" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.168 genome.fasta > output.168", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.168" - ], - "outputs": - [ - "output.168" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.169 genome.fasta > output.169", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.169" - ], - "outputs": - [ - "output.169" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.170 genome.fasta > output.170", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.170" - ], - "outputs": - [ - "output.170" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.171 genome.fasta > output.171", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.171" - ], - "outputs": - [ - "output.171" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.172 genome.fasta > output.172", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.172" - ], - "outputs": - [ - "output.172" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.173 genome.fasta > output.173", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.173" - ], - "outputs": - [ - "output.173" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.174 genome.fasta > output.174", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.174" - ], - "outputs": - [ - "output.174" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.175 genome.fasta > output.175", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.175" - ], - "outputs": - [ - "output.175" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.176 genome.fasta > output.176", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.176" - ], - "outputs": - [ - "output.176" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.177 genome.fasta > output.177", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.177" - ], - "outputs": - [ - "output.177" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.178 genome.fasta > output.178", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.178" - ], - "outputs": - [ - "output.178" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.179 genome.fasta > output.179", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.179" - ], - "outputs": - [ - "output.179" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.180 genome.fasta > output.180", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.180" - ], - "outputs": - [ - "output.180" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.181 genome.fasta > output.181", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.181" - ], - "outputs": - [ - "output.181" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.182 genome.fasta > output.182", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.182" - ], - "outputs": - [ - "output.182" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.183 genome.fasta > output.183", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.183" - ], - "outputs": - [ - "output.183" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.184 genome.fasta > output.184", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.184" - ], - "outputs": - [ - "output.184" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.185 genome.fasta > output.185", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.185" - ], - "outputs": - [ - "output.185" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.186 genome.fasta > output.186", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.186" - ], - "outputs": - [ - "output.186" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.187 genome.fasta > output.187", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.187" - ], - "outputs": - [ - "output.187" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.188 genome.fasta > output.188", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.188" - ], - "outputs": - [ - "output.188" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.189 genome.fasta > output.189", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.189" - ], - "outputs": - [ - "output.189" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.190 genome.fasta > output.190", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.190" - ], - "outputs": - [ - "output.190" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.191 genome.fasta > output.191", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.191" - ], - "outputs": - [ - "output.191" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.192 genome.fasta > output.192", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.192" - ], - "outputs": - [ - "output.192" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.193 genome.fasta > output.193", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.193" - ], - "outputs": - [ - "output.193" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.194 genome.fasta > output.194", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.194" - ], - "outputs": - [ - "output.194" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.195 genome.fasta > output.195", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.195" - ], - "outputs": - [ - "output.195" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.196 genome.fasta > output.196", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.196" - ], - "outputs": - [ - "output.196" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.197 genome.fasta > output.197", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.197" - ], - "outputs": - [ - "output.197" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.198 genome.fasta > output.198", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.198" - ], - "outputs": - [ - "output.198" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.199 genome.fasta > output.199", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.199" - ], - "outputs": - [ - "output.199" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.200 genome.fasta > output.200", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.200" - ], - "outputs": - [ - "output.200" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.201 genome.fasta > output.201", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.201" - ], - "outputs": - [ - "output.201" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.202 genome.fasta > output.202", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.202" - ], - "outputs": - [ - "output.202" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.203 genome.fasta > output.203", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.203" - ], - "outputs": - [ - "output.203" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.204 genome.fasta > output.204", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.204" - ], - "outputs": - [ - "output.204" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.205 genome.fasta > output.205", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.205" - ], - "outputs": - [ - "output.205" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.206 genome.fasta > output.206", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.206" - ], - "outputs": - [ - "output.206" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.207 genome.fasta > output.207", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.207" - ], - "outputs": - [ - "output.207" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.208 genome.fasta > output.208", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.208" - ], - "outputs": - [ - "output.208" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.209 genome.fasta > output.209", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.209" - ], - "outputs": - [ - "output.209" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.210 genome.fasta > output.210", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.210" - ], - "outputs": - [ - "output.210" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.211 genome.fasta > output.211", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.211" - ], - "outputs": - [ - "output.211" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.212 genome.fasta > output.212", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.212" - ], - "outputs": - [ - "output.212" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.213 genome.fasta > output.213", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.213" - ], - "outputs": - [ - "output.213" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.214 genome.fasta > output.214", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.214" - ], - "outputs": - [ - "output.214" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.215 genome.fasta > output.215", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.215" - ], - "outputs": - [ - "output.215" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.216 genome.fasta > output.216", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.216" - ], - "outputs": - [ - "output.216" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.217 genome.fasta > output.217", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.217" - ], - "outputs": - [ - "output.217" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.218 genome.fasta > output.218", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.218" - ], - "outputs": - [ - "output.218" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.219 genome.fasta > output.219", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.219" - ], - "outputs": - [ - "output.219" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.220 genome.fasta > output.220", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.220" - ], - "outputs": - [ - "output.220" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.221 genome.fasta > output.221", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.221" - ], - "outputs": - [ - "output.221" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.222 genome.fasta > output.222", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.222" - ], - "outputs": - [ - "output.222" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.223 genome.fasta > output.223", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.223" - ], - "outputs": - [ - "output.223" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.224 genome.fasta > output.224", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.224" - ], - "outputs": - [ - "output.224" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.225 genome.fasta > output.225", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.225" - ], - "outputs": - [ - "output.225" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.226 genome.fasta > output.226", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.226" - ], - "outputs": - [ - "output.226" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.227 genome.fasta > output.227", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.227" - ], - "outputs": - [ - "output.227" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.228 genome.fasta > output.228", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.228" - ], - "outputs": - [ - "output.228" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.229 genome.fasta > output.229", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.229" - ], - "outputs": - [ - "output.229" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.230 genome.fasta > output.230", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.230" - ], - "outputs": - [ - "output.230" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.231 genome.fasta > output.231", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.231" - ], - "outputs": - [ - "output.231" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.232 genome.fasta > output.232", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.232" - ], - "outputs": - [ - "output.232" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.233 genome.fasta > output.233", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.233" - ], - "outputs": - [ - "output.233" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.234 genome.fasta > output.234", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.234" - ], - "outputs": - [ - "output.234" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.235 genome.fasta > output.235", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.235" - ], - "outputs": - [ - "output.235" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.236 genome.fasta > output.236", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.236" - ], - "outputs": - [ - "output.236" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.237 genome.fasta > output.237", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.237" - ], - "outputs": - [ - "output.237" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.238 genome.fasta > output.238", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.238" - ], - "outputs": - [ - "output.238" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.239 genome.fasta > output.239", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.239" - ], - "outputs": - [ - "output.239" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.240 genome.fasta > output.240", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.240" - ], - "outputs": - [ - "output.240" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.241 genome.fasta > output.241", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.241" - ], - "outputs": - [ - "output.241" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.242 genome.fasta > output.242", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.242" - ], - "outputs": - [ - "output.242" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.243 genome.fasta > output.243", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.243" - ], - "outputs": - [ - "output.243" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.244 genome.fasta > output.244", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.244" - ], - "outputs": - [ - "output.244" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.245 genome.fasta > output.245", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.245" - ], - "outputs": - [ - "output.245" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.246 genome.fasta > output.246", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.246" - ], - "outputs": - [ - "output.246" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.247 genome.fasta > output.247", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.247" - ], - "outputs": - [ - "output.247" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.248 genome.fasta > output.248", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.248" - ], - "outputs": - [ - "output.248" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.249 genome.fasta > output.249", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.249" - ], - "outputs": - [ - "output.249" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.250 genome.fasta > output.250", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.250" - ], - "outputs": - [ - "output.250" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.251 genome.fasta > output.251", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.251" - ], - "outputs": - [ - "output.251" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.252 genome.fasta > output.252", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.252" - ], - "outputs": - [ - "output.252" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.253 genome.fasta > output.253", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.253" - ], - "outputs": - [ - "output.253" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.254 genome.fasta > output.254", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.254" - ], - "outputs": - [ - "output.254" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.255 genome.fasta > output.255", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.255" - ], - "outputs": - [ - "output.255" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.256 genome.fasta > output.256", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.256" - ], - "outputs": - [ - "output.256" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.257 genome.fasta > output.257", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.257" - ], - "outputs": - [ - "output.257" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.258 genome.fasta > output.258", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.258" - ], - "outputs": - [ - "output.258" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.259 genome.fasta > output.259", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.259" - ], - "outputs": - [ - "output.259" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.260 genome.fasta > output.260", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.260" - ], - "outputs": - [ - "output.260" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.261 genome.fasta > output.261", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.261" - ], - "outputs": - [ - "output.261" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.262 genome.fasta > output.262", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.262" - ], - "outputs": - [ - "output.262" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.263 genome.fasta > output.263", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.263" - ], - "outputs": - [ - "output.263" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.264 genome.fasta > output.264", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.264" - ], - "outputs": - [ - "output.264" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.265 genome.fasta > output.265", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.265" - ], - "outputs": - [ - "output.265" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.266 genome.fasta > output.266", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.266" - ], - "outputs": - [ - "output.266" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.267 genome.fasta > output.267", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.267" - ], - "outputs": - [ - "output.267" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.268 genome.fasta > output.268", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.268" - ], - "outputs": - [ - "output.268" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.269 genome.fasta > output.269", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.269" - ], - "outputs": - [ - "output.269" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.270 genome.fasta > output.270", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.270" - ], - "outputs": - [ - "output.270" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.271 genome.fasta > output.271", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.271" - ], - "outputs": - [ - "output.271" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.272 genome.fasta > output.272", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.272" - ], - "outputs": - [ - "output.272" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.273 genome.fasta > output.273", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.273" - ], - "outputs": - [ - "output.273" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.274 genome.fasta > output.274", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.274" - ], - "outputs": - [ - "output.274" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.275 genome.fasta > output.275", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.275" - ], - "outputs": - [ - "output.275" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.276 genome.fasta > output.276", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.276" - ], - "outputs": - [ - "output.276" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.277 genome.fasta > output.277", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.277" - ], - "outputs": - [ - "output.277" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.278 genome.fasta > output.278", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.278" - ], - "outputs": - [ - "output.278" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.279 genome.fasta > output.279", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.279" - ], - "outputs": - [ - "output.279" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.280 genome.fasta > output.280", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.280" - ], - "outputs": - [ - "output.280" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.281 genome.fasta > output.281", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.281" - ], - "outputs": - [ - "output.281" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.282 genome.fasta > output.282", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.282" - ], - "outputs": - [ - "output.282" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.283 genome.fasta > output.283", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.283" - ], - "outputs": - [ - "output.283" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.284 genome.fasta > output.284", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.284" - ], - "outputs": - [ - "output.284" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.285 genome.fasta > output.285", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.285" - ], - "outputs": - [ - "output.285" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.286 genome.fasta > output.286", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.286" - ], - "outputs": - [ - "output.286" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.287 genome.fasta > output.287", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.287" - ], - "outputs": - [ - "output.287" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.288 genome.fasta > output.288", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.288" - ], - "outputs": - [ - "output.288" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.289 genome.fasta > output.289", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.289" - ], - "outputs": - [ - "output.289" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.290 genome.fasta > output.290", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.290" - ], - "outputs": - [ - "output.290" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.291 genome.fasta > output.291", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.291" - ], - "outputs": - [ - "output.291" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.292 genome.fasta > output.292", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.292" - ], - "outputs": - [ - "output.292" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.293 genome.fasta > output.293", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.293" - ], - "outputs": - [ - "output.293" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.294 genome.fasta > output.294", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.294" - ], - "outputs": - [ - "output.294" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.295 genome.fasta > output.295", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.295" - ], - "outputs": - [ - "output.295" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.296 genome.fasta > output.296", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.296" - ], - "outputs": - [ - "output.296" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.297 genome.fasta > output.297", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.297" - ], - "outputs": - [ - "output.297" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.298 genome.fasta > output.298", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.298" - ], - "outputs": - [ - "output.298" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.299 genome.fasta > output.299", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.299" - ], - "outputs": - [ - "output.299" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.300 genome.fasta > output.300", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.300" - ], - "outputs": - [ - "output.300" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.301 genome.fasta > output.301", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.301" - ], - "outputs": - [ - "output.301" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.302 genome.fasta > output.302", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.302" - ], - "outputs": - [ - "output.302" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.303 genome.fasta > output.303", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.303" - ], - "outputs": - [ - "output.303" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.304 genome.fasta > output.304", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.304" - ], - "outputs": - [ - "output.304" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.305 genome.fasta > output.305", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.305" - ], - "outputs": - [ - "output.305" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.306 genome.fasta > output.306", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.306" - ], - "outputs": - [ - "output.306" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.307 genome.fasta > output.307", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.307" - ], - "outputs": - [ - "output.307" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.308 genome.fasta > output.308", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.308" - ], - "outputs": - [ - "output.308" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.309 genome.fasta > output.309", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.309" - ], - "outputs": - [ - "output.309" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.310 genome.fasta > output.310", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.310" - ], - "outputs": - [ - "output.310" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.311 genome.fasta > output.311", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.311" - ], - "outputs": - [ - "output.311" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.312 genome.fasta > output.312", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.312" - ], - "outputs": - [ - "output.312" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.313 genome.fasta > output.313", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.313" - ], - "outputs": - [ - "output.313" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.314 genome.fasta > output.314", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.314" - ], - "outputs": - [ - "output.314" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.315 genome.fasta > output.315", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.315" - ], - "outputs": - [ - "output.315" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.316 genome.fasta > output.316", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.316" - ], - "outputs": - [ - "output.316" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.317 genome.fasta > output.317", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.317" - ], - "outputs": - [ - "output.317" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.318 genome.fasta > output.318", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.318" - ], - "outputs": - [ - "output.318" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.319 genome.fasta > output.319", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.319" - ], - "outputs": - [ - "output.319" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.320 genome.fasta > output.320", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.320" - ], - "outputs": - [ - "output.320" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.321 genome.fasta > output.321", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.321" - ], - "outputs": - [ - "output.321" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.322 genome.fasta > output.322", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.322" - ], - "outputs": - [ - "output.322" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.323 genome.fasta > output.323", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.323" - ], - "outputs": - [ - "output.323" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.324 genome.fasta > output.324", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.324" - ], - "outputs": - [ - "output.324" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.325 genome.fasta > output.325", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.325" - ], - "outputs": - [ - "output.325" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.326 genome.fasta > output.326", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.326" - ], - "outputs": - [ - "output.326" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.327 genome.fasta > output.327", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.327" - ], - "outputs": - [ - "output.327" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.328 genome.fasta > output.328", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.328" - ], - "outputs": - [ - "output.328" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.329 genome.fasta > output.329", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.329" - ], - "outputs": - [ - "output.329" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.330 genome.fasta > output.330", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.330" - ], - "outputs": - [ - "output.330" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.331 genome.fasta > output.331", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.331" - ], - "outputs": - [ - "output.331" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.332 genome.fasta > output.332", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.332" - ], - "outputs": - [ - "output.332" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.333 genome.fasta > output.333", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.333" - ], - "outputs": - [ - "output.333" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.334 genome.fasta > output.334", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.334" - ], - "outputs": - [ - "output.334" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.335 genome.fasta > output.335", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.335" - ], - "outputs": - [ - "output.335" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.336 genome.fasta > output.336", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.336" - ], - "outputs": - [ - "output.336" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.337 genome.fasta > output.337", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.337" - ], - "outputs": - [ - "output.337" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.338 genome.fasta > output.338", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.338" - ], - "outputs": - [ - "output.338" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.339 genome.fasta > output.339", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.339" - ], - "outputs": - [ - "output.339" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.340 genome.fasta > output.340", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.340" - ], - "outputs": - [ - "output.340" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.341 genome.fasta > output.341", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.341" - ], - "outputs": - [ - "output.341" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.342 genome.fasta > output.342", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.342" - ], - "outputs": - [ - "output.342" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.343 genome.fasta > output.343", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.343" - ], - "outputs": - [ - "output.343" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.344 genome.fasta > output.344", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.344" - ], - "outputs": - [ - "output.344" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.345 genome.fasta > output.345", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.345" - ], - "outputs": - [ - "output.345" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.346 genome.fasta > output.346", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.346" - ], - "outputs": - [ - "output.346" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.347 genome.fasta > output.347", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.347" - ], - "outputs": - [ - "output.347" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.348 genome.fasta > output.348", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.348" - ], - "outputs": - [ - "output.348" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.349 genome.fasta > output.349", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.349" - ], - "outputs": - [ - "output.349" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.350 genome.fasta > output.350", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.350" - ], - "outputs": - [ - "output.350" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.351 genome.fasta > output.351", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.351" - ], - "outputs": - [ - "output.351" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.352 genome.fasta > output.352", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.352" - ], - "outputs": - [ - "output.352" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.353 genome.fasta > output.353", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.353" - ], - "outputs": - [ - "output.353" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.354 genome.fasta > output.354", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.354" - ], - "outputs": - [ - "output.354" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.355 genome.fasta > output.355", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.355" - ], - "outputs": - [ - "output.355" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.356 genome.fasta > output.356", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.356" - ], - "outputs": - [ - "output.356" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.357 genome.fasta > output.357", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.357" - ], - "outputs": - [ - "output.357" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.358 genome.fasta > output.358", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.358" - ], - "outputs": - [ - "output.358" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.359 genome.fasta > output.359", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.359" - ], - "outputs": - [ - "output.359" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.360 genome.fasta > output.360", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.360" - ], - "outputs": - [ - "output.360" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.361 genome.fasta > output.361", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.361" - ], - "outputs": - [ - "output.361" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.362 genome.fasta > output.362", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.362" - ], - "outputs": - [ - "output.362" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.363 genome.fasta > output.363", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.363" - ], - "outputs": - [ - "output.363" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.364 genome.fasta > output.364", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.364" - ], - "outputs": - [ - "output.364" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.365 genome.fasta > output.365", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.365" - ], - "outputs": - [ - "output.365" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.366 genome.fasta > output.366", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.366" - ], - "outputs": - [ - "output.366" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.367 genome.fasta > output.367", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.367" - ], - "outputs": - [ - "output.367" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.368 genome.fasta > output.368", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.368" - ], - "outputs": - [ - "output.368" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.369 genome.fasta > output.369", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.369" - ], - "outputs": - [ - "output.369" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.370 genome.fasta > output.370", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.370" - ], - "outputs": - [ - "output.370" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.371 genome.fasta > output.371", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.371" - ], - "outputs": - [ - "output.371" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.372 genome.fasta > output.372", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.372" - ], - "outputs": - [ - "output.372" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.373 genome.fasta > output.373", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.373" - ], - "outputs": - [ - "output.373" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.374 genome.fasta > output.374", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.374" - ], - "outputs": - [ - "output.374" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.375 genome.fasta > output.375", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.375" - ], - "outputs": - [ - "output.375" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.376 genome.fasta > output.376", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.376" - ], - "outputs": - [ - "output.376" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.377 genome.fasta > output.377", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.377" - ], - "outputs": - [ - "output.377" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.378 genome.fasta > output.378", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.378" - ], - "outputs": - [ - "output.378" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.379 genome.fasta > output.379", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.379" - ], - "outputs": - [ - "output.379" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.380 genome.fasta > output.380", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.380" - ], - "outputs": - [ - "output.380" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.381 genome.fasta > output.381", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.381" - ], - "outputs": - [ - "output.381" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.382 genome.fasta > output.382", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.382" - ], - "outputs": - [ - "output.382" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.383 genome.fasta > output.383", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.383" - ], - "outputs": - [ - "output.383" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.384 genome.fasta > output.384", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.384" - ], - "outputs": - [ - "output.384" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.385 genome.fasta > output.385", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.385" - ], - "outputs": - [ - "output.385" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.386 genome.fasta > output.386", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.386" - ], - "outputs": - [ - "output.386" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.387 genome.fasta > output.387", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.387" - ], - "outputs": - [ - "output.387" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.388 genome.fasta > output.388", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.388" - ], - "outputs": - [ - "output.388" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.389 genome.fasta > output.389", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.389" - ], - "outputs": - [ - "output.389" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.390 genome.fasta > output.390", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.390" - ], - "outputs": - [ - "output.390" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.391 genome.fasta > output.391", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.391" - ], - "outputs": - [ - "output.391" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.392 genome.fasta > output.392", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.392" - ], - "outputs": - [ - "output.392" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.393 genome.fasta > output.393", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.393" - ], - "outputs": - [ - "output.393" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.394 genome.fasta > output.394", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.394" - ], - "outputs": - [ - "output.394" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.395 genome.fasta > output.395", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.395" - ], - "outputs": - [ - "output.395" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.396 genome.fasta > output.396", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.396" - ], - "outputs": - [ - "output.396" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.397 genome.fasta > output.397", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.397" - ], - "outputs": - [ - "output.397" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.398 genome.fasta > output.398", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.398" - ], - "outputs": - [ - "output.398" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.399 genome.fasta > output.399", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.399" - ], - "outputs": - [ - "output.399" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.400 genome.fasta > output.400", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.400" - ], - "outputs": - [ - "output.400" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.401 genome.fasta > output.401", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.401" - ], - "outputs": - [ - "output.401" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.402 genome.fasta > output.402", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.402" - ], - "outputs": - [ - "output.402" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.403 genome.fasta > output.403", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.403" - ], - "outputs": - [ - "output.403" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.404 genome.fasta > output.404", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.404" - ], - "outputs": - [ - "output.404" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.405 genome.fasta > output.405", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.405" - ], - "outputs": - [ - "output.405" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.406 genome.fasta > output.406", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.406" - ], - "outputs": - [ - "output.406" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.407 genome.fasta > output.407", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.407" - ], - "outputs": - [ - "output.407" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.408 genome.fasta > output.408", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.408" - ], - "outputs": - [ - "output.408" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.409 genome.fasta > output.409", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.409" - ], - "outputs": - [ - "output.409" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.410 genome.fasta > output.410", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.410" - ], - "outputs": - [ - "output.410" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.411 genome.fasta > output.411", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.411" - ], - "outputs": - [ - "output.411" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.412 genome.fasta > output.412", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.412" - ], - "outputs": - [ - "output.412" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.413 genome.fasta > output.413", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.413" - ], - "outputs": - [ - "output.413" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.414 genome.fasta > output.414", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.414" - ], - "outputs": - [ - "output.414" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.415 genome.fasta > output.415", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.415" - ], - "outputs": - [ - "output.415" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.416 genome.fasta > output.416", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.416" - ], - "outputs": - [ - "output.416" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.417 genome.fasta > output.417", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.417" - ], - "outputs": - [ - "output.417" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.418 genome.fasta > output.418", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.418" - ], - "outputs": - [ - "output.418" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.419 genome.fasta > output.419", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.419" - ], - "outputs": - [ - "output.419" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.420 genome.fasta > output.420", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.420" - ], - "outputs": - [ - "output.420" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.421 genome.fasta > output.421", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.421" - ], - "outputs": - [ - "output.421" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.422 genome.fasta > output.422", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.422" - ], - "outputs": - [ - "output.422" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.423 genome.fasta > output.423", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.423" - ], - "outputs": - [ - "output.423" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.424 genome.fasta > output.424", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.424" - ], - "outputs": - [ - "output.424" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.425 genome.fasta > output.425", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.425" - ], - "outputs": - [ - "output.425" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.426 genome.fasta > output.426", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.426" - ], - "outputs": - [ - "output.426" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.427 genome.fasta > output.427", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.427" - ], - "outputs": - [ - "output.427" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.428 genome.fasta > output.428", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.428" - ], - "outputs": - [ - "output.428" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.429 genome.fasta > output.429", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.429" - ], - "outputs": - [ - "output.429" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.430 genome.fasta > output.430", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.430" - ], - "outputs": - [ - "output.430" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.431 genome.fasta > output.431", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.431" - ], - "outputs": - [ - "output.431" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.432 genome.fasta > output.432", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.432" - ], - "outputs": - [ - "output.432" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.433 genome.fasta > output.433", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.433" - ], - "outputs": - [ - "output.433" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.434 genome.fasta > output.434", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.434" - ], - "outputs": - [ - "output.434" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.435 genome.fasta > output.435", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.435" - ], - "outputs": - [ - "output.435" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.436 genome.fasta > output.436", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.436" - ], - "outputs": - [ - "output.436" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.437 genome.fasta > output.437", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.437" - ], - "outputs": - [ - "output.437" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.438 genome.fasta > output.438", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.438" - ], - "outputs": - [ - "output.438" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.439 genome.fasta > output.439", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.439" - ], - "outputs": - [ - "output.439" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.440 genome.fasta > output.440", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.440" - ], - "outputs": - [ - "output.440" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.441 genome.fasta > output.441", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.441" - ], - "outputs": - [ - "output.441" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.442 genome.fasta > output.442", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.442" - ], - "outputs": - [ - "output.442" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.443 genome.fasta > output.443", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.443" - ], - "outputs": - [ - "output.443" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.444 genome.fasta > output.444", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.444" - ], - "outputs": - [ - "output.444" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.445 genome.fasta > output.445", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.445" - ], - "outputs": - [ - "output.445" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.446 genome.fasta > output.446", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.446" - ], - "outputs": - [ - "output.446" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.447 genome.fasta > output.447", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.447" - ], - "outputs": - [ - "output.447" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.448 genome.fasta > output.448", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.448" - ], - "outputs": - [ - "output.448" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.449 genome.fasta > output.449", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.449" - ], - "outputs": - [ - "output.449" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.450 genome.fasta > output.450", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.450" - ], - "outputs": - [ - "output.450" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.451 genome.fasta > output.451", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.451" - ], - "outputs": - [ - "output.451" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.452 genome.fasta > output.452", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.452" - ], - "outputs": - [ - "output.452" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.453 genome.fasta > output.453", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.453" - ], - "outputs": - [ - "output.453" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.454 genome.fasta > output.454", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.454" - ], - "outputs": - [ - "output.454" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.455 genome.fasta > output.455", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.455" - ], - "outputs": - [ - "output.455" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.456 genome.fasta > output.456", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.456" - ], - "outputs": - [ - "output.456" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.457 genome.fasta > output.457", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.457" - ], - "outputs": - [ - "output.457" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.458 genome.fasta > output.458", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.458" - ], - "outputs": - [ - "output.458" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.459 genome.fasta > output.459", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.459" - ], - "outputs": - [ - "output.459" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.460 genome.fasta > output.460", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.460" - ], - "outputs": - [ - "output.460" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.461 genome.fasta > output.461", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.461" - ], - "outputs": - [ - "output.461" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.462 genome.fasta > output.462", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.462" - ], - "outputs": - [ - "output.462" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.463 genome.fasta > output.463", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.463" - ], - "outputs": - [ - "output.463" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.464 genome.fasta > output.464", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.464" - ], - "outputs": - [ - "output.464" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.465 genome.fasta > output.465", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.465" - ], - "outputs": - [ - "output.465" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.466 genome.fasta > output.466", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.466" - ], - "outputs": - [ - "output.466" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.467 genome.fasta > output.467", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.467" - ], - "outputs": - [ - "output.467" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.468 genome.fasta > output.468", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.468" - ], - "outputs": - [ - "output.468" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.469 genome.fasta > output.469", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.469" - ], - "outputs": - [ - "output.469" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.470 genome.fasta > output.470", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.470" - ], - "outputs": - [ - "output.470" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.471 genome.fasta > output.471", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.471" - ], - "outputs": - [ - "output.471" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.472 genome.fasta > output.472", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.472" - ], - "outputs": - [ - "output.472" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.473 genome.fasta > output.473", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.473" - ], - "outputs": - [ - "output.473" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.474 genome.fasta > output.474", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.474" - ], - "outputs": - [ - "output.474" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.475 genome.fasta > output.475", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.475" - ], - "outputs": - [ - "output.475" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.476 genome.fasta > output.476", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.476" - ], - "outputs": - [ - "output.476" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.477 genome.fasta > output.477", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.477" - ], - "outputs": - [ - "output.477" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.478 genome.fasta > output.478", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.478" - ], - "outputs": - [ - "output.478" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.479 genome.fasta > output.479", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.479" - ], - "outputs": - [ - "output.479" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.480 genome.fasta > output.480", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.480" - ], - "outputs": - [ - "output.480" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.481 genome.fasta > output.481", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.481" - ], - "outputs": - [ - "output.481" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.482 genome.fasta > output.482", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.482" - ], - "outputs": - [ - "output.482" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.483 genome.fasta > output.483", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.483" - ], - "outputs": - [ - "output.483" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.484 genome.fasta > output.484", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.484" - ], - "outputs": - [ - "output.484" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.485 genome.fasta > output.485", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.485" - ], - "outputs": - [ - "output.485" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.486 genome.fasta > output.486", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.486" - ], - "outputs": - [ - "output.486" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.487 genome.fasta > output.487", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.487" - ], - "outputs": - [ - "output.487" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.488 genome.fasta > output.488", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.488" - ], - "outputs": - [ - "output.488" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.489 genome.fasta > output.489", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.489" - ], - "outputs": - [ - "output.489" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.490 genome.fasta > output.490", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.490" - ], - "outputs": - [ - "output.490" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.491 genome.fasta > output.491", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.491" - ], - "outputs": - [ - "output.491" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.492 genome.fasta > output.492", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.492" - ], - "outputs": - [ - "output.492" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.493 genome.fasta > output.493", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.493" - ], - "outputs": - [ - "output.493" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.494 genome.fasta > output.494", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.494" - ], - "outputs": - [ - "output.494" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.495 genome.fasta > output.495", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.495" - ], - "outputs": - [ - "output.495" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.496 genome.fasta > output.496", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.496" - ], - "outputs": - [ - "output.496" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.497 genome.fasta > output.497", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.497" - ], - "outputs": - [ - "output.497" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.498 genome.fasta > output.498", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.498" - ], - "outputs": - [ - "output.498" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.499 genome.fasta > output.499", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.499" - ], - "outputs": - [ - "output.499" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.500 genome.fasta > output.500", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.500" - ], - "outputs": - [ - "output.500" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.501 genome.fasta > output.501", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.501" - ], - "outputs": - [ - "output.501" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.502 genome.fasta > output.502", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.502" - ], - "outputs": - [ - "output.502" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.503 genome.fasta > output.503", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.503" - ], - "outputs": - [ - "output.503" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.504 genome.fasta > output.504", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.504" - ], - "outputs": - [ - "output.504" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.505 genome.fasta > output.505", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.505" - ], - "outputs": - [ - "output.505" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.506 genome.fasta > output.506", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.506" - ], - "outputs": - [ - "output.506" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.507 genome.fasta > output.507", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.507" - ], - "outputs": - [ - "output.507" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.508 genome.fasta > output.508", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.508" - ], - "outputs": - [ - "output.508" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.509 genome.fasta > output.509", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.509" - ], - "outputs": - [ - "output.509" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.510 genome.fasta > output.510", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.510" - ], - "outputs": - [ - "output.510" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.511 genome.fasta > output.511", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.511" - ], - "outputs": - [ - "output.511" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.512 genome.fasta > output.512", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.512" - ], - "outputs": - [ - "output.512" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.513 genome.fasta > output.513", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.513" - ], - "outputs": - [ - "output.513" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.514 genome.fasta > output.514", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.514" - ], - "outputs": - [ - "output.514" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.515 genome.fasta > output.515", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.515" - ], - "outputs": - [ - "output.515" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.516 genome.fasta > output.516", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.516" - ], - "outputs": - [ - "output.516" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.517 genome.fasta > output.517", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.517" - ], - "outputs": - [ - "output.517" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.518 genome.fasta > output.518", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.518" - ], - "outputs": - [ - "output.518" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.519 genome.fasta > output.519", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.519" - ], - "outputs": - [ - "output.519" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.520 genome.fasta > output.520", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.520" - ], - "outputs": - 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"./rmapper-cs", - "genome.fasta", - "query.csfasta.525" - ], - "outputs": - [ - "output.525" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.526 genome.fasta > output.526", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.526" - ], - "outputs": - [ - "output.526" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.527 genome.fasta > output.527", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.527" - ], - "outputs": - [ - "output.527" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.528 genome.fasta > output.528", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.528" - ], - "outputs": - [ - "output.528" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.529 genome.fasta > output.529", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.529" - ], - "outputs": - [ - "output.529" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.530 genome.fasta > output.530", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.530" - ], - "outputs": - [ - "output.530" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.531 genome.fasta > output.531", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.531" - ], - "outputs": - [ - "output.531" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.532 genome.fasta > output.532", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.532" - ], - "outputs": - [ - "output.532" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.533 genome.fasta > output.533", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.533" - ], - "outputs": - [ - "output.533" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.534 genome.fasta > output.534", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.534" - ], - "outputs": - 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50bp query.csfasta.544 genome.fasta > output.544", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.544" - ], - "outputs": - [ - "output.544" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.545 genome.fasta > output.545", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.545" - ], - "outputs": - [ - "output.545" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.546 genome.fasta > output.546", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.546" - ], - "outputs": - [ - "output.546" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.547 genome.fasta > output.547", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.547" - ], - "outputs": - [ - "output.547" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.548 genome.fasta > output.548", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.548" - ], - "outputs": - 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50bp query.csfasta.558 genome.fasta > output.558", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.558" - ], - "outputs": - [ - "output.558" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.559 genome.fasta > output.559", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.559" - ], - "outputs": - [ - "output.559" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.560 genome.fasta > output.560", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.560" - ], - "outputs": - [ - "output.560" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.561 genome.fasta > output.561", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.561" - ], - "outputs": - [ - "output.561" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.562 genome.fasta > output.562", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.562" - ], - "outputs": - 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"./rmapper-cs", - "genome.fasta", - "query.csfasta.567" - ], - "outputs": - [ - "output.567" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.568 genome.fasta > output.568", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.568" - ], - "outputs": - [ - "output.568" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.569 genome.fasta > output.569", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.569" - ], - "outputs": - [ - "output.569" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.570 genome.fasta > output.570", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.570" - ], - "outputs": - [ - "output.570" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.571 genome.fasta > output.571", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.571" - ], - "outputs": - [ - "output.571" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.572 genome.fasta > output.572", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.572" - ], - "outputs": - [ - "output.572" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.573 genome.fasta > output.573", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.573" - ], - "outputs": - [ - "output.573" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.574 genome.fasta > output.574", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.574" - ], - "outputs": - [ - "output.574" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.575 genome.fasta > output.575", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.575" - ], - "outputs": - [ - "output.575" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.576 genome.fasta > output.576", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.576" - ], - "outputs": - 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"./rmapper-cs", - "genome.fasta", - "query.csfasta.581" - ], - "outputs": - [ - "output.581" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.582 genome.fasta > output.582", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.582" - ], - "outputs": - [ - "output.582" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.583 genome.fasta > output.583", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.583" - ], - "outputs": - [ - "output.583" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.584 genome.fasta > output.584", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.584" - ], - "outputs": - [ - "output.584" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.585 genome.fasta > output.585", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.585" - ], - "outputs": - [ - "output.585" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.586 genome.fasta > output.586", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.586" - ], - "outputs": - [ - "output.586" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.587 genome.fasta > output.587", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.587" - ], - "outputs": - [ - "output.587" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.588 genome.fasta > output.588", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.588" - ], - "outputs": - [ - "output.588" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.589 genome.fasta > output.589", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.589" - ], - "outputs": - [ - "output.589" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.590 genome.fasta > output.590", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.590" - ], - "outputs": - [ - "output.590" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.591 genome.fasta > output.591", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.591" - ], - "outputs": - [ - "output.591" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.592 genome.fasta > output.592", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.592" - ], - "outputs": - [ - "output.592" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.593 genome.fasta > output.593", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.593" - ], - "outputs": - [ - "output.593" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.594 genome.fasta > output.594", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.594" - ], - "outputs": - [ - "output.594" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.595 genome.fasta > output.595", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.595" - ], - "outputs": - [ - "output.595" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.596 genome.fasta > output.596", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.596" - ], - "outputs": - [ - "output.596" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.597 genome.fasta > output.597", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.597" - ], - "outputs": - [ - "output.597" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.598 genome.fasta > output.598", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.598" - ], - "outputs": - [ - "output.598" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.599 genome.fasta > output.599", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.599" - ], - "outputs": - [ - "output.599" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.600 genome.fasta > output.600", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.600" - ], - "outputs": - [ - "output.600" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.601 genome.fasta > output.601", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.601" - ], - "outputs": - [ - "output.601" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.602 genome.fasta > output.602", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.602" - ], - "outputs": - [ - "output.602" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.603 genome.fasta > output.603", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.603" - ], - "outputs": - [ - "output.603" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.604 genome.fasta > output.604", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.604" - ], - "outputs": - 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"./rmapper-cs", - "genome.fasta", - "query.csfasta.609" - ], - "outputs": - [ - "output.609" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.610 genome.fasta > output.610", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.610" - ], - "outputs": - [ - "output.610" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.611 genome.fasta > output.611", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.611" - ], - "outputs": - [ - "output.611" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.612 genome.fasta > output.612", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.612" - ], - "outputs": - [ - "output.612" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.613 genome.fasta > output.613", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.613" - ], - "outputs": - [ - "output.613" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.614 genome.fasta > output.614", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.614" - ], - "outputs": - [ - "output.614" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.615 genome.fasta > output.615", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.615" - ], - "outputs": - [ - "output.615" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.616 genome.fasta > output.616", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.616" - ], - "outputs": - [ - "output.616" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.617 genome.fasta > output.617", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.617" - ], - "outputs": - [ - "output.617" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.618 genome.fasta > output.618", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.618" - ], - "outputs": - [ - "output.618" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.619 genome.fasta > output.619", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.619" - ], - "outputs": - [ - "output.619" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.620 genome.fasta > output.620", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.620" - ], - "outputs": - [ - "output.620" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.621 genome.fasta > output.621", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.621" - ], - "outputs": - [ - "output.621" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.622 genome.fasta > output.622", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.622" - ], - "outputs": - [ - "output.622" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.623 genome.fasta > output.623", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.623" - ], - "outputs": - [ - "output.623" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.624 genome.fasta > output.624", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.624" - ], - "outputs": - [ - "output.624" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.625 genome.fasta > output.625", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.625" - ], - "outputs": - [ - "output.625" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.626 genome.fasta > output.626", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.626" - ], - "outputs": - [ - "output.626" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.627 genome.fasta > output.627", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.627" - ], - "outputs": - [ - "output.627" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.628 genome.fasta > output.628", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.628" - ], - "outputs": - [ - "output.628" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.629 genome.fasta > output.629", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.629" - ], - "outputs": - [ - "output.629" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.630 genome.fasta > output.630", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.630" - ], - "outputs": - [ - "output.630" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.631 genome.fasta > output.631", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.631" - ], - "outputs": - [ - "output.631" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.632 genome.fasta > output.632", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.632" - ], - "outputs": - [ - "output.632" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.633 genome.fasta > output.633", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.633" - ], - "outputs": - [ - "output.633" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.634 genome.fasta > output.634", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.634" - ], - "outputs": - [ - "output.634" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.635 genome.fasta > output.635", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.635" - ], - "outputs": - [ - "output.635" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.636 genome.fasta > output.636", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.636" - ], - "outputs": - [ - "output.636" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.637 genome.fasta > output.637", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.637" - ], - "outputs": - [ - "output.637" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.638 genome.fasta > output.638", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.638" - ], - "outputs": - [ - "output.638" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.639 genome.fasta > output.639", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.639" - ], - "outputs": - [ - "output.639" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.640 genome.fasta > output.640", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.640" - ], - "outputs": - [ - "output.640" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.641 genome.fasta > output.641", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.641" - ], - "outputs": - [ - "output.641" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.642 genome.fasta > output.642", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.642" - ], - "outputs": - [ - "output.642" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.643 genome.fasta > output.643", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.643" - ], - "outputs": - [ - "output.643" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.644 genome.fasta > output.644", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.644" - ], - "outputs": - [ - "output.644" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.645 genome.fasta > output.645", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.645" - ], - "outputs": - [ - "output.645" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.646 genome.fasta > output.646", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.646" - ], - "outputs": - [ - "output.646" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.647 genome.fasta > output.647", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.647" - ], - "outputs": - [ - "output.647" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.648 genome.fasta > output.648", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.648" - ], - "outputs": - [ - "output.648" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.649 genome.fasta > output.649", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.649" - ], - "outputs": - [ - "output.649" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.650 genome.fasta > output.650", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.650" - ], - "outputs": - [ - "output.650" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.651 genome.fasta > output.651", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.651" - ], - "outputs": - [ - "output.651" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.652 genome.fasta > output.652", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.652" - ], - "outputs": - [ - "output.652" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.653 genome.fasta > output.653", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.653" - ], - "outputs": - [ - "output.653" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.654 genome.fasta > output.654", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.654" - ], - "outputs": - [ - "output.654" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.655 genome.fasta > output.655", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.655" - ], - "outputs": - [ - "output.655" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.656 genome.fasta > output.656", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.656" - ], - "outputs": - [ - "output.656" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.657 genome.fasta > output.657", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.657" - ], - "outputs": - [ - "output.657" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.658 genome.fasta > output.658", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.658" - ], - "outputs": - [ - "output.658" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.659 genome.fasta > output.659", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.659" - ], - "outputs": - [ - "output.659" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.660 genome.fasta > output.660", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.660" - ], - "outputs": - [ - "output.660" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.661 genome.fasta > output.661", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.661" - ], - "outputs": - [ - "output.661" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.662 genome.fasta > output.662", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.662" - ], - "outputs": - [ - "output.662" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.663 genome.fasta > output.663", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.663" - ], - "outputs": - [ - "output.663" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.664 genome.fasta > output.664", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.664" - ], - "outputs": - [ - "output.664" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.665 genome.fasta > output.665", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.665" - ], - "outputs": - [ - "output.665" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.666 genome.fasta > output.666", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.666" - ], - "outputs": - [ - "output.666" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.667 genome.fasta > output.667", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.667" - ], - "outputs": - [ - "output.667" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.668 genome.fasta > output.668", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.668" - ], - "outputs": - [ - "output.668" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.669 genome.fasta > output.669", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.669" - ], - "outputs": - [ - "output.669" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.670 genome.fasta > output.670", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.670" - ], - "outputs": - [ - "output.670" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.671 genome.fasta > output.671", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.671" - ], - "outputs": - [ - "output.671" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.672 genome.fasta > output.672", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.672" - ], - "outputs": - [ - "output.672" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.673 genome.fasta > output.673", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.673" - ], - "outputs": - [ - "output.673" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.674 genome.fasta > output.674", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.674" - ], - "outputs": - [ - "output.674" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.675 genome.fasta > output.675", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.675" - ], - "outputs": - [ - "output.675" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.676 genome.fasta > output.676", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.676" - ], - "outputs": - [ - "output.676" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.677 genome.fasta > output.677", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.677" - ], - "outputs": - [ - "output.677" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.678 genome.fasta > output.678", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.678" - ], - "outputs": - [ - "output.678" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.679 genome.fasta > output.679", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.679" - ], - "outputs": - [ - "output.679" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.680 genome.fasta > output.680", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.680" - ], - "outputs": - [ - "output.680" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.681 genome.fasta > output.681", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.681" - ], - "outputs": - [ - "output.681" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.682 genome.fasta > output.682", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.682" - ], - "outputs": - [ - "output.682" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.683 genome.fasta > output.683", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.683" - ], - "outputs": - [ - "output.683" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.684 genome.fasta > output.684", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.684" - ], - "outputs": - [ - "output.684" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.685 genome.fasta > output.685", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.685" - ], - "outputs": - [ - "output.685" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.686 genome.fasta > output.686", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.686" - ], - "outputs": - [ - "output.686" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.687 genome.fasta > output.687", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.687" - ], - "outputs": - [ - "output.687" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.688 genome.fasta > output.688", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.688" - ], - "outputs": - 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"./rmapper-cs", - "genome.fasta", - "query.csfasta.693" - ], - "outputs": - [ - "output.693" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.694 genome.fasta > output.694", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.694" - ], - "outputs": - [ - "output.694" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.695 genome.fasta > output.695", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.695" - ], - "outputs": - [ - "output.695" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.696 genome.fasta > output.696", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.696" - ], - "outputs": - [ - "output.696" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.697 genome.fasta > output.697", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.697" - ], - "outputs": - [ - "output.697" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.698 genome.fasta > output.698", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.698" - ], - "outputs": - [ - "output.698" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.699 genome.fasta > output.699", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.699" - ], - "outputs": - [ - "output.699" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.700 genome.fasta > output.700", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.700" - ], - "outputs": - [ - "output.700" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.701 genome.fasta > output.701", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.701" - ], - "outputs": - [ - "output.701" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.702 genome.fasta > output.702", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.702" - ], - "outputs": - 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50bp query.csfasta.712 genome.fasta > output.712", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.712" - ], - "outputs": - [ - "output.712" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.713 genome.fasta > output.713", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.713" - ], - "outputs": - [ - "output.713" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.714 genome.fasta > output.714", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.714" - ], - "outputs": - [ - "output.714" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.715 genome.fasta > output.715", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.715" - ], - "outputs": - [ - "output.715" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.716 genome.fasta > output.716", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.716" - ], - "outputs": - 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50bp query.csfasta.726 genome.fasta > output.726", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.726" - ], - "outputs": - [ - "output.726" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.727 genome.fasta > output.727", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.727" - ], - "outputs": - [ - "output.727" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.728 genome.fasta > output.728", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.728" - ], - "outputs": - [ - "output.728" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.729 genome.fasta > output.729", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.729" - ], - "outputs": - [ - "output.729" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.730 genome.fasta > output.730", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.730" - ], - "outputs": - 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50bp query.csfasta.740 genome.fasta > output.740", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.740" - ], - "outputs": - [ - "output.740" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.741 genome.fasta > output.741", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.741" - ], - "outputs": - [ - "output.741" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.742 genome.fasta > output.742", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.742" - ], - "outputs": - [ - "output.742" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.743 genome.fasta > output.743", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.743" - ], - "outputs": - [ - "output.743" - ] - }, - - { - "command":"./rmapper-cs -M fast -M 50bp query.csfasta.744 genome.fasta > output.744", - "inputs": - [ - "./rmapper-cs", - "genome.fasta", - "query.csfasta.744" - ], - "outputs": - 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output.756 output.757 output.758 output.759 output.760 output.761 > output.txt" + } + ] } diff --git a/shrimp/shrimp.jx b/shrimp/shrimp.jx index e42eaf7..ea7f677 100644 --- a/shrimp/shrimp.jx +++ b/shrimp/shrimp.jx @@ -12,7 +12,7 @@ }, "rules": [ - + { "command":format("%s %d %s",SPLIT,SEQ_PER_SPLIT,QUERY), "inputs": @@ -24,9 +24,10 @@ [ format("%s.%d",QUERY,x) for x in range(ceil(TOTAL_SEQ/SEQ_PER_SPLIT)) ], - "local_job":true + "local_job":true, + "category": "preprocessing" }, - + { "command":format("%s %s %s.%d %s > output.%d",MAPPER,MOPTIONS,QUERY,x,GENOME,x), "inputs": @@ -38,9 +39,17 @@ "outputs": [ format("output.%d",x) - ] + ], + "resources" : { + "cores":1, + "memory":800, + "disk":400, + "wall-time":300 + }, + "category": "simulation" + } for x in range(ceil(TOTAL_SEQ/SEQ_PER_SPLIT)), - + { "command":format("cat %s > output.txt",join([format("output.%d",x) for x in range(ceil(TOTAL_SEQ/SEQ_PER_SPLIT))])), "inputs": @@ -51,7 +60,8 @@ [ "output.txt" ], - "local_job":true + "local_job":true, + "category": "analysis" } ] } diff --git a/shrimp/shrimp.mf b/shrimp/shrimp.mf index 092ead5..64bc82e 100644 --- a/shrimp/shrimp.mf +++ b/shrimp/shrimp.mf @@ -4,9 +4,17 @@ OPTIONS=-M fast -M 50bp +CATEGORY=preprocessing + query.csfasta.0 query.csfasta.1 query.csfasta.2 query.csfasta.3 query.csfasta.4 query.csfasta.5 query.csfasta.6 query.csfasta.7 query.csfasta.8 query.csfasta.9 query.csfasta.10 query.csfasta.11 query.csfasta.12 query.csfasta.13 query.csfasta.14 query.csfasta.15 query.csfasta.16 query.csfasta.17 query.csfasta.18 query.csfasta.19 query.csfasta.20 query.csfasta.21 query.csfasta.22 query.csfasta.23 query.csfasta.24 query.csfasta.25 query.csfasta.26 query.csfasta.27 query.csfasta.28 query.csfasta.29 query.csfasta.30 query.csfasta.31 query.csfasta.32 query.csfasta.33 query.csfasta.34 query.csfasta.35 query.csfasta.36 query.csfasta.37 query.csfasta.38 query.csfasta.39 query.csfasta.40 query.csfasta.41 query.csfasta.42 query.csfasta.43 query.csfasta.44 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query.csfasta.708 query.csfasta.709 query.csfasta.710 query.csfasta.711 query.csfasta.712 query.csfasta.713 query.csfasta.714 query.csfasta.715 query.csfasta.716 query.csfasta.717 query.csfasta.718 query.csfasta.719 query.csfasta.720 query.csfasta.721 query.csfasta.722 query.csfasta.723 query.csfasta.724 query.csfasta.725 query.csfasta.726 query.csfasta.727 query.csfasta.728 query.csfasta.729 query.csfasta.730 query.csfasta.731 query.csfasta.732 query.csfasta.733 query.csfasta.734 query.csfasta.735 query.csfasta.736 query.csfasta.737 query.csfasta.738 query.csfasta.739 query.csfasta.740 query.csfasta.741 query.csfasta.742 query.csfasta.743 query.csfasta.744 query.csfasta.745 query.csfasta.746 query.csfasta.747 query.csfasta.748 query.csfasta.749 query.csfasta.750 query.csfasta.751 query.csfasta.752 query.csfasta.753 query.csfasta.754 query.csfasta.755 query.csfasta.756 query.csfasta.757 query.csfasta.758 query.csfasta.759 query.csfasta.760 query.csfasta.761: query.csfasta LOCAL ./split_fasta 10000 query.csfasta +CATEGORY=simulation +CORES=1 +MEMORY=800 +DISK=400 +WALLTIME=300 + output.0: query.csfasta.0 genome.fasta rmapper-cs ./rmapper-cs $OPTIONS query.csfasta.0 genome.fasta > output.0 @@ -2293,5 +2301,7 @@ output.760: query.csfasta.760 genome.fasta rmapper-cs output.761: query.csfasta.761 genome.fasta rmapper-cs ./rmapper-cs $OPTIONS query.csfasta.761 genome.fasta > output.761 +CATEGORY=analysis + output.txt: output.0 output.1 output.2 output.3 output.4 output.5 output.6 output.7 output.8 output.9 output.10 output.11 output.12 output.13 output.14 output.15 output.16 output.17 output.18 output.19 output.20 output.21 output.22 output.23 output.24 output.25 output.26 output.27 output.28 output.29 output.30 output.31 output.32 output.33 output.34 output.35 output.36 output.37 output.38 output.39 output.40 output.41 output.42 output.43 output.44 output.45 output.46 output.47 output.48 output.49 output.50 output.51 output.52 output.53 output.54 output.55 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output.697 output.698 output.699 output.700 output.701 output.702 output.703 output.704 output.705 output.706 output.707 output.708 output.709 output.710 output.711 output.712 output.713 output.714 output.715 output.716 output.717 output.718 output.719 output.720 output.721 output.722 output.723 output.724 output.725 output.726 output.727 output.728 output.729 output.730 output.731 output.732 output.733 output.734 output.735 output.736 output.737 output.738 output.739 output.740 output.741 output.742 output.743 output.744 output.745 output.746 output.747 output.748 output.749 output.750 output.751 output.752 output.753 output.754 output.755 output.756 output.757 output.758 output.759 output.760 output.761 LOCAL cat output.0 output.1 output.2 output.3 output.4 output.5 output.6 output.7 output.8 output.9 output.10 output.11 output.12 output.13 output.14 output.15 output.16 output.17 output.18 output.19 output.20 output.21 output.22 output.23 output.24 output.25 output.26 output.27 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output.489 output.490 output.491 output.492 output.493 output.494 output.495 output.496 output.497 output.498 output.499 output.500 output.501 output.502 output.503 output.504 output.505 output.506 output.507 output.508 output.509 output.510 output.511 output.512 output.513 output.514 output.515 output.516 output.517 output.518 output.519 output.520 output.521 output.522 output.523 output.524 output.525 output.526 output.527 output.528 output.529 output.530 output.531 output.532 output.533 output.534 output.535 output.536 output.537 output.538 output.539 output.540 output.541 output.542 output.543 output.544 output.545 output.546 output.547 output.548 output.549 output.550 output.551 output.552 output.553 output.554 output.555 output.556 output.557 output.558 output.559 output.560 output.561 output.562 output.563 output.564 output.565 output.566 output.567 output.568 output.569 output.570 output.571 output.572 output.573 output.574 output.575 output.576 output.577 output.578 output.579 output.580 output.581 output.582 output.583 output.584 output.585 output.586 output.587 output.588 output.589 output.590 output.591 output.592 output.593 output.594 output.595 output.596 output.597 output.598 output.599 output.600 output.601 output.602 output.603 output.604 output.605 output.606 output.607 output.608 output.609 output.610 output.611 output.612 output.613 output.614 output.615 output.616 output.617 output.618 output.619 output.620 output.621 output.622 output.623 output.624 output.625 output.626 output.627 output.628 output.629 output.630 output.631 output.632 output.633 output.634 output.635 output.636 output.637 output.638 output.639 output.640 output.641 output.642 output.643 output.644 output.645 output.646 output.647 output.648 output.649 output.650 output.651 output.652 output.653 output.654 output.655 output.656 output.657 output.658 output.659 output.660 output.661 output.662 output.663 output.664 output.665 output.666 output.667 output.668 output.669 output.670 output.671 output.672 output.673 output.674 output.675 output.676 output.677 output.678 output.679 output.680 output.681 output.682 output.683 output.684 output.685 output.686 output.687 output.688 output.689 output.690 output.691 output.692 output.693 output.694 output.695 output.696 output.697 output.698 output.699 output.700 output.701 output.702 output.703 output.704 output.705 output.706 output.707 output.708 output.709 output.710 output.711 output.712 output.713 output.714 output.715 output.716 output.717 output.718 output.719 output.720 output.721 output.722 output.723 output.724 output.725 output.726 output.727 output.728 output.729 output.730 output.731 output.732 output.733 output.734 output.735 output.736 output.737 output.738 output.739 output.740 output.741 output.742 output.743 output.744 output.745 output.746 output.747 output.748 output.749 output.750 output.751 output.752 output.753 output.754 output.755 output.756 output.757 output.758 output.759 output.760 output.761 > output.txt diff --git a/ssaha/ssaha.mf b/ssaha/ssaha.mf old mode 100755 new mode 100644 index 0bf88c1..c628daf --- a/ssaha/ssaha.mf +++ b/ssaha/ssaha.mf @@ -1,7 +1,16 @@ OPTIONS=-tags 1 -rtype abi -score 30 -seeds 5 -output ssaha2 -query.fastq.0 query.fastq.1 query.fastq.2 query.fastq.3 query.fastq.4 query.fastq.5 query.fastq.6 query.fastq.7 query.fastq.8 query.fastq.9 query.fastq.10 query.fastq.11 query.fastq.12 query.fastq.13 query.fastq.14 query.fastq.15 query.fastq.16 query.fastq.17 query.fastq.18 query.fastq.19 query.fastq.20 query.fastq.21 query.fastq.22 query.fastq.23 query.fastq.24 query.fastq.25 query.fastq.26 query.fastq.27 query.fastq.28 query.fastq.29 query.fastq.30 query.fastq.31 query.fastq.32 query.fastq.33 query.fastq.34 query.fastq.35 query.fastq.36 query.fastq.37 query.fastq.38 query.fastq.39 query.fastq.40 query.fastq.41 query.fastq.42 query.fastq.43 query.fastq.44 query.fastq.45 query.fastq.46 query.fastq.47 query.fastq.48 query.fastq.49 query.fastq.50 query.fastq.51 query.fastq.52 query.fastq.53 query.fastq.54 query.fastq.55 query.fastq.56 query.fastq.57 query.fastq.58 query.fastq.59 query.fastq.60 query.fastq.61 query.fastq.62 query.fastq.63 query.fastq.64 query.fastq.65 query.fastq.66 query.fastq.67 query.fastq.68 query.fastq.69 query.fastq.70 query.fastq.71 query.fastq.72 query.fastq.73 query.fastq.74 query.fastq.75 query.fastq.76 query.fastq.77 query.fastq.78 query.fastq.79 query.fastq.80 query.fastq.81 query.fastq.82 query.fastq.83 query.fastq.84 query.fastq.85 query.fastq.86 query.fastq.87 query.fastq.88 query.fastq.89 query.fastq.90 query.fastq.91 query.fastq.92 query.fastq.93 query.fastq.94 query.fastq.95 query.fastq.96 query.fastq.97 query.fastq.98 query.fastq.99 : query.fastq fastq_reduce + +CATEGORY=preprocessing + +query.fastq.0 query.fastq.1 query.fastq.2 query.fastq.3 query.fastq.4 query.fastq.5 query.fastq.6 query.fastq.7 query.fastq.8 query.fastq.9 query.fastq.10 query.fastq.11 query.fastq.12 query.fastq.13 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query.fastq.949 query.fastq.950 query.fastq.951 query.fastq.952 query.fastq.953 query.fastq.954 query.fastq.955 query.fastq.956 query.fastq.957 query.fastq.958 query.fastq.959 query.fastq.960 query.fastq.961 query.fastq.962 query.fastq.963 query.fastq.964 query.fastq.965 query.fastq.966 query.fastq.967 query.fastq.968 query.fastq.969 query.fastq.970 query.fastq.971 query.fastq.972 query.fastq.973 query.fastq.974 query.fastq.975 query.fastq.976 query.fastq.977 query.fastq.978 query.fastq.979 query.fastq.980 query.fastq.981 query.fastq.982 query.fastq.983 query.fastq.984 query.fastq.985 query.fastq.986 query.fastq.987 query.fastq.988 query.fastq.989 query.fastq.990 query.fastq.991 query.fastq.992 query.fastq.993 query.fastq.994 query.fastq.995 query.fastq.996 query.fastq.997 query.fastq.998 query.fastq.999 : query.fastq fastq_reduce LOCAL ./fastq_reduce query.fastq 1000 +CATEGORY=simulation +CORES=1 +MEMORY=1300 +DISK=400 +WALLTIME=20 + output.fastq.0: query.fastq.0 db.fastq ssaha2 ./ssaha2 $OPTIONS db.fastq query.fastq.0 > output.fastq.0 @@ -302,6 +311,2707 @@ output.fastq.98: query.fastq.98 db.fastq ssaha2 output.fastq.99: query.fastq.99 db.fastq ssaha2 ./ssaha2 $OPTIONS db.fastq query.fastq.99 > output.fastq.99 -output.fastq: output.fastq.0 output.fastq.1 output.fastq.2 output.fastq.3 output.fastq.4 output.fastq.5 output.fastq.6 output.fastq.7 output.fastq.8 output.fastq.9 output.fastq.10 output.fastq.11 output.fastq.12 output.fastq.13 output.fastq.14 output.fastq.15 output.fastq.16 output.fastq.17 output.fastq.18 output.fastq.19 output.fastq.20 output.fastq.21 output.fastq.22 output.fastq.23 output.fastq.24 output.fastq.25 output.fastq.26 output.fastq.27 output.fastq.28 output.fastq.29 output.fastq.30 output.fastq.31 output.fastq.32 output.fastq.33 output.fastq.34 output.fastq.35 output.fastq.36 output.fastq.37 output.fastq.38 output.fastq.39 output.fastq.40 output.fastq.41 output.fastq.42 output.fastq.43 output.fastq.44 output.fastq.45 output.fastq.46 output.fastq.47 output.fastq.48 output.fastq.49 output.fastq.50 output.fastq.51 output.fastq.52 output.fastq.53 output.fastq.54 output.fastq.55 output.fastq.56 output.fastq.57 output.fastq.58 output.fastq.59 output.fastq.60 output.fastq.61 output.fastq.62 output.fastq.63 output.fastq.64 output.fastq.65 output.fastq.66 output.fastq.67 output.fastq.68 output.fastq.69 output.fastq.70 output.fastq.71 output.fastq.72 output.fastq.73 output.fastq.74 output.fastq.75 output.fastq.76 output.fastq.77 output.fastq.78 output.fastq.79 output.fastq.80 output.fastq.81 output.fastq.82 output.fastq.83 output.fastq.84 output.fastq.85 output.fastq.86 output.fastq.87 output.fastq.88 output.fastq.89 output.fastq.90 output.fastq.91 output.fastq.92 output.fastq.93 output.fastq.94 output.fastq.95 output.fastq.96 output.fastq.97 output.fastq.98 output.fastq.99 - LOCAL cat output.fastq.0 output.fastq.1 output.fastq.2 output.fastq.3 output.fastq.4 output.fastq.5 output.fastq.6 output.fastq.7 output.fastq.8 output.fastq.9 output.fastq.10 output.fastq.11 output.fastq.12 output.fastq.13 output.fastq.14 output.fastq.15 output.fastq.16 output.fastq.17 output.fastq.18 output.fastq.19 output.fastq.20 output.fastq.21 output.fastq.22 output.fastq.23 output.fastq.24 output.fastq.25 output.fastq.26 output.fastq.27 output.fastq.28 output.fastq.29 output.fastq.30 output.fastq.31 output.fastq.32 output.fastq.33 output.fastq.34 output.fastq.35 output.fastq.36 output.fastq.37 output.fastq.38 output.fastq.39 output.fastq.40 output.fastq.41 output.fastq.42 output.fastq.43 output.fastq.44 output.fastq.45 output.fastq.46 output.fastq.47 output.fastq.48 output.fastq.49 output.fastq.50 output.fastq.51 output.fastq.52 output.fastq.53 output.fastq.54 output.fastq.55 output.fastq.56 output.fastq.57 output.fastq.58 output.fastq.59 output.fastq.60 output.fastq.61 output.fastq.62 output.fastq.63 output.fastq.64 output.fastq.65 output.fastq.66 output.fastq.67 output.fastq.68 output.fastq.69 output.fastq.70 output.fastq.71 output.fastq.72 output.fastq.73 output.fastq.74 output.fastq.75 output.fastq.76 output.fastq.77 output.fastq.78 output.fastq.79 output.fastq.80 output.fastq.81 output.fastq.82 output.fastq.83 output.fastq.84 output.fastq.85 output.fastq.86 output.fastq.87 output.fastq.88 output.fastq.89 output.fastq.90 output.fastq.91 output.fastq.92 output.fastq.93 output.fastq.94 output.fastq.95 output.fastq.96 output.fastq.97 output.fastq.98 output.fastq.99 > output.fastq +output.fastq.100: query.fastq.100 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.100 > output.fastq.100 + +output.fastq.101: query.fastq.101 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.101 > output.fastq.101 + +output.fastq.102: query.fastq.102 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.102 > output.fastq.102 + +output.fastq.103: query.fastq.103 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.103 > output.fastq.103 + +output.fastq.104: query.fastq.104 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.104 > output.fastq.104 + +output.fastq.105: query.fastq.105 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.105 > output.fastq.105 + +output.fastq.106: query.fastq.106 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.106 > output.fastq.106 + +output.fastq.107: query.fastq.107 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.107 > output.fastq.107 + +output.fastq.108: query.fastq.108 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.108 > output.fastq.108 + +output.fastq.109: query.fastq.109 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.109 > output.fastq.109 + +output.fastq.110: query.fastq.110 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.110 > output.fastq.110 + +output.fastq.111: query.fastq.111 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.111 > output.fastq.111 + +output.fastq.112: query.fastq.112 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.112 > output.fastq.112 + 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$OPTIONS db.fastq query.fastq.172 > output.fastq.172 + +output.fastq.173: query.fastq.173 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.173 > output.fastq.173 + +output.fastq.174: query.fastq.174 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.174 > output.fastq.174 + +output.fastq.175: query.fastq.175 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.175 > output.fastq.175 + +output.fastq.176: query.fastq.176 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.176 > output.fastq.176 + +output.fastq.177: query.fastq.177 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.177 > output.fastq.177 + +output.fastq.178: query.fastq.178 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.178 > output.fastq.178 + +output.fastq.179: query.fastq.179 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.179 > output.fastq.179 + +output.fastq.180: query.fastq.180 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.180 > output.fastq.180 + 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$OPTIONS db.fastq query.fastq.189 > output.fastq.189 + +output.fastq.190: query.fastq.190 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.190 > output.fastq.190 + +output.fastq.191: query.fastq.191 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.191 > output.fastq.191 + +output.fastq.192: query.fastq.192 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.192 > output.fastq.192 + +output.fastq.193: query.fastq.193 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.193 > output.fastq.193 + +output.fastq.194: query.fastq.194 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.194 > output.fastq.194 + +output.fastq.195: query.fastq.195 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.195 > output.fastq.195 + +output.fastq.196: query.fastq.196 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.196 > output.fastq.196 + +output.fastq.197: query.fastq.197 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.197 > output.fastq.197 + 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$OPTIONS db.fastq query.fastq.206 > output.fastq.206 + +output.fastq.207: query.fastq.207 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.207 > output.fastq.207 + +output.fastq.208: query.fastq.208 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.208 > output.fastq.208 + +output.fastq.209: query.fastq.209 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.209 > output.fastq.209 + +output.fastq.210: query.fastq.210 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.210 > output.fastq.210 + +output.fastq.211: query.fastq.211 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.211 > output.fastq.211 + +output.fastq.212: query.fastq.212 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.212 > output.fastq.212 + +output.fastq.213: query.fastq.213 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.213 > output.fastq.213 + +output.fastq.214: query.fastq.214 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.214 > output.fastq.214 + 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$OPTIONS db.fastq query.fastq.223 > output.fastq.223 + +output.fastq.224: query.fastq.224 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.224 > output.fastq.224 + +output.fastq.225: query.fastq.225 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.225 > output.fastq.225 + +output.fastq.226: query.fastq.226 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.226 > output.fastq.226 + +output.fastq.227: query.fastq.227 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.227 > output.fastq.227 + +output.fastq.228: query.fastq.228 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.228 > output.fastq.228 + +output.fastq.229: query.fastq.229 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.229 > output.fastq.229 + +output.fastq.230: query.fastq.230 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.230 > output.fastq.230 + +output.fastq.231: query.fastq.231 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.231 > output.fastq.231 + 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$OPTIONS db.fastq query.fastq.240 > output.fastq.240 + +output.fastq.241: query.fastq.241 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.241 > output.fastq.241 + +output.fastq.242: query.fastq.242 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.242 > output.fastq.242 + +output.fastq.243: query.fastq.243 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.243 > output.fastq.243 + +output.fastq.244: query.fastq.244 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.244 > output.fastq.244 + +output.fastq.245: query.fastq.245 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.245 > output.fastq.245 + +output.fastq.246: query.fastq.246 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.246 > output.fastq.246 + +output.fastq.247: query.fastq.247 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.247 > output.fastq.247 + +output.fastq.248: query.fastq.248 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.248 > output.fastq.248 + 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$OPTIONS db.fastq query.fastq.325 > output.fastq.325 + +output.fastq.326: query.fastq.326 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.326 > output.fastq.326 + +output.fastq.327: query.fastq.327 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.327 > output.fastq.327 + +output.fastq.328: query.fastq.328 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.328 > output.fastq.328 + +output.fastq.329: query.fastq.329 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.329 > output.fastq.329 + +output.fastq.330: query.fastq.330 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.330 > output.fastq.330 + +output.fastq.331: query.fastq.331 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.331 > output.fastq.331 + +output.fastq.332: query.fastq.332 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.332 > output.fastq.332 + +output.fastq.333: query.fastq.333 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.333 > output.fastq.333 + 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$OPTIONS db.fastq query.fastq.342 > output.fastq.342 + +output.fastq.343: query.fastq.343 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.343 > output.fastq.343 + +output.fastq.344: query.fastq.344 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.344 > output.fastq.344 + +output.fastq.345: query.fastq.345 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.345 > output.fastq.345 + +output.fastq.346: query.fastq.346 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.346 > output.fastq.346 + +output.fastq.347: query.fastq.347 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.347 > output.fastq.347 + +output.fastq.348: query.fastq.348 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.348 > output.fastq.348 + +output.fastq.349: query.fastq.349 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.349 > output.fastq.349 + +output.fastq.350: query.fastq.350 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.350 > output.fastq.350 + 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$OPTIONS db.fastq query.fastq.359 > output.fastq.359 + +output.fastq.360: query.fastq.360 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.360 > output.fastq.360 + +output.fastq.361: query.fastq.361 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.361 > output.fastq.361 + +output.fastq.362: query.fastq.362 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.362 > output.fastq.362 + +output.fastq.363: query.fastq.363 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.363 > output.fastq.363 + +output.fastq.364: query.fastq.364 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.364 > output.fastq.364 + +output.fastq.365: query.fastq.365 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.365 > output.fastq.365 + +output.fastq.366: query.fastq.366 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.366 > output.fastq.366 + +output.fastq.367: query.fastq.367 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.367 > output.fastq.367 + 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$OPTIONS db.fastq query.fastq.376 > output.fastq.376 + +output.fastq.377: query.fastq.377 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.377 > output.fastq.377 + +output.fastq.378: query.fastq.378 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.378 > output.fastq.378 + +output.fastq.379: query.fastq.379 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.379 > output.fastq.379 + +output.fastq.380: query.fastq.380 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.380 > output.fastq.380 + +output.fastq.381: query.fastq.381 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.381 > output.fastq.381 + +output.fastq.382: query.fastq.382 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.382 > output.fastq.382 + +output.fastq.383: query.fastq.383 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.383 > output.fastq.383 + +output.fastq.384: query.fastq.384 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.384 > output.fastq.384 + 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$OPTIONS db.fastq query.fastq.393 > output.fastq.393 + +output.fastq.394: query.fastq.394 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.394 > output.fastq.394 + +output.fastq.395: query.fastq.395 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.395 > output.fastq.395 + +output.fastq.396: query.fastq.396 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.396 > output.fastq.396 + +output.fastq.397: query.fastq.397 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.397 > output.fastq.397 + +output.fastq.398: query.fastq.398 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.398 > output.fastq.398 + +output.fastq.399: query.fastq.399 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.399 > output.fastq.399 + +output.fastq.400: query.fastq.400 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.400 > output.fastq.400 + +output.fastq.401: query.fastq.401 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.401 > output.fastq.401 + 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$OPTIONS db.fastq query.fastq.495 > output.fastq.495 + +output.fastq.496: query.fastq.496 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.496 > output.fastq.496 + +output.fastq.497: query.fastq.497 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.497 > output.fastq.497 + +output.fastq.498: query.fastq.498 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.498 > output.fastq.498 + +output.fastq.499: query.fastq.499 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.499 > output.fastq.499 + +output.fastq.500: query.fastq.500 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.500 > output.fastq.500 + +output.fastq.501: query.fastq.501 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.501 > output.fastq.501 + +output.fastq.502: query.fastq.502 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.502 > output.fastq.502 + +output.fastq.503: query.fastq.503 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.503 > output.fastq.503 + 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$OPTIONS db.fastq query.fastq.529 > output.fastq.529 + +output.fastq.530: query.fastq.530 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.530 > output.fastq.530 + +output.fastq.531: query.fastq.531 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.531 > output.fastq.531 + +output.fastq.532: query.fastq.532 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.532 > output.fastq.532 + +output.fastq.533: query.fastq.533 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.533 > output.fastq.533 + +output.fastq.534: query.fastq.534 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.534 > output.fastq.534 + +output.fastq.535: query.fastq.535 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.535 > output.fastq.535 + +output.fastq.536: query.fastq.536 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.536 > output.fastq.536 + +output.fastq.537: query.fastq.537 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.537 > output.fastq.537 + 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$OPTIONS db.fastq query.fastq.546 > output.fastq.546 + +output.fastq.547: query.fastq.547 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.547 > output.fastq.547 + +output.fastq.548: query.fastq.548 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.548 > output.fastq.548 + +output.fastq.549: query.fastq.549 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.549 > output.fastq.549 + +output.fastq.550: query.fastq.550 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.550 > output.fastq.550 + +output.fastq.551: query.fastq.551 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.551 > output.fastq.551 + +output.fastq.552: query.fastq.552 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.552 > output.fastq.552 + +output.fastq.553: query.fastq.553 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.553 > output.fastq.553 + +output.fastq.554: query.fastq.554 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.554 > output.fastq.554 + 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$OPTIONS db.fastq query.fastq.631 > output.fastq.631 + +output.fastq.632: query.fastq.632 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.632 > output.fastq.632 + +output.fastq.633: query.fastq.633 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.633 > output.fastq.633 + +output.fastq.634: query.fastq.634 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.634 > output.fastq.634 + +output.fastq.635: query.fastq.635 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.635 > output.fastq.635 + +output.fastq.636: query.fastq.636 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.636 > output.fastq.636 + +output.fastq.637: query.fastq.637 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.637 > output.fastq.637 + +output.fastq.638: query.fastq.638 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.638 > output.fastq.638 + +output.fastq.639: query.fastq.639 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.639 > output.fastq.639 + 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$OPTIONS db.fastq query.fastq.648 > output.fastq.648 + +output.fastq.649: query.fastq.649 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.649 > output.fastq.649 + +output.fastq.650: query.fastq.650 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.650 > output.fastq.650 + +output.fastq.651: query.fastq.651 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.651 > output.fastq.651 + +output.fastq.652: query.fastq.652 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.652 > output.fastq.652 + +output.fastq.653: query.fastq.653 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.653 > output.fastq.653 + +output.fastq.654: query.fastq.654 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.654 > output.fastq.654 + +output.fastq.655: query.fastq.655 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.655 > output.fastq.655 + +output.fastq.656: query.fastq.656 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.656 > output.fastq.656 + 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$OPTIONS db.fastq query.fastq.665 > output.fastq.665 + +output.fastq.666: query.fastq.666 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.666 > output.fastq.666 + +output.fastq.667: query.fastq.667 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.667 > output.fastq.667 + +output.fastq.668: query.fastq.668 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.668 > output.fastq.668 + +output.fastq.669: query.fastq.669 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.669 > output.fastq.669 + +output.fastq.670: query.fastq.670 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.670 > output.fastq.670 + +output.fastq.671: query.fastq.671 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.671 > output.fastq.671 + +output.fastq.672: query.fastq.672 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.672 > output.fastq.672 + +output.fastq.673: query.fastq.673 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.673 > output.fastq.673 + 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$OPTIONS db.fastq query.fastq.682 > output.fastq.682 + +output.fastq.683: query.fastq.683 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.683 > output.fastq.683 + +output.fastq.684: query.fastq.684 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.684 > output.fastq.684 + +output.fastq.685: query.fastq.685 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.685 > output.fastq.685 + +output.fastq.686: query.fastq.686 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.686 > output.fastq.686 + +output.fastq.687: query.fastq.687 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.687 > output.fastq.687 + +output.fastq.688: query.fastq.688 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.688 > output.fastq.688 + +output.fastq.689: query.fastq.689 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.689 > output.fastq.689 + +output.fastq.690: query.fastq.690 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.690 > output.fastq.690 + 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$OPTIONS db.fastq query.fastq.699 > output.fastq.699 + +output.fastq.700: query.fastq.700 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.700 > output.fastq.700 + +output.fastq.701: query.fastq.701 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.701 > output.fastq.701 + +output.fastq.702: query.fastq.702 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.702 > output.fastq.702 + +output.fastq.703: query.fastq.703 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.703 > output.fastq.703 + +output.fastq.704: query.fastq.704 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.704 > output.fastq.704 + +output.fastq.705: query.fastq.705 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.705 > output.fastq.705 + +output.fastq.706: query.fastq.706 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.706 > output.fastq.706 + +output.fastq.707: query.fastq.707 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.707 > output.fastq.707 + 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$OPTIONS db.fastq query.fastq.733 > output.fastq.733 + +output.fastq.734: query.fastq.734 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.734 > output.fastq.734 + +output.fastq.735: query.fastq.735 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.735 > output.fastq.735 + +output.fastq.736: query.fastq.736 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.736 > output.fastq.736 + +output.fastq.737: query.fastq.737 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.737 > output.fastq.737 + +output.fastq.738: query.fastq.738 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.738 > output.fastq.738 + +output.fastq.739: query.fastq.739 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.739 > output.fastq.739 + +output.fastq.740: query.fastq.740 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.740 > output.fastq.740 + +output.fastq.741: query.fastq.741 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.741 > output.fastq.741 + 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$OPTIONS db.fastq query.fastq.750 > output.fastq.750 + +output.fastq.751: query.fastq.751 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.751 > output.fastq.751 + +output.fastq.752: query.fastq.752 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.752 > output.fastq.752 + +output.fastq.753: query.fastq.753 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.753 > output.fastq.753 + +output.fastq.754: query.fastq.754 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.754 > output.fastq.754 + +output.fastq.755: query.fastq.755 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.755 > output.fastq.755 + +output.fastq.756: query.fastq.756 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.756 > output.fastq.756 + +output.fastq.757: query.fastq.757 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.757 > output.fastq.757 + +output.fastq.758: query.fastq.758 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.758 > output.fastq.758 + 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$OPTIONS db.fastq query.fastq.767 > output.fastq.767 + +output.fastq.768: query.fastq.768 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.768 > output.fastq.768 + +output.fastq.769: query.fastq.769 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.769 > output.fastq.769 + +output.fastq.770: query.fastq.770 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.770 > output.fastq.770 + +output.fastq.771: query.fastq.771 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.771 > output.fastq.771 + +output.fastq.772: query.fastq.772 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.772 > output.fastq.772 + +output.fastq.773: query.fastq.773 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.773 > output.fastq.773 + +output.fastq.774: query.fastq.774 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.774 > output.fastq.774 + +output.fastq.775: query.fastq.775 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.775 > output.fastq.775 + 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$OPTIONS db.fastq query.fastq.784 > output.fastq.784 + +output.fastq.785: query.fastq.785 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.785 > output.fastq.785 + +output.fastq.786: query.fastq.786 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.786 > output.fastq.786 + +output.fastq.787: query.fastq.787 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.787 > output.fastq.787 + +output.fastq.788: query.fastq.788 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.788 > output.fastq.788 + +output.fastq.789: query.fastq.789 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.789 > output.fastq.789 + +output.fastq.790: query.fastq.790 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.790 > output.fastq.790 + +output.fastq.791: query.fastq.791 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.791 > output.fastq.791 + +output.fastq.792: query.fastq.792 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.792 > output.fastq.792 + 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$OPTIONS db.fastq query.fastq.801 > output.fastq.801 + +output.fastq.802: query.fastq.802 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.802 > output.fastq.802 + +output.fastq.803: query.fastq.803 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.803 > output.fastq.803 + +output.fastq.804: query.fastq.804 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.804 > output.fastq.804 + +output.fastq.805: query.fastq.805 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.805 > output.fastq.805 + +output.fastq.806: query.fastq.806 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.806 > output.fastq.806 + +output.fastq.807: query.fastq.807 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.807 > output.fastq.807 + +output.fastq.808: query.fastq.808 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.808 > output.fastq.808 + +output.fastq.809: query.fastq.809 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.809 > output.fastq.809 + 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$OPTIONS db.fastq query.fastq.818 > output.fastq.818 + +output.fastq.819: query.fastq.819 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.819 > output.fastq.819 + +output.fastq.820: query.fastq.820 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.820 > output.fastq.820 + +output.fastq.821: query.fastq.821 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.821 > output.fastq.821 + +output.fastq.822: query.fastq.822 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.822 > output.fastq.822 + +output.fastq.823: query.fastq.823 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.823 > output.fastq.823 + +output.fastq.824: query.fastq.824 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.824 > output.fastq.824 + +output.fastq.825: query.fastq.825 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.825 > output.fastq.825 + +output.fastq.826: query.fastq.826 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.826 > output.fastq.826 + +output.fastq.827: query.fastq.827 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.827 > output.fastq.827 + +output.fastq.828: query.fastq.828 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.828 > output.fastq.828 + +output.fastq.829: query.fastq.829 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.829 > output.fastq.829 + +output.fastq.830: query.fastq.830 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.830 > output.fastq.830 + +output.fastq.831: query.fastq.831 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.831 > output.fastq.831 + +output.fastq.832: query.fastq.832 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.832 > output.fastq.832 + +output.fastq.833: query.fastq.833 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.833 > output.fastq.833 + +output.fastq.834: query.fastq.834 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.834 > output.fastq.834 + +output.fastq.835: query.fastq.835 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.835 > output.fastq.835 + +output.fastq.836: query.fastq.836 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.836 > output.fastq.836 + +output.fastq.837: query.fastq.837 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.837 > output.fastq.837 + +output.fastq.838: query.fastq.838 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.838 > output.fastq.838 + +output.fastq.839: query.fastq.839 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.839 > output.fastq.839 + +output.fastq.840: query.fastq.840 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.840 > output.fastq.840 + +output.fastq.841: query.fastq.841 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.841 > output.fastq.841 + +output.fastq.842: query.fastq.842 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.842 > output.fastq.842 + +output.fastq.843: query.fastq.843 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.843 > output.fastq.843 + 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$OPTIONS db.fastq query.fastq.886 > output.fastq.886 + +output.fastq.887: query.fastq.887 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.887 > output.fastq.887 + +output.fastq.888: query.fastq.888 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.888 > output.fastq.888 + +output.fastq.889: query.fastq.889 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.889 > output.fastq.889 + +output.fastq.890: query.fastq.890 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.890 > output.fastq.890 + +output.fastq.891: query.fastq.891 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.891 > output.fastq.891 + +output.fastq.892: query.fastq.892 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.892 > output.fastq.892 + +output.fastq.893: query.fastq.893 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.893 > output.fastq.893 + +output.fastq.894: query.fastq.894 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.894 > output.fastq.894 + 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$OPTIONS db.fastq query.fastq.903 > output.fastq.903 + +output.fastq.904: query.fastq.904 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.904 > output.fastq.904 + +output.fastq.905: query.fastq.905 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.905 > output.fastq.905 + +output.fastq.906: query.fastq.906 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.906 > output.fastq.906 + +output.fastq.907: query.fastq.907 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.907 > output.fastq.907 + +output.fastq.908: query.fastq.908 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.908 > output.fastq.908 + +output.fastq.909: query.fastq.909 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.909 > output.fastq.909 + +output.fastq.910: query.fastq.910 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.910 > output.fastq.910 + +output.fastq.911: query.fastq.911 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.911 > output.fastq.911 + 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$OPTIONS db.fastq query.fastq.920 > output.fastq.920 + +output.fastq.921: query.fastq.921 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.921 > output.fastq.921 + +output.fastq.922: query.fastq.922 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.922 > output.fastq.922 + +output.fastq.923: query.fastq.923 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.923 > output.fastq.923 + +output.fastq.924: query.fastq.924 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.924 > output.fastq.924 + +output.fastq.925: query.fastq.925 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.925 > output.fastq.925 + +output.fastq.926: query.fastq.926 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.926 > output.fastq.926 + +output.fastq.927: query.fastq.927 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.927 > output.fastq.927 + +output.fastq.928: query.fastq.928 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.928 > output.fastq.928 + 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$OPTIONS db.fastq query.fastq.937 > output.fastq.937 + +output.fastq.938: query.fastq.938 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.938 > output.fastq.938 + +output.fastq.939: query.fastq.939 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.939 > output.fastq.939 + +output.fastq.940: query.fastq.940 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.940 > output.fastq.940 + +output.fastq.941: query.fastq.941 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.941 > output.fastq.941 + +output.fastq.942: query.fastq.942 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.942 > output.fastq.942 + +output.fastq.943: query.fastq.943 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.943 > output.fastq.943 + +output.fastq.944: query.fastq.944 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.944 > output.fastq.944 + +output.fastq.945: query.fastq.945 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.945 > output.fastq.945 + 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$OPTIONS db.fastq query.fastq.954 > output.fastq.954 + +output.fastq.955: query.fastq.955 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.955 > output.fastq.955 + +output.fastq.956: query.fastq.956 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.956 > output.fastq.956 + +output.fastq.957: query.fastq.957 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.957 > output.fastq.957 + +output.fastq.958: query.fastq.958 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.958 > output.fastq.958 + +output.fastq.959: query.fastq.959 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.959 > output.fastq.959 + +output.fastq.960: query.fastq.960 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.960 > output.fastq.960 + +output.fastq.961: query.fastq.961 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.961 > output.fastq.961 + +output.fastq.962: query.fastq.962 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.962 > output.fastq.962 + 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$OPTIONS db.fastq query.fastq.971 > output.fastq.971 + +output.fastq.972: query.fastq.972 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.972 > output.fastq.972 + +output.fastq.973: query.fastq.973 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.973 > output.fastq.973 + +output.fastq.974: query.fastq.974 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.974 > output.fastq.974 + +output.fastq.975: query.fastq.975 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.975 > output.fastq.975 + +output.fastq.976: query.fastq.976 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.976 > output.fastq.976 + +output.fastq.977: query.fastq.977 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.977 > output.fastq.977 + +output.fastq.978: query.fastq.978 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.978 > output.fastq.978 + +output.fastq.979: query.fastq.979 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.979 > output.fastq.979 + 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$OPTIONS db.fastq query.fastq.988 > output.fastq.988 + +output.fastq.989: query.fastq.989 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.989 > output.fastq.989 + +output.fastq.990: query.fastq.990 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.990 > output.fastq.990 + +output.fastq.991: query.fastq.991 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.991 > output.fastq.991 + +output.fastq.992: query.fastq.992 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.992 > output.fastq.992 + +output.fastq.993: query.fastq.993 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.993 > output.fastq.993 + +output.fastq.994: query.fastq.994 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.994 > output.fastq.994 + +output.fastq.995: query.fastq.995 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.995 > output.fastq.995 + +output.fastq.996: query.fastq.996 db.fastq ssaha2 + ./ssaha2 $OPTIONS db.fastq query.fastq.996 > output.fastq.996 + 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