Add ecology "pool of amplicons map to reference" workflow #1053

mo-mahe · 2025-12-16T15:14:50Z

Workflow for processing amplicon pool sequencing data with reference.

This workflow allows you to reconstruct a sequence from an amplicon pool using a reference sequence. To run this workflow, you need the reads from the pool library you want to analyse in FASTQ format, separated into two files: forward and reverse. You will also need your reference sequence in FASTA format. This workflow creates a consensus sequence and a metadata file containing the length of the consensus sequence, the number of reads mapped to it, and the average, minimum, and maximum coverage depth. You can also retrieve a file containing unmapped reads.

workflows/ecology/map-to-reference-workflow/test-data/visualize_consensus.html

workflows/ecology/map-to-reference-workflow/README.md

…orward.html

…aired.html

…everse.html

…e_consensus.html

mo-mahe · 2025-12-16T16:03:06Z

@yvanlebras

yvanlebras · 2025-12-16T16:08:29Z

Youhou ! Thank you Molène ! If some help needed, don't hesitate to ask! Don't hesitate Marius, we are trying to contribute to IWC thanks to Molène and Pauline work! We have around 10 workflows to push!

Copilot

Pull request overview

This PR adds a new workflow for processing amplicon pool sequencing data with a reference sequence. The workflow performs quality control, read pairing, filtering, and reference-based mapping to generate a consensus sequence and associated metadata.

Key changes:

Introduces a complete map-to-reference workflow for amplicon pool sequencing
Includes comprehensive documentation and testing infrastructure
Implements metadata generation pipeline tracking coverage and mapping statistics

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 11 comments.

Show a summary per file

File	Description
Map-to-reference.ga	Main workflow file defining the complete amplicon pool processing pipeline
Map-to-reference-tests.yml	Test configuration with input files and output assertions
README.md	Detailed workflow documentation explaining purpose, inputs, steps, and outputs
.dockstore.yml	Dockstore configuration for workflow publication
CHANGELOG.md	Version history tracking initial release
metadata.tabular	Test data file containing expected metadata output

workflows/ecology/map-to-reference-workflow/Map-to-reference.ga

workflows/ecology/map-to-reference-workflow/.dockstore.yml

Copilot · 2025-12-16T16:22:14Z

workflows/ecology/map-to-reference-workflow/Map-to-reference.ga

+                    "label": "fastqc_forward",
+                    "output_name": "html_file",


The workflow_outputs label "fastqc_forward" uses underscores. According to IWC guidelines, workflow output labels should be human-readable with spaces. Consider "FastQC forward" or "FastQC forward reads".

Copilot · 2025-12-16T16:22:14Z

workflows/ecology/map-to-reference-workflow/Map-to-reference.ga

+                    "label": "fastqc_reverse",
+                    "output_name": "html_file",


The workflow_outputs label "fastqc_reverse" uses underscores. According to IWC guidelines, workflow output labels should be human-readable with spaces. Consider "FastQC reverse" or "FastQC reverse reads".

Copilot · 2025-12-16T16:22:15Z

workflows/ecology/map-to-reference-workflow/Map-to-reference.ga

+                    "label": "visualize_consensus",
+                    "output_name": "output",


The workflow_outputs label "visualize_consensus" uses underscores. According to IWC guidelines, workflow output labels should be human-readable with spaces. Consider "Consensus visualization" or "Visualize consensus".

Copilot · 2025-12-16T16:22:15Z

workflows/ecology/map-to-reference-workflow/Map-to-reference-tests.yml

+    Forward primer: AGTGAGTTTCAACAAAACAYAAGGNCATNGG
+    Reverse primer: AGTGAGTAAACTTCAGGGTGTCCRAARAATCA
+  outputs:
+    fastqc_forward:


Test file output names must match the workflow_outputs labels exactly. If the workflow labels are updated to human-readable format (e.g., "FastQC forward"), these test output names must be updated accordingly.

Copilot · 2025-12-16T16:22:15Z

workflows/ecology/map-to-reference-workflow/Map-to-reference-tests.yml

+      asserts:
+        has_text:
+          text: html
+    fastqc_reverse:


Test file output names must match the workflow_outputs labels exactly. If the workflow labels are updated to human-readable format (e.g., "FastQC forward"), these test output names must be updated accordingly.

Copilot · 2025-12-16T16:22:15Z

workflows/ecology/map-to-reference-workflow/Map-to-reference-tests.yml

+      asserts:
+        has_text:
+          text: html
+    fastqc_paired:


Test file output names must match the workflow_outputs labels exactly. If the workflow labels are updated to human-readable format (e.g., "FastQC forward"), these test output names must be updated accordingly.

Copilot · 2025-12-16T16:22:16Z

workflows/ecology/map-to-reference-workflow/Map-to-reference-tests.yml

+      asserts:
+        has_text:
+          text: html
+    visualize_consensus:


Test file output names must match the workflow_outputs labels exactly. If the workflow labels are updated to human-readable format (e.g., "FastQC forward"), these test output names must be updated accordingly.

github-actions · 2025-12-16T18:00:19Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Map-to-reference.ga_0

Problems:

Output with path /tmp/tmpukg932j0/table rename column on dataset 43__f5ff3eed-6fb5-4bfd-9ee9-74cca15e4269.tabular different than expected, difference (using diff):
( /home/runner/work/iwc/iwc/workflows/ecology/map-to-reference-workflow/test-data/metadata.tabular v. /tmp/tmpti3benfkmetadata.tabular )
--- local_file
+++ history_data
@@ -1,2 +1,2 @@
 mapped_reads	consensus_length	min_depth	max_depth	mean_depth
-116	663	22	72	43.095744680851
+116	669	22	72	43.095744680851

Workflow invocation details

Invocation Messages

Steps

Step 1: FASTQ - Forward:
- step_state: scheduled
Step 2: FASTQ - Reverse:
- step_state: scheduled
Step 11: __ZIP_COLLECTION__:
- step_state: scheduled
- Jobs
  - Job 1:
    - Job state is ok
    Traceback:
    Job Parameters:
    - Job parameter Parameter value
      
      __workflow_invocation_uuid__ "73018df2daa211f0a3dd000d3a5ce991"

Step 12: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

times=1; yes -- 'EONForward' 2>/dev/null | head -n $times >> '/tmp/tmpa0q9y2tx/job_working_directory/000/8/outputs/dataset_4d69773e-dc80-4acb-9c96-88c61ce4d77c.dat'; times=1; yes -- 'AGTGAGTTTCAACAAAACAYAAGGNCATNGG' 2>/dev/null | head -n $times >> '/tmp/tmpa0q9y2tx/job_working_directory/000/8/outputs/dataset_4d69773e-dc80-4acb-9c96-88c61ce4d77c.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
token_set	`[{"__index__": 0, "line": "EONForward", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}, {"__index__": 1, "line": "AGTGAGTTTCAACAAAACAYAAGGNCATNGG", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}]`

Step 13: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

times=1; yes -- 'EONReverse' 2>/dev/null | head -n $times >> '/tmp/tmpa0q9y2tx/job_working_directory/000/9/outputs/dataset_d584e290-ca04-4c42-9787-cc2119453c50.dat'; times=1; yes -- 'AGTGAGTAAACTTCAGGGTGTCCRAARAATCA' 2>/dev/null | head -n $times >> '/tmp/tmpa0q9y2tx/job_working_directory/000/9/outputs/dataset_d584e290-ca04-4c42-9787-cc2119453c50.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
token_set	`[{"__index__": 0, "line": "EONReverse", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}, {"__index__": 1, "line": "AGTGAGTAAACTTCAGGGTGTCCRAARAATCA", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}]`

Step 14: toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gx-fastq-filter '/tmp/tmpa0q9y2tx/files/d/e/0/dataset_de06ef6d-54ae-458f-9eef-f90881962286.dat' '/tmp/tmpa0q9y2tx/job_working_directory/000/10/configs/tmp3swl894b' '/tmp/tmpa0q9y2tx/job_working_directory/000/10/outputs/dataset_9530dc79-ec79-49e2-83cd-1fa429d434e1.dat' '/tmp/tmpa0q9y2tx/job_working_directory/000/10/outputs/dataset_9530dc79-ec79-49e2-83cd-1fa429d434e1_files' 'sanger'

Exit Code:

```
0
```

Standard Output:

```
Kept 8562 of 8562 reads (100.00%).
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_filters	`[]`
max_num_deviants	`"0"`
max_quality	`"0.0"`
max_size	`"0"`
min_quality	`"0.0"`
min_size	`"0"`
paired_end	`false`

Step 15: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail; bowtie2-build --threads ${GALAXY_SLOTS:-4} '/tmp/tmpa0q9y2tx/files/1/8/4/dataset_18465be9-6602-4eda-bdad-e9ab59a336a0.dat' genome && ln -s -f '/tmp/tmpa0q9y2tx/files/1/8/4/dataset_18465be9-6602-4eda-bdad-e9ab59a336a0.dat' genome.fa &&   ln -f -s '/tmp/tmpa0q9y2tx/files/4/a/8/dataset_4a899d09-4768-4202-9869-e6dfb1a74628.dat' input_f.fastq &&  ln -f -s '/tmp/tmpa0q9y2tx/files/d/3/d/dataset_d3d260e7-8cd9-481c-bfc2-7811867e7278.dat' input_r.fastq &&   THREADS=${GALAXY_SLOTS:-4} && if [ "$THREADS" -gt 1 ]; then (( THREADS-- )); fi &&   bowtie2  -p "$THREADS"  -x 'genome'   -1 'input_f.fastq' -2 'input_r.fastq' --un-conc 'unaligned_reads' -I 0 -X 500 --fr                   --skip 0 --qupto 100000000 --trim5 0 --trim3 0 --phred33    -N 0 -L 28 -i 'S,1,1.15' --n-ceil 'L,0,0.15' --dpad 15 --gbar 4     --local --score-min 'G,20,8'  --ma 2 --mp '6,2' --np 1 --rdg 5,3 --rfg 5,3   -D 15 -R 2  --seed 0     | samtools sort -l 0 -T "${TMPDIR:-.}" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/tmp/tmpa0q9y2tx/job_working_directory/000/11/outputs/dataset_ed6edf45-c0a2-4a55-a1cd-5d5870d70357.dat'

Exit Code:

```
0
```

Standard Error:

Building a SMALL index
Renaming genome.3.bt2.tmp to genome.3.bt2
Renaming genome.4.bt2.tmp to genome.4.bt2
Renaming genome.1.bt2.tmp to genome.1.bt2
Renaming genome.2.bt2.tmp to genome.2.bt2
Renaming genome.rev.1.bt2.tmp to genome.rev.1.bt2
Renaming genome.rev.2.bt2.tmp to genome.rev.2.bt2
8839 reads; of these:
  8839 (100.00%) were paired; of these:
    8741 (98.89%) aligned concordantly 0 times
    98 (1.11%) aligned concordantly exactly 1 time
    0 (0.00%) aligned concordantly >1 times
    ----
    8741 pairs aligned concordantly 0 times; of these:
      23 (0.26%) aligned discordantly 1 time
    ----
    8718 pairs aligned 0 times concordantly or discordantly; of these:
      17436 mates make up the pairs; of these:
        17432 (99.98%) aligned 0 times
        2 (0.01%) aligned exactly 1 time
        2 (0.01%) aligned >1 times
1.39% overall alignment rate

Standard Output:

Settings:
  Output files: "genome.*.bt2"
  Line rate: 6 (line is 64 bytes)
  Lines per side: 1 (side is 64 bytes)
  Offset rate: 4 (one in 16)
  FTable chars: 10
  Strings: unpacked
  Max bucket size: default
  Max bucket size, sqrt multiplier: default
  Max bucket size, len divisor: 4
  Difference-cover sample period: 1024
  Endianness: little
  Actual local endianness: little
  Sanity checking: disabled
  Assertions: disabled
  Random seed: 0
  Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
  /tmp/tmpa0q9y2tx/files/1/8/4/dataset_18465be9-6602-4eda-bdad-e9ab59a336a0.dat
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
bmax according to bmaxDivN setting: 164
Using parameters --bmax 123 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 123 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:00
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:00
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:00
  Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
  (Using difference cover)
  Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 7; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 1; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 93.1429 (target: 122)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (123) for bucket 1
  Calculating Z arrays for bucket 1
  Entering block accumulator loop for bucket 1:
  bucket 1: 10%
  bucket 1: 20%
  bucket 1: 30%
  bucket 1: 40%
  bucket 1: 50%
  bucket 1: 60%
  bucket 1: 70%
  bucket 1: 80%
  bucket 1: 90%
  bucket 1: 100%
  Sorting block of length 118 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 119 for bucket 1
Getting block 2 of 7
  Reserving size (123) for bucket 2
  Calculating Z arrays for bucket 2
  Entering block accumulator loop for bucket 2:
  bucket 2: 10%
  bucket 2: 20%
  bucket 2: 30%
  bucket 2: 40%
  bucket 2: 50%
  bucket 2: 60%
  bucket 2: 70%
  bucket 2: 80%
  bucket 2: 90%
  bucket 2: 100%
  Sorting block of length 115 for bucket 2
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 116 for bucket 2
Getting block 3 of 7
  Reserving size (123) for bucket 3
  Calculating Z arrays for bucket 3
  Entering block accumulator loop for bucket 3:
  bucket 3: 10%
  bucket 3: 20%
  bucket 3: 30%
  bucket 3: 40%
  bucket 3: 50%
  bucket 3: 60%
  bucket 3: 70%
  bucket 3: 80%
  bucket 3: 90%
  bucket 3: 100%
  Sorting block of length 96 for bucket 3
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 97 for bucket 3
Getting block 4 of 7
  Reserving size (123) for bucket 4
  Calculating Z arrays for bucket 4
  Entering block accumulator loop for bucket 4:
  bucket 4: 10%
  bucket 4: 20%
  bucket 4: 30%
  bucket 4: 40%
  bucket 4: 50%
  bucket 4: 60%
  bucket 4: 70%
  bucket 4: 80%
  bucket 4: 90%
  bucket 4: 100%
  Sorting block of length 77 for bucket 4
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 78 for bucket 4
Getting block 5 of 7
  Reserving size (123) for bucket 5
  Calculating Z arrays for bucket 5
  Entering block accumulator loop for bucket 5:
  bucket 5: 10%
  bucket 5: 20%
  bucket 5: 30%
  bucket 5: 40%
  bucket 5: 50%
  bucket 5: 60%
  bucket 5: 70%
  bucket 5: 80%
  bucket 5: 90%
  bucket 5: 100%
  Sorting block of length 66 for bucket 5
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 67 for bucket 5
Getting block 6 of 7
  Reserving size (123) for bucket 6
  Calculating Z arrays for bucket 6
  Entering block accumulator loop for bucket 6:
  bucket 6: 10%
  bucket 6: 20%
  bucket 6: 30%
  bucket 6: 40%
  bucket 6: 50%
  bucket 6: 60%
  bucket 6: 70%
  bucket 6: 80%
  bucket 6: 90%
  bucket 6: 100%
  Sorting block of length 95 for bucket 6
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 96 for bucket 6
Getting block 7 of 7
  Reserving size (123) for bucket 7
  Calculating Z arrays for bucket 7
  Entering block accumulator loop for bucket 7:
  bucket 7: 10%
  bucket 7: 20%
  bucket 7: 30%
  bucket 7: 40%
  bucket 7: 50%
  bucket 7: 60%
  bucket 7: 70%
  bucket 7: 80%
  bucket 7: 90%
  bucket 7: 100%
  Sorting block of length 85 for bucket 7
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 86 for bucket 7
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 219
fchr[G]: 358
fchr[T]: 469
fchr[$]: 658
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4194838 bytes to primary EBWT file: genome.1.bt2.tmp
Wrote 172 bytes to secondary EBWT file: genome.2.bt2.tmp
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 658
    bwtLen: 659
    sz: 165
    bwtSz: 165
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 42
    offsSz: 168
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 4
    numLines: 4
    ebwtTotLen: 256
    ebwtTotSz: 256
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:00:00
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
  Time to reverse reference sequence: 00:00:00
bmax according to bmaxDivN setting: 164
Using parameters --bmax 123 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 123 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:00
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:00
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:00
  Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
  (Using difference cover)
  Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 8; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 0; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 0; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 93.1429 (target: 122)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (123) for bucket 1
  Calculating Z arrays for bucket 1
  Entering block accumulator loop for bucket 1:
  bucket 1: 10%
  bucket 1: 20%
  bucket 1: 30%
  bucket 1: 40%
  bucket 1: 50%
  bucket 1: 60%
  bucket 1: 70%
  bucket 1: 80%
  bucket 1: 90%
  bucket 1: 100%
  Sorting block of length 67 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 68 for bucket 1
Getting block 2 of 7
  Reserving size (123) for bucket 2
  Calculating Z arrays for bucket 2
  Entering block accumulator loop for bucket 2:
  bucket 2: 10%
  bucket 2: 20%
  bucket 2: 30%
  bucket 2: 40%
  bucket 2: 50%
  bucket 2: 60%
  bucket 2: 70%
  bucket 2: 80%
  bucket 2: 90%
  bucket 2: 100%
  Sorting block of length 88 for bucket 2
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 89 for bucket 2
Getting block 3 of 7
  Reserving size (123) for bucket 3
  Calculating Z arrays for bucket 3
  Entering block accumulator loop for bucket 3:
  bucket 3: 10%
  bucket 3: 20%
  bucket 3: 30%
  bucket 3: 40%
  bucket 3: 50%
  bucket 3: 60%
  bucket 3: 70%
  bucket 3: 80%
  bucket 3: 90%
  bucket 3: 100%
  Sorting block of length 103 for bucket 3
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 104 for bucket 3
Getting block 4 of 7
  Reserving size (123) for bucket 4
  Calculating Z arrays for bucket 4
  Entering block accumulator loop for bucket 4:
  bucket 4: 10%
  bucket 4: 20%
  bucket 4: 30%
  bucket 4: 40%
  bucket 4: 50%
  bucket 4: 60%
  bucket 4: 70%
  bucket 4: 80%
  bucket 4: 90%
  bucket 4: 100%
  Sorting block of length 121 for bucket 4
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 122 for bucket 4
Getting block 5 of 7
  Reserving size (123) for bucket 5
  Calculating Z arrays for bucket 5
  Entering block accumulator loop for bucket 5:
  bucket 5: 10%
  bucket 5: 20%
  bucket 5: 30%
  bucket 5: 40%
  bucket 5: 50%
  bucket 5: 60%
  bucket 5: 70%
  bucket 5: 80%
  bucket 5: 90%
  bucket 5: 100%
  Sorting block of length 90 for bucket 5
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 91 for bucket 5
Getting block 6 of 7
  Reserving size (123) for bucket 6
  Calculating Z arrays for bucket 6
  Entering block accumulator loop for bucket 6:
  bucket 6: 10%
  bucket 6: 20%
  bucket 6: 30%
  bucket 6: 40%
  bucket 6: 50%
  bucket 6: 60%
  bucket 6: 70%
  bucket 6: 80%
  bucket 6: 90%
  bucket 6: 100%
  Sorting block of length 95 for bucket 6
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 96 for bucket 6
Getting block 7 of 7
  Reserving size (123) for bucket 7
  Calculating Z arrays for bucket 7
  Entering block accumulator loop for bucket 7:
  bucket 7: 10%
  bucket 7: 20%
  bucket 7: 30%
  bucket 7: 40%
  bucket 7: 50%
  bucket 7: 60%
  bucket 7: 70%
  bucket 7: 80%
  bucket 7: 90%
  bucket 7: 100%
  Sorting block of length 88 for bucket 7
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 89 for bucket 7
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 219
fchr[G]: 358
fchr[T]: 469
fchr[$]: 658
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4194838 bytes to primary EBWT file: genome.rev.1.bt2.tmp
Wrote 172 bytes to secondary EBWT file: genome.rev.2.bt2.tmp
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 658
    bwtLen: 659
    sz: 165
    bwtSz: 165
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 42
    offsSz: 168
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 4
    numLines: 4
    ebwtTotLen: 256
    ebwtTotSz: 256
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:00:00

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
analysis_type	{"__current_case__": 1, "alignment_options": {"L": "28", "N": "0", "__current_case__": 0, "align_mode": {"__current_case__": 1, "align_mode_selector": "local", "score_min_loc": "G,20,8"}, "alignment_options_selector": "yes", "dpad": "15", "gbar": "4", "i": "S,1,1.15", "ignore_quals": false, "n_ceil": "L,0,0.15", "no_1mm_upfront": false, "nofw": false, "norc": false}, "analysis_type_selector": "full", "effort_options": {"D": "15", "R": "2", "__current_case__": 0, "effort_options_selector": "yes"}, "input_options": {"__current_case__": 0, "input_options_selector": "yes", "int_quals": false, "qupto": "100000000", "qv_encoding": "--phred33", "skip": "0", "solexa_quals": false, "trim3": "0", "trim5": "0"}, "other_options": {"__current_case__": 0, "non_deterministic": false, "other_options_selector": "yes", "seed": "0"}, "reporting_options": {"__current_case__": 0, "reporting_options_selector": "no"}, "scoring_options": {"__current_case__": 0, "ma": "2", "mp": "6,2", "np": "1", "rdg_read_extend": "3", "rdg_read_open": "5", "rfg_ref_extend": "3", "rfg_ref_open": "5", "scoring_options_selector": "yes"}}
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
library	`{"__current_case__": 1, "aligned_file": false, "input_1": {"values": [{"id": 1, "src": "hdca"}]}, "paired_options": {"I": "0", "X": "500", "__current_case__": 0, "dovetail": false, "fr_rf_ff": "--fr", "no_contain": false, "no_discordant": false, "no_mixed": false, "no_overlap": false, "paired_options_selector": "yes"}, "type": "paired_collection", "unaligned_file": true}`
reference_genome	`{"__current_case__": 1, "own_file": {"values": [{"id": 3, "src": "hda"}]}, "source": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`
sam_options	`{"__current_case__": 1, "sam_options_selector": "no"}`
save_mapping_stats	`false`

Step 16: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/503bcd6ebe4b/regex_find_replace/regex.py' --input '/tmp/tmpa0q9y2tx/files/4/d/6/dataset_4d69773e-dc80-4acb-9c96-88c61ce4d77c.dat' --output '/tmp/tmpa0q9y2tx/job_working_directory/000/12/outputs/dataset_abf889ea-a828-4b1f-a8a9-9593249bddb8.dat' --input_display_name 'Create text file' --pattern='EON' --replacement='>'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
checks	`[{"__index__": 0, "pattern": "EON", "replacement": ">"}]`
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 17: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/503bcd6ebe4b/regex_find_replace/regex.py' --input '/tmp/tmpa0q9y2tx/files/d/5/8/dataset_d584e290-ca04-4c42-9787-cc2119453c50.dat' --output '/tmp/tmpa0q9y2tx/job_working_directory/000/13/outputs/dataset_1c684c4a-e36f-4291-8264-006d511da935.dat' --input_display_name 'Create text file' --pattern='EON' --replacement='>'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
checks	`[{"__index__": 0, "pattern": "EON", "replacement": ">"}]`
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 18: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpa0q9y2tx/files/9/5/3/dataset_9530dc79-ec79-49e2-83cd-1fa429d434e1.dat' 'Filter FASTQ on dataset 8' && mkdir -p '/tmp/tmpa0q9y2tx/job_working_directory/000/14/outputs/dataset_43dbebd7-3365-478a-87a9-d700c3b9a031_files' && fastqc --outdir '/tmp/tmpa0q9y2tx/job_working_directory/000/14/outputs/dataset_43dbebd7-3365-478a-87a9-d700c3b9a031_files'   --threads ${GALAXY_SLOTS:-2} --dir ${TEMP:-$_GALAXY_JOB_TMP_DIR} --quiet --extract  --kmers 7 -f 'fastq' 'Filter FASTQ on dataset 8'  && cp '/tmp/tmpa0q9y2tx/job_working_directory/000/14/outputs/dataset_43dbebd7-3365-478a-87a9-d700c3b9a031_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpa0q9y2tx/job_working_directory/000/14/outputs/dataset_43dbebd7-3365-478a-87a9-d700c3b9a031_files'/*\.html output.html

Exit Code:

```
0
```

Standard Output:

```
null
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
adapters	`None`
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 19: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail; bowtie2-build --threads ${GALAXY_SLOTS:-4} '/tmp/tmpa0q9y2tx/files/1/8/4/dataset_18465be9-6602-4eda-bdad-e9ab59a336a0.dat' genome && ln -s -f '/tmp/tmpa0q9y2tx/files/1/8/4/dataset_18465be9-6602-4eda-bdad-e9ab59a336a0.dat' genome.fa &&   ln -f -s '/tmp/tmpa0q9y2tx/files/9/5/3/dataset_9530dc79-ec79-49e2-83cd-1fa429d434e1.dat' input_f.fastq &&   THREADS=${GALAXY_SLOTS:-4} && if [ "$THREADS" -gt 1 ]; then (( THREADS-- )); fi &&   bowtie2  -p "$THREADS"  -x 'genome'   -U 'input_f.fastq'                -N 1 -L 22 -i 'S,1,1.15' --n-ceil 'L,0,0.15' --dpad 15 --gbar 4     --local --score-min 'G,20,8'        | samtools sort -l 0 -T "${TMPDIR:-.}" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/tmp/tmpa0q9y2tx/job_working_directory/000/15/outputs/dataset_7663f9da-d3fb-48d3-82e4-833b22b79cc0.dat'

Exit Code:

```
0
```

Standard Error:

Building a SMALL index
Renaming genome.3.bt2.tmp to genome.3.bt2
Renaming genome.4.bt2.tmp to genome.4.bt2
Renaming genome.1.bt2.tmp to genome.1.bt2
Renaming genome.2.bt2.tmp to genome.2.bt2
Renaming genome.rev.1.bt2.tmp to genome.rev.1.bt2
Renaming genome.rev.2.bt2.tmp to genome.rev.2.bt2
8562 reads; of these:
  8562 (100.00%) were unpaired; of these:
    8431 (98.47%) aligned 0 times
    130 (1.52%) aligned exactly 1 time
    1 (0.01%) aligned >1 times
1.53% overall alignment rate

Standard Output:

Settings:
  Output files: "genome.*.bt2"
  Line rate: 6 (line is 64 bytes)
  Lines per side: 1 (side is 64 bytes)
  Offset rate: 4 (one in 16)
  FTable chars: 10
  Strings: unpacked
  Max bucket size: default
  Max bucket size, sqrt multiplier: default
  Max bucket size, len divisor: 4
  Difference-cover sample period: 1024
  Endianness: little
  Actual local endianness: little
  Sanity checking: disabled
  Assertions: disabled
  Random seed: 0
  Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
  /tmp/tmpa0q9y2tx/files/1/8/4/dataset_18465be9-6602-4eda-bdad-e9ab59a336a0.dat
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
bmax according to bmaxDivN setting: 164
Using parameters --bmax 123 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 123 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:00
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:00
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:00
  Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
  (Using difference cover)
  Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 7; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 1; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 93.1429 (target: 122)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (123) for bucket 1
  Calculating Z arrays for bucket 1
  Entering block accumulator loop for bucket 1:
  bucket 1: 10%
  bucket 1: 20%
  bucket 1: 30%
  bucket 1: 40%
  bucket 1: 50%
  bucket 1: 60%
  bucket 1: 70%
  bucket 1: 80%
  bucket 1: 90%
  bucket 1: 100%
  Sorting block of length 118 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 119 for bucket 1
Getting block 2 of 7
  Reserving size (123) for bucket 2
  Calculating Z arrays for bucket 2
  Entering block accumulator loop for bucket 2:
  bucket 2: 10%
  bucket 2: 20%
  bucket 2: 30%
  bucket 2: 40%
  bucket 2: 50%
  bucket 2: 60%
  bucket 2: 70%
  bucket 2: 80%
  bucket 2: 90%
  bucket 2: 100%
  Sorting block of length 115 for bucket 2
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 116 for bucket 2
Getting block 3 of 7
  Reserving size (123) for bucket 3
  Calculating Z arrays for bucket 3
  Entering block accumulator loop for bucket 3:
  bucket 3: 10%
  bucket 3: 20%
  bucket 3: 30%
  bucket 3: 40%
  bucket 3: 50%
  bucket 3: 60%
  bucket 3: 70%
  bucket 3: 80%
  bucket 3: 90%
  bucket 3: 100%
  Sorting block of length 96 for bucket 3
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 97 for bucket 3
Getting block 4 of 7
  Reserving size (123) for bucket 4
  Calculating Z arrays for bucket 4
  Entering block accumulator loop for bucket 4:
  bucket 4: 10%
  bucket 4: 20%
  bucket 4: 30%
  bucket 4: 40%
  bucket 4: 50%
  bucket 4: 60%
  bucket 4: 70%
  bucket 4: 80%
  bucket 4: 90%
  bucket 4: 100%
  Sorting block of length 77 for bucket 4
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 78 for bucket 4
Getting block 5 of 7
  Reserving size (123) for bucket 5
  Calculating Z arrays for bucket 5
  Entering block accumulator loop for bucket 5:
  bucket 5: 10%
  bucket 5: 20%
  bucket 5: 30%
  bucket 5: 40%
  bucket 5: 50%
  bucket 5: 60%
  bucket 5: 70%
  bucket 5: 80%
  bucket 5: 90%
  bucket 5: 100%
  Sorting block of length 66 for bucket 5
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 67 for bucket 5
Getting block 6 of 7
  Reserving size (123) for bucket 6
  Calculating Z arrays for bucket 6
  Entering block accumulator loop for bucket 6:
  bucket 6: 10%
  bucket 6: 20%
  bucket 6: 30%
  bucket 6: 40%
  bucket 6: 50%
  bucket 6: 60%
  bucket 6: 70%
  bucket 6: 80%
  bucket 6: 90%
  bucket 6: 100%
  Sorting block of length 95 for bucket 6
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 96 for bucket 6
Getting block 7 of 7
  Reserving size (123) for bucket 7
  Calculating Z arrays for bucket 7
  Entering block accumulator loop for bucket 7:
  bucket 7: 10%
  bucket 7: 20%
  bucket 7: 30%
  bucket 7: 40%
  bucket 7: 50%
  bucket 7: 60%
  bucket 7: 70%
  bucket 7: 80%
  bucket 7: 90%
  bucket 7: 100%
  Sorting block of length 85 for bucket 7
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 86 for bucket 7
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 219
fchr[G]: 358
fchr[T]: 469
fchr[$]: 658
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4194838 bytes to primary EBWT file: genome.1.bt2.tmp
Wrote 172 bytes to secondary EBWT file: genome.2.bt2.tmp
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 658
    bwtLen: 659
    sz: 165
    bwtSz: 165
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 42
    offsSz: 168
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 4
    numLines: 4
    ebwtTotLen: 256
    ebwtTotSz: 256
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:00:00
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
  Time to reverse reference sequence: 00:00:00
bmax according to bmaxDivN setting: 164
Using parameters --bmax 123 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 123 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:00
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:00
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:00
  Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
  (Using difference cover)
  Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 8; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 0; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 0; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 93.1429 (target: 122)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (123) for bucket 1
  Calculating Z arrays for bucket 1
  Entering block accumulator loop for bucket 1:
  bucket 1: 10%
  bucket 1: 20%
  bucket 1: 30%
  bucket 1: 40%
  bucket 1: 50%
  bucket 1: 60%
  bucket 1: 70%
  bucket 1: 80%
  bucket 1: 90%
  bucket 1: 100%
  Sorting block of length 67 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 68 for bucket 1
Getting block 2 of 7
  Reserving size (123) for bucket 2
  Calculating Z arrays for bucket 2
  Entering block accumulator loop for bucket 2:
  bucket 2: 10%
  bucket 2: 20%
  bucket 2: 30%
  bucket 2: 40%
  bucket 2: 50%
  bucket 2: 60%
  bucket 2: 70%
  bucket 2: 80%
  bucket 2: 90%
  bucket 2: 100%
  Sorting block of length 88 for bucket 2
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 89 for bucket 2
Getting block 3 of 7
  Reserving size (123) for bucket 3
  Calculating Z arrays for bucket 3
  Entering block accumulator loop for bucket 3:
  bucket 3: 10%
  bucket 3: 20%
  bucket 3: 30%
  bucket 3: 40%
  bucket 3: 50%
  bucket 3: 60%
  bucket 3: 70%
  bucket 3: 80%
  bucket 3: 90%
  bucket 3: 100%
  Sorting block of length 103 for bucket 3
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 104 for bucket 3
Getting block 4 of 7
  Reserving size (123) for bucket 4
  Calculating Z arrays for bucket 4
  Entering block accumulator loop for bucket 4:
  bucket 4: 10%
  bucket 4: 20%
  bucket 4: 30%
  bucket 4: 40%
  bucket 4: 50%
  bucket 4: 60%
  bucket 4: 70%
  bucket 4: 80%
  bucket 4: 90%
  bucket 4: 100%
  Sorting block of length 121 for bucket 4
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 122 for bucket 4
Getting block 5 of 7
  Reserving size (123) for bucket 5
  Calculating Z arrays for bucket 5
  Entering block accumulator loop for bucket 5:
  bucket 5: 10%
  bucket 5: 20%
  bucket 5: 30%
  bucket 5: 40%
  bucket 5: 50%
  bucket 5: 60%
  bucket 5: 70%
  bucket 5: 80%
  bucket 5: 90%
  bucket 5: 100%
  Sorting block of length 90 for bucket 5
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 91 for bucket 5
Getting block 6 of 7
  Reserving size (123) for bucket 6
  Calculating Z arrays for bucket 6
  Entering block accumulator loop for bucket 6:
  bucket 6: 10%
  bucket 6: 20%
  bucket 6: 30%
  bucket 6: 40%
  bucket 6: 50%
  bucket 6: 60%
  bucket 6: 70%
  bucket 6: 80%
  bucket 6: 90%
  bucket 6: 100%
  Sorting block of length 95 for bucket 6
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 96 for bucket 6
Getting block 7 of 7
  Reserving size (123) for bucket 7
  Calculating Z arrays for bucket 7
  Entering block accumulator loop for bucket 7:
  bucket 7: 10%
  bucket 7: 20%
  bucket 7: 30%
  bucket 7: 40%
  bucket 7: 50%
  bucket 7: 60%
  bucket 7: 70%
  bucket 7: 80%
  bucket 7: 90%
  bucket 7: 100%
  Sorting block of length 88 for bucket 7
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 89 for bucket 7
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 219
fchr[G]: 358
fchr[T]: 469
fchr[$]: 658
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4194838 bytes to primary EBWT file: genome.rev.1.bt2.tmp
Wrote 172 bytes to secondary EBWT file: genome.rev.2.bt2.tmp
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 658
    bwtLen: 659
    sz: 165
    bwtSz: 165
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 42
    offsSz: 168
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 4
    numLines: 4
    ebwtTotLen: 256
    ebwtTotSz: 256
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:00:00

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
analysis_type	{"__current_case__": 1, "alignment_options": {"L": "22", "N": "1", "__current_case__": 0, "align_mode": {"__current_case__": 1, "align_mode_selector": "local", "score_min_loc": "G,20,8"}, "alignment_options_selector": "yes", "dpad": "15", "gbar": "4", "i": "S,1,1.15", "ignore_quals": false, "n_ceil": "L,0,0.15", "no_1mm_upfront": false, "nofw": false, "norc": false}, "analysis_type_selector": "full", "effort_options": {"__current_case__": 1, "effort_options_selector": "no"}, "input_options": {"__current_case__": 1, "input_options_selector": "no"}, "other_options": {"__current_case__": 1, "other_options_selector": "no"}, "reporting_options": {"__current_case__": 0, "reporting_options_selector": "no"}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "no"}}
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
library	`{"__current_case__": 0, "aligned_file": false, "input_1": {"values": [{"id": 13, "src": "hda"}]}, "type": "single", "unaligned_file": false}`
reference_genome	`{"__current_case__": 1, "own_file": {"values": [{"id": 3, "src": "hda"}]}, "source": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`
sam_options	`{"__current_case__": 1, "sam_options_selector": "no"}`
save_mapping_stats	`false`

Step 20: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.4+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -o | grep -q pipefail && set -o pipefail; bowtie2-build --threads ${GALAXY_SLOTS:-4} '/tmp/tmpa0q9y2tx/files/1/8/4/dataset_18465be9-6602-4eda-bdad-e9ab59a336a0.dat' genome && ln -s -f '/tmp/tmpa0q9y2tx/files/1/8/4/dataset_18465be9-6602-4eda-bdad-e9ab59a336a0.dat' genome.fa &&   ln -f -s '/tmp/tmpa0q9y2tx/files/3/0/9/dataset_3099eb14-6a80-442d-a22b-f388b3bf600a.dat' input_f.fastq &&  ln -f -s '/tmp/tmpa0q9y2tx/files/2/0/a/dataset_20a66c05-9546-43c9-963c-cff23d87c2a6.dat' input_r.fastq &&   THREADS=${GALAXY_SLOTS:-4} && if [ "$THREADS" -gt 1 ]; then (( THREADS-- )); fi &&   bowtie2  -p "$THREADS"  -x 'genome'   -1 'input_f.fastq' -2 'input_r.fastq' --un-conc 'unaligned_reads' -I 0 -X 500 --rf                   --skip 0 --qupto 100000000 --trim5 0 --trim3 0 --phred33    -N 0 -L 28 -i 'S,1,1.15' --n-ceil 'L,0,0.15' --dpad 15 --gbar 4     --local --score-min 'G,20,8'  --ma 2 --mp '6,2' --np 1 --rdg 5,3 --rfg 5,3   -D 15 -R 2  --seed 0     | samtools sort -l 0 -T "${TMPDIR:-.}" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/tmp/tmpa0q9y2tx/job_working_directory/000/16/outputs/dataset_3a4814cf-2e95-4018-9f55-f2ab52cff535.dat'

Exit Code:

```
0
```

Standard Error:

Building a SMALL index
Renaming genome.3.bt2.tmp to genome.3.bt2
Renaming genome.4.bt2.tmp to genome.4.bt2
Renaming genome.1.bt2.tmp to genome.1.bt2
Renaming genome.2.bt2.tmp to genome.2.bt2
Renaming genome.rev.1.bt2.tmp to genome.rev.1.bt2
Renaming genome.rev.2.bt2.tmp to genome.rev.2.bt2
8741 reads; of these:
  8741 (100.00%) were paired; of these:
    8723 (99.79%) aligned concordantly 0 times
    17 (0.19%) aligned concordantly exactly 1 time
    1 (0.01%) aligned concordantly >1 times
    ----
    8723 pairs aligned concordantly 0 times; of these:
      6 (0.07%) aligned discordantly 1 time
    ----
    8717 pairs aligned 0 times concordantly or discordantly; of these:
      17434 mates make up the pairs; of these:
        17432 (99.99%) aligned 0 times
        2 (0.01%) aligned exactly 1 time
        0 (0.00%) aligned >1 times
0.29% overall alignment rate

Standard Output:

Settings:
  Output files: "genome.*.bt2"
  Line rate: 6 (line is 64 bytes)
  Lines per side: 1 (side is 64 bytes)
  Offset rate: 4 (one in 16)
  FTable chars: 10
  Strings: unpacked
  Max bucket size: default
  Max bucket size, sqrt multiplier: default
  Max bucket size, len divisor: 4
  Difference-cover sample period: 1024
  Endianness: little
  Actual local endianness: little
  Sanity checking: disabled
  Assertions: disabled
  Random seed: 0
  Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
  /tmp/tmpa0q9y2tx/files/1/8/4/dataset_18465be9-6602-4eda-bdad-e9ab59a336a0.dat
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
bmax according to bmaxDivN setting: 164
Using parameters --bmax 123 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 123 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:00
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:00
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:00
  Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
  (Using difference cover)
  Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 7; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 1; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 93.1429 (target: 122)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (123) for bucket 1
  Calculating Z arrays for bucket 1
  Entering block accumulator loop for bucket 1:
  bucket 1: 10%
  bucket 1: 20%
  bucket 1: 30%
  bucket 1: 40%
  bucket 1: 50%
  bucket 1: 60%
  bucket 1: 70%
  bucket 1: 80%
  bucket 1: 90%
  bucket 1: 100%
  Sorting block of length 118 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 119 for bucket 1
Getting block 2 of 7
  Reserving size (123) for bucket 2
  Calculating Z arrays for bucket 2
  Entering block accumulator loop for bucket 2:
  bucket 2: 10%
  bucket 2: 20%
  bucket 2: 30%
  bucket 2: 40%
  bucket 2: 50%
  bucket 2: 60%
  bucket 2: 70%
  bucket 2: 80%
  bucket 2: 90%
  bucket 2: 100%
  Sorting block of length 115 for bucket 2
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 116 for bucket 2
Getting block 3 of 7
  Reserving size (123) for bucket 3
  Calculating Z arrays for bucket 3
  Entering block accumulator loop for bucket 3:
  bucket 3: 10%
  bucket 3: 20%
  bucket 3: 30%
  bucket 3: 40%
  bucket 3: 50%
  bucket 3: 60%
  bucket 3: 70%
  bucket 3: 80%
  bucket 3: 90%
  bucket 3: 100%
  Sorting block of length 96 for bucket 3
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 97 for bucket 3
Getting block 4 of 7
  Reserving size (123) for bucket 4
  Calculating Z arrays for bucket 4
  Entering block accumulator loop for bucket 4:
  bucket 4: 10%
  bucket 4: 20%
  bucket 4: 30%
  bucket 4: 40%
  bucket 4: 50%
  bucket 4: 60%
  bucket 4: 70%
  bucket 4: 80%
  bucket 4: 90%
  bucket 4: 100%
  Sorting block of length 77 for bucket 4
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 78 for bucket 4
Getting block 5 of 7
  Reserving size (123) for bucket 5
  Calculating Z arrays for bucket 5
  Entering block accumulator loop for bucket 5:
  bucket 5: 10%
  bucket 5: 20%
  bucket 5: 30%
  bucket 5: 40%
  bucket 5: 50%
  bucket 5: 60%
  bucket 5: 70%
  bucket 5: 80%
  bucket 5: 90%
  bucket 5: 100%
  Sorting block of length 66 for bucket 5
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 67 for bucket 5
Getting block 6 of 7
  Reserving size (123) for bucket 6
  Calculating Z arrays for bucket 6
  Entering block accumulator loop for bucket 6:
  bucket 6: 10%
  bucket 6: 20%
  bucket 6: 30%
  bucket 6: 40%
  bucket 6: 50%
  bucket 6: 60%
  bucket 6: 70%
  bucket 6: 80%
  bucket 6: 90%
  bucket 6: 100%
  Sorting block of length 95 for bucket 6
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 96 for bucket 6
Getting block 7 of 7
  Reserving size (123) for bucket 7
  Calculating Z arrays for bucket 7
  Entering block accumulator loop for bucket 7:
  bucket 7: 10%
  bucket 7: 20%
  bucket 7: 30%
  bucket 7: 40%
  bucket 7: 50%
  bucket 7: 60%
  bucket 7: 70%
  bucket 7: 80%
  bucket 7: 90%
  bucket 7: 100%
  Sorting block of length 85 for bucket 7
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 86 for bucket 7
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 219
fchr[G]: 358
fchr[T]: 469
fchr[$]: 658
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4194838 bytes to primary EBWT file: genome.1.bt2.tmp
Wrote 172 bytes to secondary EBWT file: genome.2.bt2.tmp
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 658
    bwtLen: 659
    sz: 165
    bwtSz: 165
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 42
    offsSz: 168
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 4
    numLines: 4
    ebwtTotLen: 256
    ebwtTotSz: 256
    color: 0
    reverse: 0
Total time for call to driver() for forward index: 00:00:00
Reading reference sizes
  Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:00
  Time to reverse reference sequence: 00:00:00
bmax according to bmaxDivN setting: 164
Using parameters --bmax 123 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 123 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
  Building sPrime
  Building sPrimeOrder
  V-Sorting samples
  V-Sorting samples time: 00:00:00
  Allocating rank array
  Ranking v-sort output
  Ranking v-sort output time: 00:00:00
  Invoking Larsson-Sadakane on ranks
  Invoking Larsson-Sadakane on ranks time: 00:00:00
  Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
  (Using difference cover)
  Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
  Splitting and merging time: 00:00:00
Split 2, merged 8; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 0; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Split 1, merged 0; iterating...
Splitting and merging
  Splitting and merging time: 00:00:00
Avg bucket size: 93.1429 (target: 122)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
  Reserving size (123) for bucket 1
  Calculating Z arrays for bucket 1
  Entering block accumulator loop for bucket 1:
  bucket 1: 10%
  bucket 1: 20%
  bucket 1: 30%
  bucket 1: 40%
  bucket 1: 50%
  bucket 1: 60%
  bucket 1: 70%
  bucket 1: 80%
  bucket 1: 90%
  bucket 1: 100%
  Sorting block of length 67 for bucket 1
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 68 for bucket 1
Getting block 2 of 7
  Reserving size (123) for bucket 2
  Calculating Z arrays for bucket 2
  Entering block accumulator loop for bucket 2:
  bucket 2: 10%
  bucket 2: 20%
  bucket 2: 30%
  bucket 2: 40%
  bucket 2: 50%
  bucket 2: 60%
  bucket 2: 70%
  bucket 2: 80%
  bucket 2: 90%
  bucket 2: 100%
  Sorting block of length 88 for bucket 2
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 89 for bucket 2
Getting block 3 of 7
  Reserving size (123) for bucket 3
  Calculating Z arrays for bucket 3
  Entering block accumulator loop for bucket 3:
  bucket 3: 10%
  bucket 3: 20%
  bucket 3: 30%
  bucket 3: 40%
  bucket 3: 50%
  bucket 3: 60%
  bucket 3: 70%
  bucket 3: 80%
  bucket 3: 90%
  bucket 3: 100%
  Sorting block of length 103 for bucket 3
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 104 for bucket 3
Getting block 4 of 7
  Reserving size (123) for bucket 4
  Calculating Z arrays for bucket 4
  Entering block accumulator loop for bucket 4:
  bucket 4: 10%
  bucket 4: 20%
  bucket 4: 30%
  bucket 4: 40%
  bucket 4: 50%
  bucket 4: 60%
  bucket 4: 70%
  bucket 4: 80%
  bucket 4: 90%
  bucket 4: 100%
  Sorting block of length 121 for bucket 4
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 122 for bucket 4
Getting block 5 of 7
  Reserving size (123) for bucket 5
  Calculating Z arrays for bucket 5
  Entering block accumulator loop for bucket 5:
  bucket 5: 10%
  bucket 5: 20%
  bucket 5: 30%
  bucket 5: 40%
  bucket 5: 50%
  bucket 5: 60%
  bucket 5: 70%
  bucket 5: 80%
  bucket 5: 90%
  bucket 5: 100%
  Sorting block of length 90 for bucket 5
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 91 for bucket 5
Getting block 6 of 7
  Reserving size (123) for bucket 6
  Calculating Z arrays for bucket 6
  Entering block accumulator loop for bucket 6:
  bucket 6: 10%
  bucket 6: 20%
  bucket 6: 30%
  bucket 6: 40%
  bucket 6: 50%
  bucket 6: 60%
  bucket 6: 70%
  bucket 6: 80%
  bucket 6: 90%
  bucket 6: 100%
  Sorting block of length 95 for bucket 6
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 96 for bucket 6
Getting block 7 of 7
  Reserving size (123) for bucket 7
  Calculating Z arrays for bucket 7
  Entering block accumulator loop for bucket 7:
  bucket 7: 10%
  bucket 7: 20%
  bucket 7: 30%
  bucket 7: 40%
  bucket 7: 50%
  bucket 7: 60%
  bucket 7: 70%
  bucket 7: 80%
  bucket 7: 90%
  bucket 7: 100%
  Sorting block of length 88 for bucket 7
  (Using difference cover)
  Sorting block time: 00:00:00
Returning block of 89 for bucket 7
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 219
fchr[G]: 358
fchr[T]: 469
fchr[$]: 658
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4194838 bytes to primary EBWT file: genome.rev.1.bt2.tmp
Wrote 172 bytes to secondary EBWT file: genome.rev.2.bt2.tmp
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
    len: 658
    bwtLen: 659
    sz: 165
    bwtSz: 165
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 20
    eftabSz: 80
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 42
    offsSz: 168
    lineSz: 64
    sideSz: 64
    sideBwtSz: 48
    sideBwtLen: 192
    numSides: 4
    numLines: 4
    ebwtTotLen: 256
    ebwtTotSz: 256
    color: 0
    reverse: 1
Total time for backward call to driver() for mirror index: 00:00:00

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
analysis_type	{"__current_case__": 1, "alignment_options": {"L": "28", "N": "0", "__current_case__": 0, "align_mode": {"__current_case__": 1, "align_mode_selector": "local", "score_min_loc": "G,20,8"}, "alignment_options_selector": "yes", "dpad": "15", "gbar": "4", "i": "S,1,1.15", "ignore_quals": false, "n_ceil": "L,0,0.15", "no_1mm_upfront": false, "nofw": false, "norc": false}, "analysis_type_selector": "full", "effort_options": {"D": "15", "R": "2", "__current_case__": 0, "effort_options_selector": "yes"}, "input_options": {"__current_case__": 0, "input_options_selector": "yes", "int_quals": false, "qupto": "100000000", "qv_encoding": "--phred33", "skip": "0", "solexa_quals": false, "trim3": "0", "trim5": "0"}, "other_options": {"__current_case__": 0, "non_deterministic": false, "other_options_selector": "yes", "seed": "0"}, "reporting_options": {"__current_case__": 0, "reporting_options_selector": "no"}, "scoring_options": {"__current_case__": 0, "ma": "2", "mp": "6,2", "np": "1", "rdg_read_extend": "3", "rdg_read_open": "5", "rfg_ref_extend": "3", "rfg_ref_open": "5", "scoring_options_selector": "yes"}}
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
library	`{"__current_case__": 1, "aligned_file": false, "input_1": {"values": [{"id": 2, "src": "hdca"}]}, "paired_options": {"I": "0", "X": "500", "__current_case__": 0, "dovetail": false, "fr_rf_ff": "--rf", "no_contain": false, "no_discordant": false, "no_mixed": false, "no_overlap": false, "paired_options_selector": "yes"}, "type": "paired_collection", "unaligned_file": true}`
reference_genome	`{"__current_case__": 1, "own_file": {"values": [{"id": 3, "src": "hda"}]}, "source": "history"}`
rg	`{"__current_case__": 3, "rg_selector": "do_not_set"}`
sam_options	`{"__current_case__": 1, "sam_options_selector": "no"}`
save_mapping_stats	`false`

Step 3: Filter FASTQ - Minimum size:
- step_state: scheduled

Step 21: toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.21+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) &&        ln -s '/tmp/tmpa0q9y2tx/files/7/6/6/dataset_7663f9da-d3fb-48d3-82e4-833b22b79cc0.dat' infile && ln -s '/tmp/tmpa0q9y2tx/files/_metadata_files/a/d/d/metadata_add066c2-92b6-4ca8-890e-02763bf03fe1.dat' infile.bai &&               samtools view -@ $addthreads -b  -q 30 -f 0 -F 4 -G 0   -o outfile      infile

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
addref_cond	`{"__current_case__": 0, "addref_select": "no"}`
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	{"__current_case__": 1, "filter_config": {"cigarcons": null, "cond_expr": {"__current_case__": 0, "select_expr": "no"}, "cond_region": {"__current_case__": 0, "select_region": "no"}, "cond_rg": {"__current_case__": 0, "select_rg": "no"}, "exclusive_filter": ["4"], "exclusive_filter_all": null, "inclusive_filter": null, "library": null, "qname_file": null, "quality": "30", "tag": null}, "output_options": {"__current_case__": 0, "adv_output": {"collapsecigar": false, "readtags": []}, "complementary_output": false, "output_format": {"__current_case__": 2, "oformat": "bam"}, "reads_report_type": "retained"}, "outtype": "selected_reads", "subsample_config": {"subsampling_mode": {"__current_case__": 0, "factor": "1.0", "seed": null, "select_subsample": "fraction"}}}

Step 22: toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/jbrowse2/3.6.5+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p '/tmp/tmpa0q9y2tx/job_working_directory/000/18/outputs/dataset_c45076b5-12d5-4658-bd32-396a84511d4e_files/data';   cp '/tmp/tmpa0q9y2tx/job_working_directory/000/18/configs/tmpymcmg0bd' '/tmp/tmpa0q9y2tx/job_working_directory/000/18/outputs/dataset_c45076b5-12d5-4658-bd32-396a84511d4e_files/galaxy.xml';  export JBROWSE2_SOURCE_DIR=$(dirname $(which jbrowse))/../opt/jbrowse2;  python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/93fdd696c281/jbrowse2/jbrowse2.py' --jbrowse ${JBROWSE2_SOURCE_DIR}   --outdir '/tmp/tmpa0q9y2tx/job_working_directory/000/18/outputs/dataset_c45076b5-12d5-4658-bd32-396a84511d4e_files' '/tmp/tmpa0q9y2tx/job_working_directory/000/18/configs/tmpymcmg0bd';  cp '/tmp/tmpa0q9y2tx/job_working_directory/000/18/outputs/dataset_c45076b5-12d5-4658-bd32-396a84511d4e_files/index.html' '/tmp/tmpa0q9y2tx/job_working_directory/000/18/outputs/dataset_c45076b5-12d5-4658-bd32-396a84511d4e.dat';

Exit Code:

```
0
```

Standard Error:

DEBUG:jbrowse:Processing genome
DEBUG:jbrowse:cd /tmp/tmpa0q9y2tx/job_working_directory/000/18/outputs/dataset_c45076b5-12d5-4658-bd32-396a84511d4e_files && bgzip /tmp/tmpa0q9y2tx/job_working_directory/000/18/outputs/dataset_c45076b5-12d5-4658-bd32-396a84511d4e_files/data/astrotoma_agassizii_COI.fasta.fasta
DEBUG:jbrowse:cd /tmp/tmpa0q9y2tx/job_working_directory/000/18/outputs/dataset_c45076b5-12d5-4658-bd32-396a84511d4e_files && samtools faidx /tmp/tmpa0q9y2tx/job_working_directory/000/18/outputs/dataset_c45076b5-12d5-4658-bd32-396a84511d4e_files/data/astrotoma_agassizii_COI.fasta.fasta.gz
DEBUG:jbrowse:cd /tmp/tmpa0q9y2tx/job_working_directory/000/18/outputs/dataset_c45076b5-12d5-4658-bd32-396a84511d4e_files && jbrowse add-assembly --load inPlace --name astrotoma_agassizii_COI.fasta --type bgzipFasta --out /tmp/tmpa0q9y2tx/job_working_directory/000/18/outputs/dataset_c45076b5-12d5-4658-bd32-396a84511d4e_files --skipCheck data/astrotoma_agassizii_COI.fasta.fasta.gz
/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/93fdd696c281/jbrowse2/jbrowse2.py:1692: DeprecationWarning: Testing an element's truth value will always return True in future versions.  Use specific 'len(elem)' or 'elem is not None' test instead.
  item.tag: parse_style_conf(item) for item in (track.find("options/style") or [])
/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/fubar/jbrowse2/93fdd696c281/jbrowse2/jbrowse2.py:1696: DeprecationWarning: Testing an element's truth value will always return True in future versions.  Use specific 'len(elem)' or 'elem is not None' test instead.
  item.tag: parse_style_conf(item) for item in (track.find("options/style") or [])
INFO:jbrowse:-----> Processing track Default / Samtools view on dataset 23: filtered alignments (bam, 1 files)
DEBUG:jbrowse:cd /tmp/tmpa0q9y2tx/job_working_directory/000/18/outputs/dataset_c45076b5-12d5-4658-bd32-396a84511d4e_files && cp /tmp/tmpa0q9y2tx/files/3/5/3/dataset_3532dc6e-c719-4bcd-a28d-664ec6648fd3.dat /tmp/tmpa0q9y2tx/job_working_directory/000/18/outputs/dataset_c45076b5-12d5-4658-bd32-396a84511d4e_files/data/1b2854c0f868ff4c0c3eb4b60f809316_0_0.bam
DEBUG:jbrowse:cd /tmp/tmpa0q9y2tx/job_working_directory/000/18/outputs/dataset_c45076b5-12d5-4658-bd32-396a84511d4e_files && cp /tmp/tmpa0q9y2tx/files/_metadata_files/e/c/b/metadata_ecbcf22c-d98e-41e6-b3aa-242944f8f3ee.dat /tmp/tmpa0q9y2tx/job_working_directory/000/18/outputs/dataset_c45076b5-12d5-4658-bd32-396a84511d4e_files/data/1b2854c0f868ff4c0c3eb4b60f809316_0_0.bam.bai
DEBUG:jbrowse:cd /tmp/tmpa0q9y2tx/job_working_directory/000/18/outputs/dataset_c45076b5-12d5-4658-bd32-396a84511d4e_files && jbrowse add-track --name Samtools view on dataset 23: filtered alignments --category Default --target /tmp/tmpa0q9y2tx/job_working_directory/000/18/outputs/dataset_c45076b5-12d5-4658-bd32-396a84511d4e_files --trackId 1b2854c0f868ff4c0c3eb4b60f809316_0_0 --assemblyNames astrotoma_agassizii_COI.fasta --load inPlace --config {"displays": [{"type": "LinearAlignmentsDisplay", "displayId": "1b2854c0f868ff4c0c3eb4b60f809316_0_0_LinearAlignmentsDisplay"}], "metadata": {"dataset_id": "ec802ce356817933", "dataset_hid": "28", "dataset_size": "8.4 KB", "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_2572\">bam</a>", "dataset_file_ext": "bam", "history_id": "c1f821c882229aee", "history_user_email": "<a href=\"mailto:[email protected]\">[email protected]</a>", "history_user_id": "1", "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/c1f821c882229aee\">CWL Target History</a>", "metadata_dbkey": "?", "metadata_columns": "12", "metadata_column_names": "[\"QNAME\", \"FLAG\", \"RNAME\", \"POS\", \"MAPQ\", \"CIGAR\", \"MRNM\", \"MPOS\", \"ISIZE\", \"SEQ\", \"QUAL\", \"OPT\"]", "metadata_bam_version": "1.5", "metadata_sort_order": "coordinate", "metadata_read_groups": "[]", "metadata_reference_names": "[\"KY986589.1\"]", "metadata_reference_lengths": "[658]", "metadata_metadata_incomplete": "False", "metadata_bam_index": "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX", "tool_tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.21+galaxy0", "tool_tool_version": "1.21+galaxy0", "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/ec802ce356817933/show_params\">toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.21+galaxy0</a>"}} data/1b2854c0f868ff4c0c3eb4b60f809316_0_0.bam

Standard Output:

Added assembly "astrotoma_agassizii_COI.fasta" to /tmp/tmpa0q9y2tx/job_working_directory/000/18/outputs/dataset_c45076b5-12d5-4658-bd32-396a84511d4e_files/config.json
Added track with name "Samtools view on dataset 23: filtered alignments" and trackId "1b2854c0f868ff4c0c3eb4b60f809316_0_0" to /tmp/tmpa0q9y2tx/job_working_directory/000/18/outputs/dataset_c45076b5-12d5-4658-bd32-396a84511d4e_files/config.json

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
action	`{"__current_case__": 0, "action_select": "create"}`
assemblies	[{"__index__": 0, "cytobands": null, "defaultLocation": "", "ref_name_aliases": null, "reference_genome": {"__current_case__": 1, "genome": {"values": [{"id": 3, "src": "hda"}]}, "genome_type_select": "history"}, "track_groups": [{"__index__": 0, "category": "Default", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 1, "annotation_cond": {"__current_case__": 0, "annotation": {"values": [{"id": 25, "src": "hda"}]}, "annotation_source": "history"}, "data_format_select": "pileup", "jbstyle": {"track_style": {"__current_case__": 0, "display": "LinearAlignmentsDisplay"}}, "metadata": {"galaxy_metadata": true, "metadata_bonus": null}, "track_visibility": "default_on"}}]}]}]
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
jbgen	`{"enableAnalytics": false, "font_size": "10", "primary_color": "#0d233f", "quaternary_color": "#ffb11d", "secondary_color": "#721e63", "tertiary_color": "#135560"}`

Step 23: toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.21+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&  samtools sort -@ $addthreads -n '/tmp/tmpa0q9y2tx/files/3/5/3/dataset_3532dc6e-c719-4bcd-a28d-664ec6648fd3.dat' -T "${TMPDIR:-.}" > input &&   samtools fasta     -f 0   -F 2304   -G 0  input  > output.fasta && ln -s output.fasta output

Exit Code:

```
0
```

Standard Error:

[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 116 reads

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
copy_arb_tags	`None`
copy_tags	`false`
dbkey	`"?"`
exclusive_filter	`["256", "2048"]`
exclusive_filter_all	`None`
idxout_cond	`{"__current_case__": 0, "idxout_select": "no"}`
inclusive_filter	`None`
output_fmt_cond	`{"__current_case__": 1, "output_fmt_select": "fasta"}`
outputs	`"other"`
read_numbering	`""`

Step 24: toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.7:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&   ln -s '/tmp/tmpa0q9y2tx/files/3/5/3/dataset_3532dc6e-c719-4bcd-a28d-664ec6648fd3.dat' infile && ln -s '/tmp/tmpa0q9y2tx/files/_metadata_files/e/c/b/metadata_ecbcf22c-d98e-41e6-b3aa-242944f8f3ee.dat' infile.bai &&  samtools idxstats -@ $addthreads infile  > '/tmp/tmpa0q9y2tx/job_working_directory/000/20/outputs/dataset_1cedb3b4-d2fa-400e-9bfb-10634a6924cf.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 25: toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.21+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpa0q9y2tx/files/3/5/3/dataset_3532dc6e-c719-4bcd-a28d-664ec6648fd3.dat' '0' && ln -s '/tmp/tmpa0q9y2tx/files/_metadata_files/e/c/b/metadata_ecbcf22c-d98e-41e6-b3aa-242944f8f3ee.dat' '0.bai' &&   samtools depth  0   -g 0   -G 1796    > '/tmp/tmpa0q9y2tx/job_working_directory/000/21/outputs/dataset_b5f952d9-dd55-48dd-b5cf-fc1a3fbbeaa2.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
additional_options	`{"deletions": false, "required_flags": null, "single_read": false, "skipped_flags": ["4", "256", "512", "1024"]}`
all	`""`
basequality	`None`
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond_region	`{"__current_case__": 0, "select_region": "no"}`
dbkey	`"?"`
mapquality	`None`
maxdepth	`None`
minlength	`None`
output_options	`{"header": false}`

Step 26: toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

if [[ -n "$GALAXY_MEMORY_MB" ]]; then MEMORY="-m $((GALAXY_MEMORY_MB * 1024))"; fi;  megahit --num-cpu-threads ${GALAXY_SLOTS:-4} -r '/tmp/tmpa0q9y2tx/files/1/b/e/dataset_1bed602d-bd1f-4b12-bb3a-37b8f804ecef.dat' --min-count '2' --k-list '21,29,39,59,79,99,119,141'  --bubble-level '2' --merge-level '20,0.95' --prune-level '2' --prune-depth '2' --disconnect-ratio '0.1' --low-local-ratio '0.2' --cleaning-rounds '5'   --min-contig-len '200' $MEMORY

Exit Code:

```
0
```

Standard Error:

2025-12-16 17:15:23 - MEGAHIT v1.2.9
2025-12-16 17:15:23 - Using megahit_core with POPCNT and BMI2 support
2025-12-16 17:15:23 - Convert reads to binary library
2025-12-16 17:15:23 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 0 (/tmp/tmpa0q9y2tx/files/1/b/e/dataset_1bed602d-bd1f-4b12-bb3a-37b8f804ecef.dat): se, 116 reads, 449 max length'
2025-12-16 17:15:23 - b'INFO  utils/utils.h                 :  152 - Real: 0.0005\tuser: 0.0000\tsys: 0.0019\tmaxrss: 16732'
2025-12-16 17:15:23 - Start assembly. Number of CPU threads 1 
2025-12-16 17:15:23 - k list: 21,29,39,59,79,99,119,141 
2025-12-16 17:15:23 - Memory used: 15095321395
2025-12-16 17:15:23 - Extract solid (k+1)-mers for k = 21 
2025-12-16 17:15:23 - Build graph for k = 21 
2025-12-16 17:15:24 - Assemble contigs from SdBG for k = 21
2025-12-16 17:15:24 - Local assembly for k = 21
2025-12-16 17:15:24 - Extract iterative edges from k = 21 to 29 
2025-12-16 17:15:24 - Build graph for k = 29 
2025-12-16 17:15:24 - Assemble contigs from SdBG for k = 29
2025-12-16 17:15:24 - Local assembly for k = 29
2025-12-16 17:15:24 - Extract iterative edges from k = 29 to 39 
2025-12-16 17:15:24 - Build graph for k = 39 
2025-12-16 17:15:24 - Assemble contigs from SdBG for k = 39
2025-12-16 17:15:24 - Local assembly for k = 39
2025-12-16 17:15:24 - Extract iterative edges from k = 39 to 59 
2025-12-16 17:15:24 - Build graph for k = 59 
2025-12-16 17:15:25 - Assemble contigs from SdBG for k = 59
2025-12-16 17:15:25 - Local assembly for k = 59
2025-12-16 17:15:25 - Extract iterative edges from k = 59 to 79 
2025-12-16 17:15:25 - Build graph for k = 79 
2025-12-16 17:15:25 - Assemble contigs from SdBG for k = 79
2025-12-16 17:15:25 - Local assembly for k = 79
2025-12-16 17:15:25 - Extract iterative edges from k = 79 to 99 
2025-12-16 17:15:25 - Build graph for k = 99 
2025-12-16 17:15:25 - Assemble contigs from SdBG for k = 99
2025-12-16 17:15:25 - Local assembly for k = 99
2025-12-16 17:15:25 - Extract iterative edges from k = 99 to 119 
2025-12-16 17:15:25 - Build graph for k = 119 
2025-12-16 17:15:25 - Assemble contigs from SdBG for k = 119
2025-12-16 17:15:26 - Local assembly for k = 119
2025-12-16 17:15:26 - Extract iterative edges from k = 119 to 141 
2025-12-16 17:15:26 - Build graph for k = 141 
2025-12-16 17:15:26 - Assemble contigs from SdBG for k = 141
2025-12-16 17:15:26 - Merging to output final contigs 
2025-12-16 17:15:26 - 1 contigs, total 669 bp, min 669 bp, max 669 bp, avg 669 bp, N50 669 bp
2025-12-16 17:15:26 - ALL DONE. Time elapsed: 2.665113 seconds

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
advanced_section	`{"bubble_level": "2", "cleaning_rounds": "5", "disconnect_ratio": "0.1", "kmin1pass": false, "low_local_ratio": "0.2", "merge_level": "20,0.95", "nolocal": false, "nomercy": false, "prune_depth": "2", "prune_level": "2"}`
basic_section	`{"k_mer": {"__current_case__": 0, "k_list": "21,29,39,59,79,99,119,141", "k_mer_method": "klist_method"}, "min_count": "2"}`
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_option	`{"__current_case__": 0, "choice": "single", "single_files": {"values": [{"id": 27, "src": "hda"}]}}`
output_section	`{"log_file": false, "min_contig_len": "200", "show_intermediate_contigs": false}`

Step 27: toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

echo 'rucio' >> '/tmp/tmpa0q9y2tx/job_working_directory/000/23/outputs/dataset_85e9ae2b-4e54-46df-bbe7-25b234421b21.dat' && cat '/tmp/tmpa0q9y2tx/files/1/c/e/dataset_1cedb3b4-d2fa-400e-9bfb-10634a6924cf.dat' >> '/tmp/tmpa0q9y2tx/job_working_directory/000/23/outputs/dataset_85e9ae2b-4e54-46df-bbe7-25b234421b21.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
options	`"header"`
text_input	`"rucio"`

Step 28: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.9+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash  --header-out       min 3 max 3 mean 3 < /tmp/tmpa0q9y2tx/files/b/5/f/dataset_b5f952d9-dd55-48dd-b5cf-fc1a3fbbeaa2.dat > '/tmp/tmpa0q9y2tx/job_working_directory/000/24/outputs/dataset_c6180f2e-1f24-44e1-a877-e72843a8c7db.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`None`
header_in	`false`
header_out	`true`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "min"}, {"__index__": 1, "op_column": "3", "op_name": "max"}, {"__index__": 2, "op_column": "3", "op_name": "mean"}]`
print_full_line	`false`

Step 29: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/5.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmpa0q9y2tx/files/f/6/f/dataset_f6f113c0-faff-4237-b9fc-7babeb323e0f.dat' 'Assembly with MEGAHIT on dataset 30.fa' &&  cutadapt  -j=${GALAXY_SLOTS:-4}   -a file:'/tmp/tmpa0q9y2tx/files/1/c/6/dataset_1c684c4a-e36f-4291-8264-006d511da935.dat'   -g file:'/tmp/tmpa0q9y2tx/files/a/b/f/dataset_abf889ea-a828-4b1f-a8a9-9593249bddb8.dat'    --error-rate=0.2 --times=1 --overlap=20    --action=trim         --minimum-length=1      -o 'out1.fa'  'Assembly with MEGAHIT on dataset 30.fa'

Exit Code:

```
0
```

Standard Output:

This is cutadapt 5.1 with Python 3.12.10
Command line parameters: -j=1 -a file:/tmp/tmpa0q9y2tx/files/1/c/6/dataset_1c684c4a-e36f-4291-8264-006d511da935.dat -g file:/tmp/tmpa0q9y2tx/files/a/b/f/dataset_abf889ea-a828-4b1f-a8a9-9593249bddb8.dat --error-rate=0.2 --times=1 --overlap=20 --action=trim --minimum-length=1 -o out1.fa Assembly with MEGAHIT on dataset 30.fa
Processing single-end reads on 1 core ...

=== Summary ===

Total reads processed:                       1
Reads with adapters:                         0 (0.0%)

== Read fate breakdown ==
Reads that were too short:                   0 (0.0%)
Reads written (passing filters):             1 (100.0%)

Total basepairs processed:           669 bp
Total written (filtered):            669 bp (100.0%)

=== Adapter Reverse ===

Sequence: AGTGAGTAAACTTCAGGGTGTCCRAARAATCA; Type: regular 3'; Length: 32; Trimmed: 0 times

=== Adapter Forward ===

Sequence: AGTGAGTTTCAACAAAACAYAAGGNCATNGG; Type: regular 5'; Length: 31; Trimmed: 0 times

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
adapter_options	`{"action": "trim", "error_rate": "0.2", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "20", "revcomp": false, "times": "1"}`
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
filter_options	`{"discard_casava": false, "discard_trimmed": false, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "maximum_length2": null, "minimum_length": "1", "minimum_length2": null, "pair_filter": "any"}`
library	{"__current_case__": 0, "input_1": {"values": [{"id": 30, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 2, "adapter_file": {"values": [{"id": 18, "src": "hda"}]}, "adapter_source_list": "file"}, "single_noindels": false}], "anywhere_adapters": [], "front_adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 2, "adapter_file": {"values": [{"id": 17, "src": "hda"}]}, "adapter_source_list": "file"}, "single_noindels": false}]}, "type": "single"}
other_trimming_options	`{"cut": "0", "cut2": "0", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "quality_cutoff2": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "shorten_options_r2": {"__current_case__": 1, "shorten_values_r2": "False"}, "trim_n": false}`
output_selector	`None`
read_mod_options	`{"length_tag": null, "rename": null, "strip_suffix": null, "zero_cap": false}`

Step 30: Show beginning1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

head -n 2 '/tmp/tmpa0q9y2tx/files/8/5/e/dataset_85e9ae2b-4e54-46df-bbe7-25b234421b21.dat' > '/tmp/tmpa0q9y2tx/job_working_directory/000/26/outputs/dataset_b03f7a5e-de2a-4e0f-8448-0f171d399ddb.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
header	`true`
lineNum	`"1"`

Step 4: Filter FASTQ - Maximum size:
- step_state: scheduled

Step 31: toolshed.g2.bx.psu.edu/repos/iuc/seqkit_stats/seqkit_stats/2.10.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpa0q9y2tx/files/3/8/b/dataset_38bdf06f-9b3c-4a12-b8f4-660375d56f0b.dat' 'Cutadapt on dataset 19_ 20_ and 33_ Read 1 Output' &&  seqkit stats 'Cutadapt on dataset 19_ 20_ and 33_ Read 1 Output'    --tabular > '/tmp/tmpa0q9y2tx/job_working_directory/000/27/outputs/dataset_6a397858-fedb-43c7-bad1-43fb7c20aeed.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
all	`false`
basename	`false`
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
skip_err	`false`
tabular	`true`

Step 32: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpa0q9y2tx/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpa0q9y2tx/files/b/0/3/dataset_b03f7a5e-de2a-4e0f-8448-0f171d399ddb.dat' 'c3' T '/tmp/tmpa0q9y2tx/job_working_directory/000/28/outputs/dataset_0438bd0c-ea67-4937-af30-feea61fcf8b5.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c3"`
dbkey	`"?"`
delimiter	`"T"`

Step 33: Show tail1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

set -eo pipefail; ( head -n 1 '/tmp/tmpa0q9y2tx/files/6/a/3/dataset_6a397858-fedb-43c7-bad1-43fb7c20aeed.dat' && tail -n +2 '/tmp/tmpa0q9y2tx/files/6/a/3/dataset_6a397858-fedb-43c7-bad1-43fb7c20aeed.dat' | tail -n 1 ) > '/tmp/tmpa0q9y2tx/job_working_directory/000/29/outputs/dataset_491cb49f-bf58-420e-a429-56f8212636ad.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
header	`true`
lineNum	`"1"`

Step 34: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpa0q9y2tx/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpa0q9y2tx/files/4/9/1/dataset_491cb49f-bf58-420e-a429-56f8212636ad.dat' 'c8' T '/tmp/tmpa0q9y2tx/job_working_directory/000/30/outputs/dataset_88d7bef4-bea7-4561-9bef-9b6108c61f8a.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c8"`
dbkey	`"?"`
delimiter	`"T"`

Step 35: Paste1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

paste '/tmp/tmpa0q9y2tx/files/8/8/d/dataset_88d7bef4-bea7-4561-9bef-9b6108c61f8a.dat' '/tmp/tmpa0q9y2tx/files/c/6/1/dataset_c6180f2e-1f24-44e1-a877-e72843a8c7db.dat' > '/tmp/tmpa0q9y2tx/job_working_directory/000/31/outputs/dataset_d4c75af3-22a8-4bd3-b14c-6a90f3e21b35.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
delimiter	`"T"`

Step 36: Paste1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

paste '/tmp/tmpa0q9y2tx/files/0/4/3/dataset_0438bd0c-ea67-4937-af30-feea61fcf8b5.dat' '/tmp/tmpa0q9y2tx/files/d/4/c/dataset_d4c75af3-22a8-4bd3-b14c-6a90f3e21b35.dat' > '/tmp/tmpa0q9y2tx/job_working_directory/000/32/outputs/dataset_893d2474-7586-4ae0-9f26-468396f05959.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
delimiter	`"T"`

Step 37: toolshed.g2.bx.psu.edu/repos/recetox/table_pandas_rename_column/table_pandas_rename_column/2.2.3+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python3 '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/recetox/table_pandas_rename_column/3f54cd56a65e/table_pandas_rename_column/table_pandas_rename_column.py' --input_dataset '/tmp/tmpa0q9y2tx/files/8/9/3/dataset_893d2474-7586-4ae0-9f26-468396f05959.dat' 'tabular' --rename 1=mapped_reads 2=consensus_length 3=min_depth 4=max_depth 5=mean_depth --output_dataset '/tmp/tmpa0q9y2tx/job_working_directory/000/33/outputs/dataset_f5ff3eed-6fb5-4bfd-9ee9-74cca15e4269.dat' 'tabular'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columns_selection	`[{"__index__": 0, "column": "1", "new_name": "mapped_reads"}, {"__index__": 1, "column": "2", "new_name": "consensus_length"}, {"__index__": 2, "column": "3", "new_name": "min_depth"}, {"__index__": 3, "column": "4", "new_name": "max_depth"}, {"__index__": 4, "column": "5", "new_name": "mean_depth"}]`
dbkey	`"?"`

Step 5: Reference sequence:
- step_state: scheduled
Step 6: Forward primer:
- step_state: scheduled
Step 7: Reverse primer:
- step_state: scheduled

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpa0q9y2tx/files/4/a/8/dataset_4a899d09-4768-4202-9869-e6dfb1a74628.dat' 'Banque-02_S2_L001_R1_001_fastq' && mkdir -p '/tmp/tmpa0q9y2tx/job_working_directory/000/4/outputs/dataset_8514c286-4e45-47d6-9787-45c8b9260e89_files' && fastqc --outdir '/tmp/tmpa0q9y2tx/job_working_directory/000/4/outputs/dataset_8514c286-4e45-47d6-9787-45c8b9260e89_files'   --threads ${GALAXY_SLOTS:-2} --dir ${TEMP:-$_GALAXY_JOB_TMP_DIR} --quiet --extract  --kmers 7 -f 'fastq' 'Banque-02_S2_L001_R1_001_fastq'  && cp '/tmp/tmpa0q9y2tx/job_working_directory/000/4/outputs/dataset_8514c286-4e45-47d6-9787-45c8b9260e89_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpa0q9y2tx/job_working_directory/000/4/outputs/dataset_8514c286-4e45-47d6-9787-45c8b9260e89_files'/*\.html output.html

Exit Code:

```
0
```

Standard Output:

```
null
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
adapters	`None`
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 9: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpa0q9y2tx/files/d/3/d/dataset_d3d260e7-8cd9-481c-bfc2-7811867e7278.dat' 'Banque-02_S2_L001_R2_001_fastq' && mkdir -p '/tmp/tmpa0q9y2tx/job_working_directory/000/5/outputs/dataset_9f3298d9-a805-4996-a791-d37d2c4d0142_files' && fastqc --outdir '/tmp/tmpa0q9y2tx/job_working_directory/000/5/outputs/dataset_9f3298d9-a805-4996-a791-d37d2c4d0142_files'   --threads ${GALAXY_SLOTS:-2} --dir ${TEMP:-$_GALAXY_JOB_TMP_DIR} --quiet --extract  --kmers 7 -f 'fastq' 'Banque-02_S2_L001_R2_001_fastq'  && cp '/tmp/tmpa0q9y2tx/job_working_directory/000/5/outputs/dataset_9f3298d9-a805-4996-a791-d37d2c4d0142_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpa0q9y2tx/job_working_directory/000/5/outputs/dataset_9f3298d9-a805-4996-a791-d37d2c4d0142_files'/*\.html output.html

Exit Code:

```
0
```

Standard Output:

```
null
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
adapters	`None`
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contaminants	`None`
dbkey	`"?"`
kmers	`"7"`
limits	`None`
min_length	`None`
nogroup	`false`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/pear/iuc_pear/0.9.6.4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

pear -f '/tmp/tmpa0q9y2tx/files/4/a/8/dataset_4a899d09-4768-4202-9869-e6dfb1a74628.dat' -r '/tmp/tmpa0q9y2tx/files/d/3/d/dataset_d3d260e7-8cd9-481c-bfc2-7811867e7278.dat' --phred-base 33  --output pear --p-value 0.01 --min-overlap 10 --min-asm-length 50 --min-trim-length 1 --quality-theshold 0 --max-uncalled-base 1.0 --test-method 1 --threads "${GALAXY_SLOTS:-8}" --score-method 2 --cap 40

Exit Code:

```
0
```

Standard Output:

 ____  _____    _    ____ 
|  _ \| ____|  / \  |  _ \
| |_) |  _|   / _ \ | |_) |
|  __/| |___ / ___ \|  _ <
|_|   |_____/_/   \_\_| \_\

PEAR v0.9.6 [January 15, 2015]

Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR
Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593

Forward reads file.................: /tmp/tmpa0q9y2tx/files/4/a/8/dataset_4a899d09-4768-4202-9869-e6dfb1a74628.dat
Reverse reads file.................: /tmp/tmpa0q9y2tx/files/d/3/d/dataset_d3d260e7-8cd9-481c-bfc2-7811867e7278.dat
PHRED..............................: 33
Using empirical frequencies........: YES
Statistical method.................: OES
Maximum assembly length............: 999999
Minimum assembly length............: 50
p-value............................: 0.010000
Quality score threshold (trimming).: 0
Minimum read size after trimming...: 1
Maximal ratio of uncalled bases....: 1.000000
Minimum overlap....................: 10
Scoring method.....................: Scaled score
Threads............................: 1

Allocating memory..................: 200,000,000 bytes
Computing empirical frequencies....: DONE
  A: 0.308304
  C: 0.192901
  G: 0.198973
  T: 0.299822
  0 uncalled bases
Assemblying reads: 0%
Assemblying reads: 100%

Assembled reads ...................: 8,562 / 8,839 (96.866%)
Discarded reads ...................: 0 / 8,839 (0.000%)
Not assembled reads ...............: 277 / 8,839 (3.134%)
Assembled reads file...............: pear.assembled.fastq
Discarded reads file...............: pear.discarded.fastq
Unassembled forward reads file.....: pear.unassembled.forward.fastq
Unassembled reverse reads file.....: pear.unassembled.reverse.fastq

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"73018df2daa211f0a3dd000d3a5ce991"`
cap	`"40"`
chromInfo	`"/tmp/tmpa0q9y2tx/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
empirical_freqs	`false`
library	`{"__current_case__": 0, "forward": {"values": [{"id": 1, "src": "hda"}]}, "reverse": {"values": [{"id": 2, "src": "hda"}]}, "type": "paired"}`
max_assembly_length	`"0"`
max_uncalled_base	`"1.0"`
min_assembly_length	`"50"`
min_overlap	`"10"`
min_trim_length	`"1"`
nbase	`false`
outputs	`"assembled"`
pvalue	`"0.01"`
quality_threshold	`"0"`
score_method	`"2"`
test_method	`"1"`

Other invocation details
- history_id
  - c1f821c882229aee
- history_state
  - ok
- invocation_id
  - c1f821c882229aee
- invocation_state
  - scheduled
- workflow_id
  - c1f821c882229aee

Co-authored-by: Copilot <[email protected]>

Change the name of the workflow. Line 111.

Change the name of the workflow. Line 3.

mo-mahe added 5 commits December 16, 2025 14:10

Create README.md

97597b1

Add files via upload

88fcbee

Add files via upload

0fba5d9

Rename dockstore.yml to .dockstore.yml

dce0ce7

Update README.md

9526e32

mvdbeek reviewed Dec 16, 2025

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mvdbeek reviewed Dec 16, 2025

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mvdbeek requested a review from Copilot December 16, 2025 15:43

mo-mahe added 4 commits December 16, 2025 16:59

Delete workflows/ecology/map-to-reference-workflow/test-data/fastqc_f…

5c4ebf8

…orward.html

Delete workflows/ecology/map-to-reference-workflow/test-data/fastqc_p…

18a4a52

…aired.html

Delete workflows/ecology/map-to-reference-workflow/test-data/fastqc_r…

7137c7e

…everse.html

Delete workflows/ecology/map-to-reference-workflow/test-data/visualiz…

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…e_consensus.html

Rename workflow in README.md

a300d5b

yvanlebras changed the title ~~Add map to reference workflow~~ Add ecology "pool of amplicons map to reference" workflow Dec 16, 2025

Copilot AI reviewed Dec 16, 2025

View reviewed changes

mo-mahe and others added 5 commits December 17, 2025 09:56

Update workflows/ecology/map-to-reference-workflow/Map-to-reference.ga

12501f1

Co-authored-by: Copilot <[email protected]>

Update Map-to-reference-tests.yml

eeafc62

Delete workflows/ecology/map-to-reference-workflow/test-data directory

f51d4f6

Update Map-to-reference.ga

2dc527c

Change the name of the workflow. Line 111.

Update .dockstore.yml

d7726ce

Change the name of the workflow. Line 3.

Add ecology "pool of amplicons map to reference" workflow #1053

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