Updating workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads from 0.3 to 0.4

[gxydevbot]

Hello! This is an automated update of the following workflow: workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:

• toolshed.g2.bx.psu.edu/repos/iuc/bamtools_split_mapped/bamtools_split_mapped/2.5.2+galaxy2 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/bamtools_split_mapped/bamtools_split_mapped/2.5.3+galaxy0

The workflow release number has been updated from 0.3 to 0.4.

If you want to skip this change, close this PR without deleting the branch. It will be reopened if another change is detected.
Any commit from another author than 'planemo-autoupdate' will prevent more auto-updates.
To ignore manual changes and allow autoupdates, delete the branch.

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ host-or-contamination-removal-on-long-reads.ga_0

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: Host/Contaminant Reference Genome (long-reads):

      • step_state: scheduled

    • Step 2: Long-reads:

      • step_state: scheduled

    • Step 3: Profile of preset options for the mapping (long-read):

      • step_state: scheduled

    • Step 4: minimap2 (toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy2):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:3a70f8bc7e17b723591f6132418640cfdbc88246-0

          Command Line:

          • ln -f -s '/cvmfs/data.galaxyproject.org/byhand/apiMel3/seq/apiMel3.fa' reference.fa && minimap2 -x map-pb    --q-occ-frac 0.01       -t ${GALAXY_SLOTS:-4} reference.fa '/tmp/tmpmkc09v6r/files/0/f/c/dataset_0fc39fb7-e9e6-49a0-a8d9-423d6cd135d9.dat' -a | samtools view --no-PG -hT reference.fa | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O BAM -o '/tmp/tmpmkc09v6r/job_working_directory/000/3/outputs/dataset_597dcaaf-a864-4e91-9a55-9fb40ac889cd.dat'

          Exit Code:

          • 0

          Standard Error:

          • [M::mm_idx_gen::13.797*0.49] collected minimizers
            [M::mm_idx_gen::15.687*0.55] sorted minimizers
            [M::main::15.688*0.55] loaded/built the index for 17 target sequence(s)
            [M::mm_mapopt_update::15.942*0.55] mid_occ = 138
            [M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 1; #seq: 17
            [M::mm_idx_stat::16.115*0.56] distinct minimizers: 17801079 (80.12% are singletons); average occurrences: 1.615; average spacing: 20.392; total length: 586300787
            [M::worker_pipeline::17.900*0.59] mapped 24877 sequences
            [M::main] Version: 2.28-r1209
            [M::main] CMD: minimap2 -x map-pb --q-occ-frac 0.01 -t 1 -a reference.fa /tmp/tmpmkc09v6r/files/0/f/c/dataset_0fc39fb7-e9e6-49a0-a8d9-423d6cd135d9.dat
            [M::main] Real time: 17.916 sec; CPU: 10.625 sec; Peak RSS: 2.067 GB
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"dd7922f40b0711f1aadf6045bd023583"
            alignment_options	{"A": null, "B": null, "E": null, "E2": null, "O": null, "O2": null, "no_end_flt": true, "s": null, "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": null, "z2": null}
            chromInfo	"/tmp/tmpmkc09v6r/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            fastq_input	{"__current_case__": 0, "analysis_type_selector": "map-pb", "fastq_input1": {"values": [{"id": 1, "src": "dce"}]}, "fastq_input_selector": "single"}
            indexing_options	{"H": false, "I": null, "k": null, "w": null}
            io_options	{"K": null, "L": false, "Q": false, "Y": false, "c": false, "cs": null, "eqx": false, "output_format": "BAM"}
            mapping_options	{"F": null, "N": null, "X": false, "f": null, "g": null, "kmer_ocurrence_interval": {"__current_case__": 1, "interval": ""}, "m": null, "mask_len": null, "max_chain_iter": null, "max_chain_skip": null, "min_occ_floor": null, "n": null, "p": null, "q_occ_frac": "0.01", "r": null}
            reference_source	{"__current_case__": 0, "ref_file": "apiMel3", "reference_source_selector": "cached"}

        • Job 2:

          • Job state is ok

          Container:

          • quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:3a70f8bc7e17b723591f6132418640cfdbc88246-0

          Command Line:

          • ln -f -s '/cvmfs/data.galaxyproject.org/byhand/apiMel3/seq/apiMel3.fa' reference.fa && minimap2 -x map-pb    --q-occ-frac 0.01       -t ${GALAXY_SLOTS:-4} reference.fa '/tmp/tmpmkc09v6r/files/f/7/d/dataset_f7d5db48-c9f5-432b-b53c-4a3987763141.dat' -a | samtools view --no-PG -hT reference.fa | samtools sort -@${GALAXY_SLOTS:-2} -T "${TMPDIR:-.}" -O BAM -o '/tmp/tmpmkc09v6r/job_working_directory/000/4/outputs/dataset_7452a5fa-75ad-4707-8f97-f8fe1b0bd19d.dat'

          Exit Code:

          • 0

          Standard Error:

          • [M::mm_idx_gen::13.579*0.49] collected minimizers
            [M::mm_idx_gen::15.462*0.55] sorted minimizers
            [M::main::15.462*0.55] loaded/built the index for 17 target sequence(s)
            [M::mm_mapopt_update::15.715*0.56] mid_occ = 138
            [M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 1; #seq: 17
            [M::mm_idx_stat::15.888*0.56] distinct minimizers: 17801079 (80.12% are singletons); average occurrences: 1.615; average spacing: 20.392; total length: 586300787
            [M::worker_pipeline::17.482*0.59] mapped 16951 sequences
            [M::main] Version: 2.28-r1209
            [M::main] CMD: minimap2 -x map-pb --q-occ-frac 0.01 -t 1 -a reference.fa /tmp/tmpmkc09v6r/files/f/7/d/dataset_f7d5db48-c9f5-432b-b53c-4a3987763141.dat
            [M::main] Real time: 17.496 sec; CPU: 10.348 sec; Peak RSS: 2.066 GB
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"dd7922f40b0711f1aadf6045bd023583"
            alignment_options	{"A": null, "B": null, "E": null, "E2": null, "O": null, "O2": null, "no_end_flt": true, "s": null, "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": null, "z2": null}
            chromInfo	"/tmp/tmpmkc09v6r/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            fastq_input	{"__current_case__": 0, "analysis_type_selector": "map-pb", "fastq_input1": {"values": [{"id": 2, "src": "dce"}]}, "fastq_input_selector": "single"}
            indexing_options	{"H": false, "I": null, "k": null, "w": null}
            io_options	{"K": null, "L": false, "Q": false, "Y": false, "c": false, "cs": null, "eqx": false, "output_format": "BAM"}
            mapping_options	{"F": null, "N": null, "X": false, "f": null, "g": null, "kmer_ocurrence_interval": {"__current_case__": 1, "interval": ""}, "m": null, "mask_len": null, "max_chain_iter": null, "max_chain_skip": null, "min_occ_floor": null, "n": null, "p": null, "q_occ_frac": "0.01", "r": null}
            reference_source	{"__current_case__": 0, "ref_file": "apiMel3", "reference_source_selector": "cached"}

    • Step 5: QualiMap (toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/qualimap:2.3--hdfd78af_0

          Command Line:

          • export JAVA_OPTS="-Djava.awt.headless=true -Xmx${GALAXY_MEMORY_MB:-1024}m" &&    ln -s '/tmp/tmpmkc09v6r/files/5/9/7/dataset_597dcaaf-a864-4e91-9a55-9fb40ac889cd.dat' 'Spike3bBarcode10' &&  qualimap bamqc -bam 'Spike3bBarcode10' -outdir results -outformat html --collect-overlap-pairs -nw 400 --paint-chromosome-limits -hm 3  --skip-duplicated --skip-dup-mode 0 -nt ${GALAXY_SLOTS:-1} &&   sed 's|images_qualimapReport/||g;s|css/||g' results/qualimapReport.html > '/tmp/tmpmkc09v6r/job_working_directory/000/5/outputs/dataset_4214a6b7-c077-4669-b5c8-21eee756e66a.dat' && mkdir '/tmp/tmpmkc09v6r/job_working_directory/000/5/outputs/dataset_4214a6b7-c077-4669-b5c8-21eee756e66a_files' && mv results/css/*.css '/tmp/tmpmkc09v6r/job_working_directory/000/5/outputs/dataset_4214a6b7-c077-4669-b5c8-21eee756e66a_files' && mv results/css/*.png '/tmp/tmpmkc09v6r/job_working_directory/000/5/outputs/dataset_4214a6b7-c077-4669-b5c8-21eee756e66a_files' && if [ -d results/images_qualimapReport ]; then mv results/images_qualimapReport/* '/tmp/tmpmkc09v6r/job_working_directory/000/5/outputs/dataset_4214a6b7-c077-4669-b5c8-21eee756e66a_files' && for file in $(ls -A results/raw_data_qualimapReport); do mv "results/raw_data_qualimapReport/$file" `echo "results/$file" | sed 's/(//;s/)//'`; done fi && mv results/genome_results.txt results/summary_report.txt

          Exit Code:

          • 0

          Standard Output:

          • Java memory size is set to 1200M
            Launching application...
            
            detected environment java options -Djava.awt.headless=true -Xmx1024m
            QualiMap v.2.3
            Built on 2023-05-19 16:57
            
            Selected tool: bamqc
            Available memory (Mb): 264
            Max memory (Mb): 1073
            Starting bam qc....
            Loading sam header...
            Loading locator...
            Loading reference...
            Only flagged duplicate alignments will be skipped...
            Number of windows: 400, effective number of windows: 416
            Chunk of reads size: 1000
            Number of threads: 1
            Processed 50 out of 416 windows...
            Processed 100 out of 416 windows...
            Processed 150 out of 416 windows...
            Processed 200 out of 416 windows...
            Processed 250 out of 416 windows...
            Processed 300 out of 416 windows...
            Processed 350 out of 416 windows...
            Processed 400 out of 416 windows...
            Total processed windows:416
            Number of reads: 24877
            Number of valid reads: 30
            Number of correct strand reads:0
            
            Inside of regions...
            Num mapped reads: 15
            Num mapped first of pair: 0
            Num mapped second of pair: 0
            Num singletons: 0
            Time taken to analyze reads: 4
            Computing descriptors...
            numberOfMappedBases: 6267
            referenceSize: 586300787
            numberOfSequencedBases: 5873
            numberOfAs: 822
            Computing per chromosome statistics...
            Computing histograms...
            Overall analysis time: 4
            end of bam qc
            Computing report...
            Writing HTML report...
            HTML report created successfully
            
            Finished
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"dd7922f40b0711f1aadf6045bd023583"
            chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/apiMel3.len"
            dbkey	"apiMel3"
            duplicate_skipping	"0"
            per_base_coverage	false
            plot_specific	{"genome_gc_distr": null, "homopolymer_size": "3", "n_bins": "400", "paint_chromosome_limits": true}
            stats_regions	{"__current_case__": 0, "region_select": "all"}

        • Job 2:

          • Job state is ok

          Container:

          • quay.io/biocontainers/qualimap:2.3--hdfd78af_0

          Command Line:

          • export JAVA_OPTS="-Djava.awt.headless=true -Xmx${GALAXY_MEMORY_MB:-1024}m" &&    ln -s '/tmp/tmpmkc09v6r/files/7/4/5/dataset_7452a5fa-75ad-4707-8f97-f8fe1b0bd19d.dat' 'Spike3bBarcode12' &&  qualimap bamqc -bam 'Spike3bBarcode12' -outdir results -outformat html --collect-overlap-pairs -nw 400 --paint-chromosome-limits -hm 3  --skip-duplicated --skip-dup-mode 0 -nt ${GALAXY_SLOTS:-1} &&   sed 's|images_qualimapReport/||g;s|css/||g' results/qualimapReport.html > '/tmp/tmpmkc09v6r/job_working_directory/000/6/outputs/dataset_2cfe8b61-08cf-4f91-8c3f-28803ce41423.dat' && mkdir '/tmp/tmpmkc09v6r/job_working_directory/000/6/outputs/dataset_2cfe8b61-08cf-4f91-8c3f-28803ce41423_files' && mv results/css/*.css '/tmp/tmpmkc09v6r/job_working_directory/000/6/outputs/dataset_2cfe8b61-08cf-4f91-8c3f-28803ce41423_files' && mv results/css/*.png '/tmp/tmpmkc09v6r/job_working_directory/000/6/outputs/dataset_2cfe8b61-08cf-4f91-8c3f-28803ce41423_files' && if [ -d results/images_qualimapReport ]; then mv results/images_qualimapReport/* '/tmp/tmpmkc09v6r/job_working_directory/000/6/outputs/dataset_2cfe8b61-08cf-4f91-8c3f-28803ce41423_files' && for file in $(ls -A results/raw_data_qualimapReport); do mv "results/raw_data_qualimapReport/$file" `echo "results/$file" | sed 's/(//;s/)//'`; done fi && mv results/genome_results.txt results/summary_report.txt

          Exit Code:

          • 0

          Standard Output:

          • Java memory size is set to 1200M
            Launching application...
            
            detected environment java options -Djava.awt.headless=true -Xmx1024m
            QualiMap v.2.3
            Built on 2023-05-19 16:57
            
            Selected tool: bamqc
            Available memory (Mb): 264
            Max memory (Mb): 1073
            Starting bam qc....
            Loading sam header...
            Loading locator...
            Loading reference...
            Only flagged duplicate alignments will be skipped...
            Number of windows: 400, effective number of windows: 416
            Chunk of reads size: 1000
            Number of threads: 1
            Processed 50 out of 416 windows...
            Processed 100 out of 416 windows...
            Processed 150 out of 416 windows...
            Processed 200 out of 416 windows...
            Processed 250 out of 416 windows...
            Processed 300 out of 416 windows...
            Processed 350 out of 416 windows...
            Processed 400 out of 416 windows...
            Total processed windows:416
            Number of reads: 16951
            Number of valid reads: 10
            Number of correct strand reads:0
            
            Inside of regions...
            Num mapped reads: 10
            Num mapped first of pair: 0
            Num mapped second of pair: 0
            Num singletons: 0
            Time taken to analyze reads: 3
            Computing descriptors...
            numberOfMappedBases: 2240
            referenceSize: 586300787
            numberOfSequencedBases: 2165
            numberOfAs: 635
            Computing per chromosome statistics...
            Computing histograms...
            Overall analysis time: 3
            end of bam qc
            Computing report...
            Writing HTML report...
            HTML report created successfully
            
            Finished
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"dd7922f40b0711f1aadf6045bd023583"
            chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/apiMel3.len"
            dbkey	"apiMel3"
            duplicate_skipping	"0"
            per_base_coverage	false
            plot_specific	{"genome_gc_distr": null, "homopolymer_size": "3", "n_bins": "400", "paint_chromosome_limits": true}
            stats_regions	{"__current_case__": 0, "region_select": "all"}

    • Step 6: Split BAM (toolshed.g2.bx.psu.edu/repos/iuc/bamtools_split_mapped/bamtools_split_mapped/2.5.3+galaxy0):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/local/mulled-v2-0560a8046fc82aa4338588eca29ff18edab2c5aa:a5d29a3763e96bdce12142816d06b607a8d00eeb-0

          Command Line:

          • ln -s '/tmp/tmpmkc09v6r/files/5/9/7/dataset_597dcaaf-a864-4e91-9a55-9fb40ac889cd.dat' 'localbam.bam' && ln -s '/tmp/tmpmkc09v6r/files/_metadata_files/a/1/2/metadata_a12b19c2-bb45-42ae-9c0d-64992d37bfa9.dat' 'localbam.bam.bai' && bamtools split -mapped -in localbam.bam -stub split_bam

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"dd7922f40b0711f1aadf6045bd023583"
            chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/apiMel3.len"
            dbkey	"apiMel3"

        • Job 2:

          • Job state is error

          Command Line:

          • ln -s '/tmp/tmpmkc09v6r/files/7/4/5/dataset_7452a5fa-75ad-4707-8f97-f8fe1b0bd19d.dat' 'localbam.bam' && ln -s '/tmp/tmpmkc09v6r/files/_metadata_files/1/a/0/metadata_1a0c61dd-aa28-4ad1-86c6-1672f12a0c51.dat' 'localbam.bam.bai' && bamtools split -mapped -in localbam.bam -stub split_bam

          Exit Code:

          • 127

          Standard Error:

          • /tmp/tmpmkc09v6r/job_working_directory/000/8/tool_script.sh: line 10: bamtools: command not found
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"dd7922f40b0711f1aadf6045bd023583"
            chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/apiMel3.len"
            dbkey	"apiMel3"

    • Step 7: Flatten collection (__FLATTEN__):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __workflow_invocation_uuid__	"dd7922f40b0711f1aadf6045bd023583"
            input	{"values": [{"id": 3, "src": "hdca"}]}
            join_identifier	"_"

    • Step 8: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.22+galaxy1):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/samtools:1.22--h96c455f_0

          Command Line:

          • addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) &&  samtools sort -@ $addthreads -n '/tmp/tmpmkc09v6r/files/4/5/4/dataset_45460724-b293-4788-a3da-bd9693e75a24.dat' -T "${TMPDIR:-.}" > input &&   samtools fastq       -f 0   -F 2304   -G 0  input  > output.fastqsanger && ln -s output.fastqsanger output

          Exit Code:

          • 0

          Standard Error:

          • [M::bam2fq_mainloop] discarded 0 singletons
            [M::bam2fq_mainloop] processed 24862 reads
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"dd7922f40b0711f1aadf6045bd023583"
            chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/apiMel3.len"
            copy_arb_tags	None
            copy_tags	false
            dbkey	"apiMel3"
            exclusive_filter	["256", "2048"]
            exclusive_filter_all	None
            idxout_cond	{"__current_case__": 0, "idxout_select": "no"}
            inclusive_filter	None
            output_fmt_cond	{"__current_case__": 0, "default_quality": null, "ilumina_casava": false, "output_fmt_select": "fastqsanger", "output_quality": false}
            outputs	"other"
            read_numbering	""

        • Job 2:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"dd7922f40b0711f1aadf6045bd023583"
            chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/apiMel3.len"
            copy_arb_tags	None
            copy_tags	false
            dbkey	"apiMel3"
            exclusive_filter	["256", "2048"]
            exclusive_filter_all	None
            idxout_cond	{"__current_case__": 0, "idxout_select": "no"}
            inclusive_filter	None
            output_fmt_cond	{"__current_case__": 0, "default_quality": null, "ilumina_casava": false, "output_fmt_select": "fastqsanger", "output_quality": false}
            outputs	"other"
            read_numbering	""

    • Step 9: MultiQC (toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy0):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/multiqc:1.33--pyhdfd78af_0

          Command Line:

          • die() { echo "$@" 1>&2 ; exit 1; } &&  mkdir multiqc_WDir &&   mkdir multiqc_WDir/qualimap_0 &&  sample="$(grep 'bam file = ' /tmp/tmpmkc09v6r/files/8/c/6/dataset_8c6f8625-dc50-478a-b01f-2ccb70d42159.dat | sed 's/bam file = //g' | sed 's: ::g')" && dir_name="multiqc_WDir/qualimap_0/${sample}" && mkdir -p ${dir_name} && filepath_1="${dir_name}/genome_results.txt" && ln -sf '/tmp/tmpmkc09v6r/files/8/c/6/dataset_8c6f8625-dc50-478a-b01f-2ccb70d42159.dat' ${filepath_1} && nested_dir_name="${dir_name}/raw_data_qualimapReport/" && mkdir -p ${nested_dir_name} && filepath_2="${nested_dir_name}/coverage_histogram.txt" && ln -sf '/tmp/tmpmkc09v6r/files/8/6/b/dataset_86b84499-fdbc-4dee-982f-6693d4de1eac.dat' ${filepath_2} && nested_dir_name="${dir_name}/raw_data_qualimapReport/" && mkdir -p ${nested_dir_name} && filepath_3="${nested_dir_name}/mapped_reads_gc-content_distribution.txt" && ln -sf '/tmp/tmpmkc09v6r/files/0/b/f/dataset_0bf813ac-68ad-4a0c-90e8-a869f8cac192.dat' ${filepath_3} && sample="$(grep 'bam file = ' /tmp/tmpmkc09v6r/files/7/6/f/dataset_76f28fbc-7cd3-41bf-aff3-a5b685f70f78.dat | sed 's/bam file = //g' | sed 's: ::g')" && dir_name="multiqc_WDir/qualimap_0/${sample}" && mkdir -p ${dir_name} && filepath_1="${dir_name}/genome_results.txt" && ln -sf '/tmp/tmpmkc09v6r/files/7/6/f/dataset_76f28fbc-7cd3-41bf-aff3-a5b685f70f78.dat' ${filepath_1} && nested_dir_name="${dir_name}/raw_data_qualimapReport/" && mkdir -p ${nested_dir_name} && filepath_2="${nested_dir_name}/coverage_histogram.txt" && ln -sf '/tmp/tmpmkc09v6r/files/f/8/6/dataset_f86d8f07-7e15-416a-9823-ce48892d1d34.dat' ${filepath_2} && nested_dir_name="${dir_name}/raw_data_qualimapReport/" && mkdir -p ${nested_dir_name} && filepath_3="${nested_dir_name}/mapped_reads_gc-content_distribution.txt" && ln -sf '/tmp/tmpmkc09v6r/files/c/c/9/dataset_cc9117ed-7007-4242-a9fa-2ddb786a850e.dat' ${filepath_3} &&    multiqc multiqc_WDir --filename 'report'  --title 'HostContamination Removal'      && mkdir -p ./plots && ls -l ./report_data/ && cp ./report_data/*plot*.txt ./plots/ | true

          Exit Code:

          • 0

          Standard Error:

          • /// MultiQC 🔍 v1.33
            
                 update_config | Report title: HostContamination Removal
                   file_search | Search path: /tmp/tmpmkc09v6r/job_working_directory/000/12/working/multiqc_WDir
            
                      qualimap | Found 2 BamQC reports
            
                 write_results | Data        : report_data
                 write_results | Report      : report.html
                       multiqc | MultiQC complete
            cp: cannot stat './report_data/*plot*.txt': No such file or directory
            

          Standard Output:

          • total 892
            -rw-r--r-- 1 1001 1001  10718 Feb 16 07:22 llms-full.txt
            -rw-r--r-- 1 1001 1001  10870 Feb 16 07:22 multiqc.log
            -rw-r--r-- 1 1001 1001 682958 Feb 16 07:22 multiqc.parquet
            -rw-r--r-- 1 1001 1001    186 Feb 16 07:22 multiqc_citations.txt
            -rw-r--r-- 1 1001 1001 174715 Feb 16 07:22 multiqc_data.json
            -rw-r--r-- 1 1001 1001    704 Feb 16 07:22 multiqc_general_stats.txt
            -rw-r--r-- 1 1001 1001    422 Feb 16 07:22 multiqc_qualimap_bamqc_genome_results.txt
            -rw-r--r-- 1 1001 1001   1136 Feb 16 07:22 multiqc_sources.txt
            -rw-r--r-- 1 1001 1001    246 Feb 16 07:22 qualimap_coverage_histogram.txt
            -rw-r--r-- 1 1001 1001   2552 Feb 16 07:22 qualimap_gc_content.txt
            -rw-r--r-- 1 1001 1001    759 Feb 16 07:22 qualimap_genome_fraction.txt
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"dd7922f40b0711f1aadf6045bd023583"
            chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/apiMel3.len"
            comment	""
            dbkey	"apiMel3"
            export	false
            flat	false
            image_content_input	None
            png_plots	false
            results	[{"__index__": 0, "software_cond": {"__current_case__": 20, "input": {"values": [{"id": 7, "src": "hdca"}]}, "software": "qualimap"}}]
            title	"Host/Contamination Removal"

  • Other invocation details

    • history_id

      • 88e62ae3f0ce651e

    • history_state

      • error

    • invocation_id

      • 88e62ae3f0ce651e

    • invocation_state

      • scheduled

    • workflow_id

      • 88e62ae3f0ce651e