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20 hours ago •
galaxyproject
galaxyproject
add taxonomic analysis and human reads removal wf
@bebatut @wm75 This is workflow for Taxonomic Analysis of SARS-CoV-2 Wastewater Samples with Human Read Removal. Would be a first part of metagenomic data variant analysis
Test Results (powered by Planemo)
Test Summary
| Test State | Count |
|---|---|
| Total | 1 |
| Passed | 0 |
| Error | 1 |
| Failure | 0 |
| Skipped | 0 |
Errored Tests
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❌ Taxonomic-Analysis-of-SARS-CoV-2-Wastewater-Samples-with-Human-Read-Removal.ga_0
Execution Problem:
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Failed to run workflow, at least one job is in [error] state.
Workflow invocation details
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Invocation Messages
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Steps
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Step 1: SARS-CoV-2 reference genome:
- step_state: scheduled
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Step 2: Paired Collection:
- step_state: scheduled
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Step 3: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0:
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step_state: scheduled
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Jobs
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Job 1:
- Job state is ok
Command Line:
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ln -s '/tmp/tmpvp1vnw0g/files/d/3/0/dataset_d30a72ce-4a42-4ef0-8b6c-48da70a66eec.dat' 'SRR12596170_fastq.fastq.gz' && ln -s '/tmp/tmpvp1vnw0g/files/4/5/7/dataset_4576cabe-e687-45d1-bb99-c0f24069cb39.dat' 'SRR12596170_fastq_R2.fastq.gz' && fastp --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for SRR12596170_fastq.fastq.gz' -i 'SRR12596170_fastq.fastq.gz' -o first.fastq.gz -I 'SRR12596170_fastq_R2.fastq.gz' -O second.fastq.gz --detect_adapter_for_pe && mv first.fastq.gz '/tmp/tmpvp1vnw0g/job_working_directory/000/6/outputs/dataset_9b59d290-9dee-469a-8932-9966a0a4d674.dat' && mv second.fastq.gz '/tmp/tmpvp1vnw0g/job_working_directory/000/6/outputs/dataset_91e7a8e9-be16-4bb8-9811-c2fbacf66e9a.dat'
Exit Code:
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0
Standard Error:
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Detecting adapter sequence for read1... No adapter detected for read1 Detecting adapter sequence for read2... No adapter detected for read2 Read1 before filtering: total reads: 167374 total bases: 12425652 Q20 bases: 11614277(93.4702%) Q30 bases: 11368920(91.4956%) Read2 before filtering: total reads: 167374 total bases: 12265824 Q20 bases: 11350710(92.5393%) Q30 bases: 11085935(90.3807%) Read1 after filtering: total reads: 155144 total bases: 11496170 Q20 bases: 10977759(95.4906%) Q30 bases: 10795701(93.9069%) Read2 aftering filtering: total reads: 155144 total bases: 11348252 Q20 bases: 10851896(95.6261%) Q30 bases: 10659366(93.9296%) Filtering result: reads passed filter: 310288 reads failed due to low quality: 24088 reads failed due to too many N: 372 reads failed due to too short: 0 reads with adapter trimmed: 1800 bases trimmed due to adapters: 37303 Duplication rate: 12.3851% Insert size peak (evaluated by paired-end reads): 116 JSON report: fastp.json HTML report: fastp.html fastp --thread 1 --report_title fastp report for SRR12596170_fastq.fastq.gz -i SRR12596170_fastq.fastq.gz -o first.fastq.gz -I SRR12596170_fastq_R2.fastq.gz -O second.fastq.gz --detect_adapter_for_pe fastp v0.20.1, time used: 7 seconds
Job Parameters:
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Job parameter Parameter value __input_ext "fastqsanger.gz"__workflow_invocation_uuid__ "4dc0b42fdb4311eeaad6fbf0711a9142"chromInfo "/tmp/tmpvp1vnw0g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"dbkey "?"filter_options {"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}output_options {"report_html": true, "report_json": true}overrepresented_sequence_analysis {"overrepresentation_analysis": false, "overrepresentation_sampling": null}read_mod_options {"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}single_paired {"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "paired_input": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "paired_collection"}
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Job 2:
- Job state is ok
Command Line:
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ln -s '/tmp/tmpvp1vnw0g/files/5/c/4/dataset_5c41e464-70bf-4ca3-ab35-b684ecf945fc.dat' 'SRR12596172_fastq.fastq.gz' && ln -s '/tmp/tmpvp1vnw0g/files/f/3/c/dataset_f3c2d737-1ea5-4bbe-a418-86cfe41c8882.dat' 'SRR12596172_fastq_R2.fastq.gz' && fastp --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for SRR12596172_fastq.fastq.gz' -i 'SRR12596172_fastq.fastq.gz' -o first.fastq.gz -I 'SRR12596172_fastq_R2.fastq.gz' -O second.fastq.gz --detect_adapter_for_pe && mv first.fastq.gz '/tmp/tmpvp1vnw0g/job_working_directory/000/7/outputs/dataset_00406541-0045-4332-bc59-40fba66ebfb7.dat' && mv second.fastq.gz '/tmp/tmpvp1vnw0g/job_working_directory/000/7/outputs/dataset_28b581d3-871a-40f8-93dc-7ccd60fe556e.dat'
Exit Code:
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0
Standard Error:
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Detecting adapter sequence for read1... No adapter detected for read1 Detecting adapter sequence for read2... No adapter detected for read2 Read1 before filtering: total reads: 167374 total bases: 12425652 Q20 bases: 11614277(93.4702%) Q30 bases: 11368920(91.4956%) Read2 before filtering: total reads: 167374 total bases: 12265824 Q20 bases: 11350710(92.5393%) Q30 bases: 11085935(90.3807%) Read1 after filtering: total reads: 155144 total bases: 11496170 Q20 bases: 10977759(95.4906%) Q30 bases: 10795701(93.9069%) Read2 aftering filtering: total reads: 155144 total bases: 11348252 Q20 bases: 10851896(95.6261%) Q30 bases: 10659366(93.9296%) Filtering result: reads passed filter: 310288 reads failed due to low quality: 24088 reads failed due to too many N: 372 reads failed due to too short: 0 reads with adapter trimmed: 1800 bases trimmed due to adapters: 37303 Duplication rate: 12.3851% Insert size peak (evaluated by paired-end reads): 116 JSON report: fastp.json HTML report: fastp.html fastp --thread 1 --report_title fastp report for SRR12596172_fastq.fastq.gz -i SRR12596172_fastq.fastq.gz -o first.fastq.gz -I SRR12596172_fastq_R2.fastq.gz -O second.fastq.gz --detect_adapter_for_pe fastp v0.20.1, time used: 7 seconds
Job Parameters:
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Job parameter Parameter value __input_ext "fastqsanger.gz"__workflow_invocation_uuid__ "4dc0b42fdb4311eeaad6fbf0711a9142"chromInfo "/tmp/tmpvp1vnw0g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"dbkey "?"filter_options {"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}output_options {"report_html": true, "report_json": true}overrepresented_sequence_analysis {"overrepresentation_analysis": false, "overrepresentation_sampling": null}read_mod_options {"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}single_paired {"__current_case__": 2, "adapter_trimming_options": {"adapter_sequence1": "", "adapter_sequence2": "", "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "paired_input": {"values": [{"id": 4, "src": "dce"}]}, "single_paired_selector": "paired_collection"}
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Step 4: toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1:
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step_state: scheduled
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Jobs
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Job 1:
- Job state is ok
Command Line:
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kraken2 --threads ${GALAXY_SLOTS:-1} --db '/cvmfs/data.galaxyproject.org/managed/kraken2_databases/kraken2_viral_db' --paired '/tmp/tmpvp1vnw0g/files/d/3/0/dataset_d30a72ce-4a42-4ef0-8b6c-48da70a66eec.dat' '/tmp/tmpvp1vnw0g/files/4/5/7/dataset_4576cabe-e687-45d1-bb99-c0f24069cb39.dat' --confidence '0.0' --minimum-base-quality '0' --minimum-hit-groups '2' --report '/tmp/tmpvp1vnw0g/job_working_directory/000/8/outputs/dataset_bd438a34-cc3d-44c8-9c3d-ac96c62dec9b.dat' > '/tmp/tmpvp1vnw0g/job_working_directory/000/8/outputs/dataset_75337e88-8056-4f07-97ce-0342825854d6.dat'
Exit Code:
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0
Standard Error:
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Loading database information... done. 167374 sequences (24.69 Mbp) processed in 1.468s (6841.7 Kseq/m, 1009.31 Mbp/m). 5662 sequences classified (3.38%) 161712 sequences unclassified (96.62%)
Job Parameters:
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Job parameter Parameter value __input_ext "fastqsanger.gz"__workflow_invocation_uuid__ "4dc0b42fdb4311eeaad6fbf0711a9142"chromInfo "/tmp/tmpvp1vnw0g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"confidence "0.0"dbkey "?"kraken2_database "viral2019-03"min_base_quality "0"minimum_hit_groups "2"quick falsereport {"create_report": true, "report_minimizer_data": false, "report_zero_counts": false, "use_mpa_style": false}single_paired {"__current_case__": 0, "input_pair": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "collection"}split_reads falseuse_names false
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Job 2:
- Job state is ok
Command Line:
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kraken2 --threads ${GALAXY_SLOTS:-1} --db '/cvmfs/data.galaxyproject.org/managed/kraken2_databases/kraken2_viral_db' --paired '/tmp/tmpvp1vnw0g/files/5/c/4/dataset_5c41e464-70bf-4ca3-ab35-b684ecf945fc.dat' '/tmp/tmpvp1vnw0g/files/f/3/c/dataset_f3c2d737-1ea5-4bbe-a418-86cfe41c8882.dat' --confidence '0.0' --minimum-base-quality '0' --minimum-hit-groups '2' --report '/tmp/tmpvp1vnw0g/job_working_directory/000/9/outputs/dataset_87d986a5-c189-45a3-a5a0-5cfd386b4bf5.dat' > '/tmp/tmpvp1vnw0g/job_working_directory/000/9/outputs/dataset_26b4a608-3368-413e-a783-758b86df10cc.dat'
Exit Code:
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0
Standard Error:
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Loading database information... done. 167374 sequences (24.69 Mbp) processed in 1.475s (6806.6 Kseq/m, 1004.13 Mbp/m). 5662 sequences classified (3.38%) 161712 sequences unclassified (96.62%)
Job Parameters:
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Job parameter Parameter value __input_ext "fastqsanger.gz"__workflow_invocation_uuid__ "4dc0b42fdb4311eeaad6fbf0711a9142"chromInfo "/tmp/tmpvp1vnw0g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"confidence "0.0"dbkey "?"kraken2_database "viral2019-03"min_base_quality "0"minimum_hit_groups "2"quick falsereport {"create_report": true, "report_minimizer_data": false, "report_zero_counts": false, "use_mpa_style": false}single_paired {"__current_case__": 0, "input_pair": {"values": [{"id": 4, "src": "dce"}]}, "single_paired_selector": "collection"}split_reads falseuse_names false
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Step 5: toolshed.g2.bx.psu.edu/repos/iuc/read_it_and_keep/read_it_and_keep/0.2.2+galaxy0:
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step_state: scheduled
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Jobs
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Job 1:
- Job state is ok
Command Line:
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ln -s '/tmp/tmpvp1vnw0g/files/7/e/7/dataset_7e74610b-a616-4717-9b1c-dba7a2ba6168.dat' ref_untrimmed.fasta && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/read_it_and_keep/1563b58905f4/read_it_and_keep/trim_reference.py' ref_untrimmed.fasta ref.fasta && ln -s '/tmp/tmpvp1vnw0g/files/9/b/5/dataset_9b59d290-9dee-469a-8932-9966a0a4d674.dat' read1 && ln -s '/tmp/tmpvp1vnw0g/files/9/1/e/dataset_91e7a8e9-be16-4bb8-9811-c2fbacf66e9a.dat' read2 && readItAndKeep --tech illumina --ref_fasta ref.fasta --min_map_length 50 --min_map_length_pc 50.0 --reads1 read1 --reads2 read2 -o output
Exit Code:
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0
Standard Error:
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Processed 100000 reads (or read pairs)
Standard Output:
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Input reads file 1 155144 Input reads file 2 155144 Kept reads 1 24959 Kept reads 2 24959
Job Parameters:
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Job parameter Parameter value __input_ext "input"__workflow_invocation_uuid__ "4dc0b42fdb4311eeaad6fbf0711a9142"adv {"enumerate_names": false, "min_map_length": "50", "min_map_length_pc": "50.0"}chromInfo "/tmp/tmpvp1vnw0g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"dbkey "?"reads {"__current_case__": 1, "paired_reads": {"values": [{"id": 7, "src": "dce"}]}, "read_type": "paired_collection"}ref_source {"__current_case__": 0, "ref_fasta": {"values": [{"id": 1, "src": "hda"}]}, "source": "history"}sequencing_tech "illumina"trim_reference true
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Job 2:
- Job state is ok
Command Line:
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ln -s '/tmp/tmpvp1vnw0g/files/7/e/7/dataset_7e74610b-a616-4717-9b1c-dba7a2ba6168.dat' ref_untrimmed.fasta && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/read_it_and_keep/1563b58905f4/read_it_and_keep/trim_reference.py' ref_untrimmed.fasta ref.fasta && ln -s '/tmp/tmpvp1vnw0g/files/0/0/4/dataset_00406541-0045-4332-bc59-40fba66ebfb7.dat' read1 && ln -s '/tmp/tmpvp1vnw0g/files/2/8/b/dataset_28b581d3-871a-40f8-93dc-7ccd60fe556e.dat' read2 && readItAndKeep --tech illumina --ref_fasta ref.fasta --min_map_length 50 --min_map_length_pc 50.0 --reads1 read1 --reads2 read2 -o output
Exit Code:
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0
Standard Error:
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Processed 100000 reads (or read pairs)
Standard Output:
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Input reads file 1 155144 Input reads file 2 155144 Kept reads 1 24959 Kept reads 2 24959
Job Parameters:
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Job parameter Parameter value __input_ext "input"__workflow_invocation_uuid__ "4dc0b42fdb4311eeaad6fbf0711a9142"adv {"enumerate_names": false, "min_map_length": "50", "min_map_length_pc": "50.0"}chromInfo "/tmp/tmpvp1vnw0g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"dbkey "?"reads {"__current_case__": 1, "paired_reads": {"values": [{"id": 8, "src": "dce"}]}, "read_type": "paired_collection"}ref_source {"__current_case__": 0, "ref_fasta": {"values": [{"id": 1, "src": "hda"}]}, "source": "history"}sequencing_tech "illumina"trim_reference true
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Step 6: toolshed.g2.bx.psu.edu/repos/devteam/kraken2tax/Kraken2Tax/1.1:
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step_state: scheduled
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Jobs
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Job 1:
- Job state is running
Command Line:
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awk '{ print $2, $3 }' OFS="\t" "/tmp/tmpvp1vnw0g/files/b/d/4/dataset_bd438a34-cc3d-44c8-9c3d-ac96c62dec9b.dat" | taxonomy-reader "/cvmfs/data.galaxyproject.org/managed/ncbi_taxonomy/ncbi-2015-10-05/names.dmp" "/cvmfs/data.galaxyproject.org/managed/ncbi_taxonomy/ncbi-2015-10-05/nodes.dmp" 1 > "/tmp/tmpvp1vnw0g/job_working_directory/000/12/outputs/dataset_61c4bc80-cc86-41a5-98f3-7577945e8bf7.dat"
Job Parameters:
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Job parameter Parameter value __input_ext "tabular"__workflow_invocation_uuid__ "4dc0b42fdb4311eeaad6fbf0711a9142"chromInfo "/tmp/tmpvp1vnw0g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"dbkey "?"ncbi_taxonomy "ncbi-2015-10-05"read_name "2"tax_id 5bc3b5997ae36e38
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Job 2:
- Job state is error
Command Line:
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awk '{ print $2, $3 }' OFS="\t" "/tmp/tmpvp1vnw0g/files/8/7/d/dataset_87d986a5-c189-45a3-a5a0-5cfd386b4bf5.dat" | taxonomy-reader "/cvmfs/data.galaxyproject.org/managed/ncbi_taxonomy/ncbi-2015-10-05/names.dmp" "/cvmfs/data.galaxyproject.org/managed/ncbi_taxonomy/ncbi-2015-10-05/nodes.dmp" 1 > "/tmp/tmpvp1vnw0g/job_working_directory/000/13/outputs/dataset_11ecc157-8193-468d-a152-8f217a33da1b.dat"
Exit Code:
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127
Standard Error:
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/tmp/tmpvp1vnw0g/job_working_directory/000/13/tool_script.sh: line 9: taxonomy-reader: command not found
Job Parameters:
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Job parameter Parameter value __input_ext "tabular"__workflow_invocation_uuid__ "4dc0b42fdb4311eeaad6fbf0711a9142"chromInfo "/tmp/tmpvp1vnw0g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"dbkey "?"ncbi_taxonomy "ncbi-2015-10-05"read_name "2"tax_id 5bc3b5997ae36e38
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Step 7: toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1:
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step_state: scheduled
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Jobs
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Job 1:
- Job state is paused
Job Parameters:
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Job parameter Parameter value __input_ext "taxonomy"__workflow_invocation_uuid__ "4dc0b42fdb4311eeaad6fbf0711a9142"chromInfo "/tmp/tmpvp1vnw0g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"combine_inputs falsedbkey "?"root_name "Root"type_of_data {"__current_case__": 0, "input": {"values": [{"id": 8, "src": "hdca"}]}, "max_rank": "8", "type_of_data_selector": "taxonomy"}
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Step 8: toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1:
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step_state: scheduled
-
Jobs
-
Job 1:
- Job state is paused
Job Parameters:
-
Job parameter Parameter value __input_ext "taxonomy"__workflow_invocation_uuid__ "4dc0b42fdb4311eeaad6fbf0711a9142"chromInfo "/tmp/tmpvp1vnw0g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"combine_inputs truedbkey "?"root_name "Root"type_of_data {"__current_case__": 0, "input": {"values": [{"id": 8, "src": "hdca"}]}, "max_rank": "8", "type_of_data_selector": "taxonomy"}
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Other invocation details
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error_message
- Failed to run workflow, at least one job is in [error] state.
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history_id
- b718e6261924da2c
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history_state
- error
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invocation_id
- b718e6261924da2c
-
invocation_state
- scheduled
-
workflow_id
- b718e6261924da2c
-
-
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