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Add abromics bacterial hybrid assembly and annotation workflow #324

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Add abromics bacterial hybrid assembly and annotation workflow #324

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pimarin
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@pimarin pimarin commented Jan 26, 2024

This workflow com from the abromics project in genomic :
Bacterial assembly from illumina paired-end short reads and long-reads and some annotations

We followed the recommandaion to publish the workflow (licence, author list and email, steps annotations...)

  • Workflow inported from usegalaxy.fr using planemo workflow_test_init to use a valid invocation
  • Workflow tests passed using planemo test command on the usegalaxy.fr server
  • Readme.md written
  • CHANGELOG.md written
  • CHANGELOG.md written
  • .dockstore.yml written

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pimarin commented Jan 26, 2024

I'm wainting to fix the PR323 to try to pass the test with this WF

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Test Results (powered by Planemo)

Test Summary

Test State Count
Total 1
Passed 0
Error 1
Failure 0
Skipped 0
Errored Tests
  • ❌ abromics_genomic_hybrid_long_reads.ga_0

    Execution Problem:

    • Failed to run workflow, at least one job is in [error] state.

    Workflow invocation details

    • Invocation Messages

    • Steps

      • Step 1: select_bracken_database:

        • step_state: scheduled

      • Step 2: select_kraken2_database:

        • step_state: scheduled

      • Step 11: fastp_triming:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • ln -s '/tmp/tmpjqyyf1wb/files/d/e/0/dataset_de03a00d-6ef2-4dee-b498-023e312af668.dat' 'paired_r1_fastqsanger_gz.fastq.gz' &&  ln -s '/tmp/tmpjqyyf1wb/files/a/1/0/dataset_a10b265e-ef1a-4308-8612-4fdaaa4b85f7.dat' 'paired_r2_fastqsanger_gz_R2.fastq.gz' &&    fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for paired_r1_fastqsanger_gz.fastq.gz'   -i 'paired_r1_fastqsanger_gz.fastq.gz' -o first.fastq.gz  -I 'paired_r2_fastqsanger_gz_R2.fastq.gz' -O second.fastq.gz       --detect_adapter_for_pe                                        -c  &&  mv first.fastq.gz '/tmp/tmpjqyyf1wb/job_working_directory/000/5/outputs/dataset_082ecd66-55b4-4021-8850-670b613a3292.dat' && mv second.fastq.gz '/tmp/tmpjqyyf1wb/job_working_directory/000/5/outputs/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat'

            Exit Code:

            • 0

            Standard Error:

            • 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: 400000
total bases: 103519948
Q20 bases: 102769299(99.2749%)
Q30 bases: 99758884(96.3668%)

Read2 before filtering:
total reads: 400000
total bases: 95635965
Q20 bases: 93004830(97.2488%)
Q30 bases: 85930009(89.8511%)

Read1 after filtering:
total reads: 400000
total bases: 103502171
Q20 bases: 102766762(99.2895%)
Q30 bases: 99758999(96.3835%)

Read2 after filtering:
total reads: 400000
total bases: 95621214
Q20 bases: 93046338(97.3072%)
Q30 bases: 85975954(89.9131%)

Filtering result:
reads passed filter: 800000
reads failed due to low quality: 0
reads failed due to too many N: 0
reads failed due to too short: 0
reads with adapter trimmed: 6012
bases trimmed due to adapters: 32528
reads corrected by overlap analysis: 54309
bases corrected by overlap analysis: 67520

Duplication rate: 0.007%

Insert size peak (evaluated by paired-end reads): 301

JSON report: fastp.json
HTML report: fastp.html

fastp --thread 1 --report_title fastp report for paired_r1_fastqsanger_gz.fastq.gz -i paired_r1_fastqsanger_gz.fastq.gz -o first.fastq.gz -I paired_r2_fastqsanger_gz_R2.fastq.gz -O second.fastq.gz --detect_adapter_for_pe -c 
fastp v0.23.2, time used: 33 seconds

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "fastqsanger.gz"
              __workflow_invocation_uuid__ "fea8dd5bbc3c11eea726e997ec892c65"
              chromInfo "/tmp/tmpjqyyf1wb/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": true}, "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": null, "umi_prefix": null}}
              single_paired {"__current_case__": 1, "adapter_trimming_options": {"adapter_sequence1": null, "adapter_sequence2": null, "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_front2": null, "trim_tail1": null, "trim_tail2": null}, "in1": {"values": [{"id": 2, "src": "hda"}]}, "in2": {"values": [{"id": 1, "src": "hda"}]}, "single_paired_selector": "paired"}

      • Step 12: filtlong_trimming:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • filtlong --keep_percent '90.0' --min_length '1000' --illumina_1 '/tmp/tmpjqyyf1wb/files/0/8/2/dataset_082ecd66-55b4-4021-8850-670b613a3292.dat' --illumina_2 '/tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat' --length_weight '1.0' --mean_q_weight '1.0' --window_q_weight '1.0'  --window_size '250' '/tmp/tmpjqyyf1wb/files/b/d/9/dataset_bd92873c-8a28-490f-b800-d7d52c949efd.dat' > output.fastq

            Exit Code:

            • 0

            Standard Error:

            • Hashing 16-mers from Illumina reads

  /tmp/tmpjqyyf1wb/files/0/8/2/dataset_082ecd66-55b4-4021-8850-670b613a3292.dat (483797 bp)
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31f-ae89-26c1bedadee3.dat (40150131 bp)
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  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (81268903 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (81752665 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (82236368 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (82720083 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (83203854 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (83687648 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (84171277 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (84655061 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (85138731 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (85622490 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (86106257 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (86590148 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (87073760 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (87557406 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (88041066 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (88524744 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (89008547 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (89492366 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (89976054 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (90459681 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (90943375 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (91427068 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (91910681 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (92394407 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (92878057 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (93361747 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (93845595 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (94329480 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (94813290 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (95297132 bp)
  /tmp/tmpjqyyf1wb/files/6/d/b/dataset_6dbf6233-5ea1-431f-ae89-26c1bedadee3.dat (95621214 bp)
  800000 reads, 10878792 16-mers

Scoring long reads

  387 reads (483816 bp)
  726 reads (967475 bp)
  1071 reads (1454165 bp)
  1416 reads (1937914 bp)
  1784 reads (2422403 bp)
  2109 reads (2908036 bp)
  2464 reads (3391674 bp)
  2825 reads (3877299 bp)
  3194 reads (4363582 bp)
  3583 reads (4849218 bp)
  3949 reads (5333157 bp)
  4328 reads (5816911 bp)
  4694 reads (6300796 bp)
  5023 reads (6787967 bp)
  5395 reads (7272816 bp)
  5728 reads (7761392 bp)
  6114 reads (8246053 bp)
  6473 reads (8732855 bp)
  6820 reads (9223168 bp)
  7167 reads (9708928 bp)
  7574 reads (10195347 bp)
  7961 reads (10679045 bp)
  8381 reads (11163011 bp)
  8724 reads (11648254 bp)
  9063 reads (12135182 bp)
  9419 reads (12619186 bp)
  9786 reads (13103460 bp)
  10155 reads (13587851 bp)
  10482 reads (14073214 bp)
  10798 reads (14556848 bp)
  11209 reads (15040473 bp)
  11537 reads (15525836 bp)
  11890 reads (16010851 bp)
  12265 reads (16494882 bp)
  12619 reads (16979540 bp)
  12985 reads (17464572 bp)
  13296 reads (17948452 bp)
  13698 reads (18432407 bp)
  14057 reads (18919005 bp)
  14352 reads (19405560 bp)
  14675 reads (19891240 bp)
  15040 reads (20374966 bp)
  15422 reads (20859447 bp)
  15773 reads (21343934 bp)
  16089 reads (21827977 bp)
  16441 reads (22311940 bp)
  16800 reads (22804129 bp)
  17197 reads (23289124 bp)
  17568 reads (23775803 bp)
  17960 reads (24259638 bp)
  18318 reads (24747018 bp)
  18664 reads (25237038 bp)
  19012 reads (25721985 bp)
  19365 reads (26205867 bp)
  19719 reads (26690219 bp)
  20061 reads (27176739 bp)
  20416 reads (27660588 bp)
  20769 reads (28145309 bp)
  21135 reads (28629430 bp)
  21503 reads (29117124 bp)
  21887 reads (29604921 bp)
  22255 reads (30089585 bp)
  22629 reads (30577664 bp)
  22987 reads (31061429 bp)
  23385 reads (31545159 bp)
  23780 reads (32031742 bp)
  24153 reads (32517432 bp)
  24487 reads (33002401 bp)
  24844 reads (33486466 bp)
  25208 reads (33971118 bp)
  25570 reads (34454829 bp)
  25962 reads (34940244 bp)
  26335 reads (35426393 bp)
  26694 reads (35910481 bp)
  27032 reads (36394219 bp)
  27415 reads (36880796 bp)
  27751 reads (37366233 bp)
  28123 reads (37851846 bp)
  28490 reads (38336253 bp)
  28835 reads (38821371 bp)
  29171 reads (39308357 bp)
  29525 reads (39792012 bp)
  29896 reads (40276105 bp)
  30257 reads (40760606 bp)
  30638 reads (41245396 bp)
  30953 reads (41729153 bp)
  31303 reads (42213693 bp)
  31653 reads (42698539 bp)
  32023 reads (43182628 bp)
  32402 reads (43666932 bp)
  32776 reads (44153872 bp)
  33156 reads (44637557 bp)
  33499 reads (45123064 bp)
  33855 reads (45606858 bp)
  34229 reads (46097366 bp)
  34582 reads (46583499 bp)
  34914 reads (47067544 bp)
  35292 reads (47551537 bp)
  35681 reads (48035595 bp)
  36027 reads (48519468 bp)
  36425 reads (49004930 bp)
  36775 reads (49488661 bp)
  37151 reads (49973670 bp)
  37532 reads (50457519 bp)
  37935 reads (50941154 bp)
  38289 reads (51426180 bp)
  38654 reads (51913352 bp)
  39036 reads (52398660 bp)
  39383 reads (52885271 bp)
  39747 reads (53371612 bp)
  40137 reads (53855278 bp)
  40499 reads (54340275 bp)
  40864 reads (54829973 bp)
  41206 reads (55315027 bp)
  41585 reads (55799553 bp)
  41970 reads (56283991 bp)
  42333 reads (56784082 bp)
  42686 reads (57272681 bp)
  43057 reads (57757732 bp)
  43397 reads (58242393 bp)
  43778 reads (58730342 bp)
  44077 reads (59216207 bp)
  44501 reads (59700315 bp)
  44873 reads (60185415 bp)
  45208 reads (60670110 bp)
  45582 reads (61154861 bp)
  45995 reads (61639333 bp)
  46382 reads (62122949 bp)
  46744 reads (62609895 bp)
  47154 reads (63093849 bp)
  47585 reads (63577896 bp)
  47944 reads (64063325 bp)
  48333 reads (64548032 bp)
  48741 reads (65031869 bp)
  49099 reads (65516614 bp)
  49435 reads (66002084 bp)
  49763 reads (66486906 bp)
  50101 reads (66970532 bp)
  50441 reads (67458303 bp)
  50769 reads (67943434 bp)
  51092 reads (68431494 bp)
  51410 reads (68915434 bp)
  51763 reads (69399469 bp)
  52125 reads (69884676 bp)
  52490 reads (70368653 bp)
  52854 reads (70852647 bp)
  53181 reads (71336260 bp)
  53574 reads (71824482 bp)
  53955 reads (72309765 bp)
  54349 reads (72794053 bp)
  54685 reads (73278465 bp)
  55058 reads (73762879 bp)
  55447 reads (74247770 bp)
  55826 reads (74731453 bp)
  56193 reads (75215292 bp)
  56596 reads (75704949 bp)
  56989 reads (76188615 bp)
  57358 reads (76672689 bp)
  57757 reads (77157740 bp)
  58108 reads (77641361 bp)
  58466 reads (78126110 bp)
  58874 reads (78610286 bp)
  59233 reads (79094778 bp)
  59582 reads (79578575 bp)
  59919 reads (80067588 bp)
  60270 reads (80551394 bp)
  60616 reads (81036109 bp)
  60962 reads (81519948 bp)
  61347 reads (82005296 bp)
  61777 reads (82489525 bp)
  62129 reads (82973916 bp)
  62513 reads (83459282 bp)
  62886 reads (83946756 bp)
  63256 reads (84430678 bp)
  63639 reads (84916286 bp)
  64029 reads (85401239 bp)
  64379 reads (85885546 bp)
  64731 reads (86369256 bp)
  65096 reads (86861967 bp)
  65485 reads (87346155 bp)
  65840 reads (87832080 bp)
  66279 reads (88316035 bp)
  66688 reads (88803495 bp)
  67070 reads (89288967 bp)
  67451 reads (89773007 bp)
  67808 reads (90258059 bp)
  68177 reads (90744918 bp)
  68529 reads (91234416 bp)
  68864 reads (91718412 bp)
  69236 reads (92202739 bp)
  69644 reads (92686811 bp)
  69994 reads (93175797 bp)
  70000 reads (93181572 bp)

Filtering long reads
  target: 83863414 bp
  reads already fall below target after filtering

Outputting passed long reads

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "fea8dd5bbc3c11eea726e997ec892c65"
              chromInfo "/tmp/tmpjqyyf1wb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              external_references {"assembly": null, "illumina_1": {"values": [{"id": 6, "src": "hda"}]}, "illumina_2": {"values": [{"id": 7, "src": "hda"}]}}
              other {"window_size": "250"}
              output_thresholds {"keep_percent": "90.0", "max_length": null, "min_length": "1000", "min_mean_q": null, "min_window_q": null, "target_bases": null}
              read_manipulation {"split": null, "trim": false}
              score_weights {"length_weight": "1.0", "mean_q_weight": "1.0", "window_q_weight": "1.0"}

      • Step 13: kraken_taxonomy_assignation:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • kraken2 --threads ${GALAXY_SLOTS:-1} --db '/cvmfs/data.galaxyproject.org/managed/kraken2_databases/2022-02-02T162959Z_silva_kmer-len_35_minimizer-len_31_minimizer-spaces_6_load-factor_0.7'    '/tmp/tmpjqyyf1wb/files/3/7/8/dataset_3788230a-8e29-43d1-bee2-31a253685f49.dat'   --confidence '0.0' --minimum-base-quality '10' --minimum-hit-groups '2'    --report '/tmp/tmpjqyyf1wb/job_working_directory/000/7/outputs/dataset_fd7d1ea5-a2e5-48bd-b224-9ada0d8aa76f.dat'     > '/tmp/tmpjqyyf1wb/job_working_directory/000/7/outputs/dataset_d76986de-fef2-4dff-9f42-3a020741efd9.dat'

            Exit Code:

            • 0

            Standard Error:

            • Loading database information... done.
29137 sequences (76.23 Mbp) processed in 1.126s (1552.1 Kseq/m, 4060.48 Mbp/m).
  198 sequences classified (0.68%)
  28939 sequences unclassified (99.32%)

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "fastqsanger"
              __workflow_invocation_uuid__ "fea8dd5bbc3c11eea726e997ec892c65"
              chromInfo "/tmp/tmpjqyyf1wb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              confidence "0.0"
              dbkey "?"
              kraken2_database "2022-02-02T162959Z_silva_kmer-len_35_minimizer-len_31_minimizer-spaces_6_load-factor_0.7"
              min_base_quality "10"
              minimum_hit_groups "2"
              quick false
              report {"create_report": true, "report_minimizer_data": false, "report_zero_counts": false, "use_mpa_style": false}
              single_paired {"__current_case__": 2, "input_sequences": {"values": [{"id": 10, "src": "hda"}]}, "single_paired_selector": "no"}
              split_reads false
              use_names false

      • Step 14: fastqc_quality_after:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • ln -s '/tmp/tmpjqyyf1wb/files/3/7/8/dataset_3788230a-8e29-43d1-bee2-31a253685f49.dat' 'filtered_long_reads' && mkdir -p '/tmp/tmpjqyyf1wb/job_working_directory/000/8/outputs/dataset_ab08b1b4-0e37-476b-a674-3228adfd889c_files' && fastqc --outdir '/tmp/tmpjqyyf1wb/job_working_directory/000/8/outputs/dataset_ab08b1b4-0e37-476b-a674-3228adfd889c_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'filtered_long_reads'  && cp '/tmp/tmpjqyyf1wb/job_working_directory/000/8/outputs/dataset_ab08b1b4-0e37-476b-a674-3228adfd889c_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpjqyyf1wb/job_working_directory/000/8/outputs/dataset_ab08b1b4-0e37-476b-a674-3228adfd889c_files'/*\.html output.html

            Exit Code:

            • 0

            Standard Error:

            • Fontconfig error: No writable cache directories

            Standard Output:

            • null

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "fastqsanger"
              __workflow_invocation_uuid__ "fea8dd5bbc3c11eea726e997ec892c65"
              adapters None
              chromInfo "/tmp/tmpjqyyf1wb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              contaminants None
              dbkey "?"
              kmers "7"
              limits None
              min_length None
              nogroup false

      • Step 15: flye_long_reads_assembly:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is running

            Command Line:

            • ln -s '/tmp/tmpjqyyf1wb/files/3/7/8/dataset_3788230a-8e29-43d1-bee2-31a253685f49.dat' ./input_0.fastq && flye --nano-corr ./input_0.fastq -o out_dir -t ${GALAXY_SLOTS:-4} -i 1

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "fea8dd5bbc3c11eea726e997ec892c65"
              asm {"__current_case__": 1, "asm_select": "false"}
              chromInfo "/tmp/tmpjqyyf1wb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              generate_log false
              iterations "1"
              keep_haplotypes false
              meta false
              min_overlap None
              mode_conditional {"__current_case__": 1, "mode": "--nano-corr"}
              no_alt_contigs false
              scaffold false

      • Step 16: bracken_abundance_estimation:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is error

            Traceback:

            • Traceback (most recent call last):
  File "/tmp/tmpjqyyf1wb/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 293, in prepare_job
    job_wrapper.prepare()
  File "/tmp/tmpjqyyf1wb/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1255, in prepare
    tool_evaluator.set_compute_environment(compute_environment, get_special=get_special)
  File "/tmp/tmpjqyyf1wb/galaxy-dev/lib/galaxy/tools/evaluation.py", line 139, in set_compute_environment
    self._validate_incoming(incoming)
  File "/tmp/tmpjqyyf1wb/galaxy-dev/lib/galaxy/tools/evaluation.py", line 282, in _validate_incoming
    visit_input_values(self.tool.inputs, incoming, validate_inputs)
  File "/tmp/tmpjqyyf1wb/galaxy-dev/lib/galaxy/tools/parameters/__init__.py", line 224, in visit_input_values
    callback_helper(
  File "/tmp/tmpjqyyf1wb/galaxy-dev/lib/galaxy/tools/parameters/__init__.py", line 159, in callback_helper
    new_value = callback(**args)
                ^^^^^^^^^^^^^^^^
  File "/tmp/tmpjqyyf1wb/galaxy-dev/lib/galaxy/tools/evaluation.py", line 279, in validate_inputs
    value = input.from_json(value, request_context, context)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpjqyyf1wb/galaxy-dev/lib/galaxy/tools/parameters/basic.py", line 1030, in from_json
    raise ParameterValueError(
galaxy.tools.parameters.basic.ParameterValueError: parameter 'kmer_distr': requires a value, but no legal values defined

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "fea8dd5bbc3c11eea726e997ec892c65"
              chromInfo "/tmp/tmpjqyyf1wb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              kmer_distr "2022-02-02T162959Z_silva_kmer-len_35_minimizer-len_31_minimizer-spaces_6_load-factor_0.7"
              level "S"
              logfile_output false
              out_report true
              threshold "10"

      • Step 17: recentrifuge_taxonomy_visualization:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is queued

            Command Line:

            • mkdir input_dir && ln -s '/tmp/tmpjqyyf1wb/files/d/7/6/dataset_d76986de-fef2-4dff-9f42-3a020741efd9.dat' 'input_dir/kraken_report_reads.krk' && rcf -n /cvmfs/data.galaxyproject.org/managed/ncbi_taxonomy/ncbi-2015-10-05  -k input_dir  -e TSV -o output  --scoring 'KRAKEN'  --summary ADD   --strain  | tee "/tmp/tmpjqyyf1wb/job_working_directory/000/11/outputs/dataset_29f7c40c-a126-4a4c-a56e-a1db732059d4.dat"

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "fea8dd5bbc3c11eea726e997ec892c65"
              advanced_option {"avoidcross": false, "controls": "0", "exclude_taxa_name": null, "include_taxa_name": null, "minscore_value": "0", "mintaxa": "0", "scoring": null}
              chromInfo "/tmp/tmpjqyyf1wb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              database {"database_name": "ncbi-2015-10-05"}
              dbkey "?"
              file_type {"__current_case__": 3, "filetype": "kraken"}
              more_advanced_option {"ctrlminscore": "0", "ctrlmintaxa": "0", "nokollapse": false, "sequential": false, "strain": true, "summary": "ADD", "takeoutroot": false}
              output_option {"extra": "TSV", "no_logfile": false, "nohtml": false}

      • Step 18: bwa_alignment_R1:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is new

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "fea8dd5bbc3c11eea726e997ec892c65"
              analysis_type {"__current_case__": 4, "algorithmic_options": {"__current_case__": 1, "algorithmic_options_selector": "do_not_set"}, "analysis_type_selector": "full", "io_options": {"C": false, "K": null, "M": false, "T": "30", "V": false, "Y": false, "__current_case__": 0, "a": true, "five": false, "h": "5", "io_options_selector": "set", "q": false}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}
              chromInfo "/tmp/tmpjqyyf1wb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              fastq_input {"__current_case__": 1, "fastq_input1": {"values": [{"id": 6, "src": "hda"}]}, "fastq_input_selector": "single"}
              output_sort "unsorted"
              reference_source {"__current_case__": 1, "ref_file": {"values": [{"id": 15, "src": "hda"}]}, "reference_source_selector": "history"}
              rg {"__current_case__": 3, "rg_selector": "do_not_set"}

      • Step 19: bwa_alignment_R2:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is new

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "fea8dd5bbc3c11eea726e997ec892c65"
              analysis_type {"__current_case__": 4, "algorithmic_options": {"__current_case__": 1, "algorithmic_options_selector": "do_not_set"}, "analysis_type_selector": "full", "io_options": {"C": false, "K": null, "M": false, "T": "30", "V": false, "Y": false, "__current_case__": 0, "a": true, "five": false, "h": "5", "io_options_selector": "set", "q": false}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}
              chromInfo "/tmp/tmpjqyyf1wb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              fastq_input {"__current_case__": 1, "fastq_input1": {"values": [{"id": 7, "src": "hda"}]}, "fastq_input_selector": "single"}
              output_sort "unsorted"
              reference_source {"__current_case__": 1, "ref_file": {"values": [{"id": 15, "src": "hda"}]}, "reference_source_selector": "history"}
              rg {"__current_case__": 3, "rg_selector": "do_not_set"}

      • Step 20: bandage_contig_graph_stats:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is new

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "fea8dd5bbc3c11eea726e997ec892c65"
              chromInfo "/tmp/tmpjqyyf1wb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              tsv false

      • Step 3: select_ncbi_taxonomy_database:

        • step_state: scheduled

      • Step 21: polypolish_polish:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is new

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "fea8dd5bbc3c11eea726e997ec892c65"
              chromInfo "/tmp/tmpjqyyf1wb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              input {"fasta_file": {"values": [{"id": 15, "src": "hda"}]}, "sam_data_type": {"R1_sam": {"values": [{"id": 25, "src": "hda"}]}, "R2_sam": {"values": [{"id": 26, "src": "hda"}]}, "__current_case__": 1, "insert_filter": {"__current_case__": 0, "filter_select": "filter", "high": "99.9", "low": "0.1"}, "sam_selector": "paired"}}
              options {"debug": false, "fraction_invalid": "0.2", "fraction_valid": "0.5", "keep_logfile": false, "max_errors": "10", "min_depth": "5"}

      • Step 22: quast_quality:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is new

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "fea8dd5bbc3c11eea726e997ec892c65"
              advanced {"contig_thresholds": "0,1000", "extensive_mis_size": "1000", "fragmented_max_indent": null, "report_all_metrics": false, "scaffold_gap_max_size": "1000", "skip_unaligned_mis_contigs": true, "strict_NA": false, "unaligned_part_size": "500", "x_for_Nx": "90"}
              alignments {"ambiguity_score": "0.99", "ambiguity_usage": "one", "fragmented": false, "local_mis_size": "200", "min_alignment": "65", "upper_bound_assembly": false, "upper_bound_min_con": null, "use_all_alignments": false}
              assembly {"__current_case__": 0, "min_identity": "95.0", "orga_type": "", "ref": {"__current_case__": 1, "est_ref_size": null, "use_ref": "false"}, "type": "genome"}
              chromInfo "/tmp/tmpjqyyf1wb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              genes {"conserved_genes_finding": true, "gene_finding": {"__current_case__": 0, "tool": "none"}, "rna_finding": false}
              large false
              min_contig "500"
              mode {"__current_case__": 0, "in": {"__current_case__": 1, "custom": "false", "inputs": {"values": [{"id": 28, "src": "hda"}]}}, "mode": "individual", "reads": {"__current_case__": 7, "input_1": {"values": [{"id": 10, "src": "hda"}]}, "reads_option": "nanopore"}}
              output_files ["html", "pdf", "tabular", "log", "summary", "krona"]
              split_scaffolds false

      • Step 23: isescan_IS_annotation:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is new

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "fea8dd5bbc3c11eea726e997ec892c65"
              chromInfo "/tmp/tmpjqyyf1wb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              log_activate true
              remove_short_is false

      • Step 24: refseqmasher_genome:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is new

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "fasta"
              __workflow_invocation_uuid__ "fea8dd5bbc3c11eea726e997ec892c65"
              adv {"min_kmer_threshold": "8", "output_type": "tab", "verbosity": "-vv"}
              chromInfo "/tmp/tmpjqyyf1wb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              input {"__current_case__": 0, "fasta": {"values": [{"id": 28, "src": "hda"}]}, "type": "fasta"}
              top_n_results "3"

      • Step 25: genome_annotation_with_bakta:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is new

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "fea8dd5bbc3c11eea726e997ec892c65"
              annotation {"complete": false, "compliant": false, "keep_contig_headers": true, "meta": false, "prodigal": null, "proteins": null, "replicons": null, "translation_table": "11"}
              chromInfo "/tmp/tmpjqyyf1wb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              input_option {"amrfinder_db_select": "amrfinderplus_V3.11_2023-04-17.1", "bakta_db_select": "V5.0light_2023-02-20", "input_file": {"values": [{"id": 28, "src": "hda"}]}, "min_contig_length": null}
              organism {"genus": null, "plasmid": null, "species": null, "strain": null}
              output_files {"output_selection": ["file_tsv", "file_gff3", "file_ffn", "file_plot", "file_gbff", "file_embl", "file_fna", "file_faa", "hypo_tsv", "hypo_fa", "sum_txt", "file_json", "log_txt"]}
              workflow {"skip_analysis": null}

      • Step 26: bandage_contig_graph_plot:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is new

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "fea8dd5bbc3c11eea726e997ec892c65"
              chromInfo "/tmp/tmpjqyyf1wb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              fontsize None
              height "1000"
              lengths false
              names false
              nodewidth None
              output_format "svg"
              width "1000"

      • Step 27: genomic_annotation_plasmid_plasmidfinder:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is new

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "fea8dd5bbc3c11eea726e997ec892c65"
              chromInfo "/tmp/tmpjqyyf1wb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              input {"database_name": "plasmidfinder_314d85f_2023_03_17", "input_file": {"values": [{"id": 28, "src": "hda"}]}}
              options {"min_cov": "0.6", "threshold": "0.95"}
              output_files {"output_selection": ["hit_fasta", "plasmid_fasta", "result_tsv", "result_txt", "data_json"]}

      • Step 28: staramr_amr_genes:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is new

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "fea8dd5bbc3c11eea726e997ec892c65"
              advanced {"complex_mutations": {"__current_case__": 0, "complex_mutations_condition": "default"}, "exclude_genes": {"__current_case__": 0, "exclude_genes_condition": "default"}, "exclude_negatives": false, "exclude_resistance_phenotypes": false, "genome_size_lower_bound": "4000000", "genome_size_upper_bound": "6000000", "minimum_N50_value": "10000", "minimum_contig_length": "300", "mlst_scheme": "auto", "pid_threshold": "98.0", "plasmidfinder_type": "include_all", "plength_plasmidfinder": "60.0", "plength_pointfinder": "95.0", "plength_resfinder": "60.0", "report_all_blast": false, "unacceptable_number_contigs": "1000"}
              chromInfo "/tmp/tmpjqyyf1wb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              pointfinder_db {"__current_case__": 0, "use_pointfinder": "disabled"}

      • Step 29: genomic_annotation_integron:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is new

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "fea8dd5bbc3c11eea726e997ec892c65"
              chromInfo "/tmp/tmpjqyyf1wb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"
              gbk false
              local_max true
              no_logfile false
              pdf false
              promoter_attI true
              settings {"attc_settings": {"calin_threshold": "2", "covar_matrix": null, "dist_thresh": "4000", "keep_palindromes": false, "max_attc_size": "200", "min_attc_size": "40"}, "protein_settings": {"func_annot": false, "no_proteins": false, "union_integrases": false}}
              topology_file None
              type_replicon None

      • Step 30: abricate_virulence:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is new

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "fea8dd5bbc3c11eea726e997ec892c65"
              adv {"db": "vfdb", "min_cov": "80.0", "min_dna_id": "80.0", "no_header": false}
              chromInfo "/tmp/tmpjqyyf1wb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              dbkey "?"

      • Step 4: long_reads_input:

        • step_state: scheduled

      • Step 31: multiqc_report:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is new

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "input"
              __workflow_invocation_uuid__ "fea8dd5bbc3c11eea726e997ec892c65"
              chromInfo "/tmp/tmpjqyyf1wb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              comment "QUALITY_REPORT"
              dbkey "?"
              export false
              flat false
              results [{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 9, "src": "hda"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 21, "input": {"values": [{"id": 29, "src": "hda"}]}, "software": "quast"}}, {"__index__": 2, "software_cond": {"__current_case__": 8, "output": [{"__index__": 0, "input": {"values": [{"id": 5, "src": "hda"}]}, "type": "data"}, {"__index__": 1, "input": {"values": [{"id": 14, "src": "hda"}]}, "type": "data"}], "software": "fastqc"}}]
              saveLog false
              title "QUALITY_REPORT"

      • Step 5: select_bakta_database:

        • step_state: scheduled

      • Step 6: select_amrfinderplus_to_bakta_database:

        • step_state: scheduled

      • Step 7: select_plasmidfinder_database:

        • step_state: scheduled

      • Step 8: paired_r1:

        • step_state: scheduled

      • Step 9: paired_r2:

        • step_state: scheduled

      • Step 10: fastcqc_quality_before:

        • step_state: scheduled

        • Jobs

          • Job 1:

            • Job state is ok

            Command Line:

            • ln -s '/tmp/tmpjqyyf1wb/files/b/d/9/dataset_bd92873c-8a28-490f-b800-d7d52c949efd.dat' 'long_reads_input_fastqsanger_gz.gz' && mkdir -p '/tmp/tmpjqyyf1wb/job_working_directory/000/4/outputs/dataset_c1a6919f-3e3e-4f35-bc3c-213f22c6c7cf_files' && fastqc --outdir '/tmp/tmpjqyyf1wb/job_working_directory/000/4/outputs/dataset_c1a6919f-3e3e-4f35-bc3c-213f22c6c7cf_files'   --threads ${GALAXY_SLOTS:-2} --quiet --extract  --kmers 7 -f 'fastq' 'long_reads_input_fastqsanger_gz.gz'  && cp '/tmp/tmpjqyyf1wb/job_working_directory/000/4/outputs/dataset_c1a6919f-3e3e-4f35-bc3c-213f22c6c7cf_files'/*/fastqc_data.txt output.txt && cp '/tmp/tmpjqyyf1wb/job_working_directory/000/4/outputs/dataset_c1a6919f-3e3e-4f35-bc3c-213f22c6c7cf_files'/*\.html output.html

            Exit Code:

            • 0

            Standard Error:

            • Fontconfig error: No writable cache directories

            Standard Output:

            • application/gzip

            Job Parameters:

            • Job parameter Parameter value
              __input_ext "fastqsanger.gz"
              __workflow_invocation_uuid__ "fea8dd5bbc3c11eea726e997ec892c65"
              adapters None
              chromInfo "/tmp/tmpjqyyf1wb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
              contaminants None
              dbkey "?"
              kmers "7"
              limits None
              min_length None
              nogroup false
    • Other invocation details

      • error_message

        • Failed to run workflow, at least one job is in [error] state.

      • history_id

        • c51e8e37efa65d4f

      • history_state

        • error

      • invocation_id

        • c51e8e37efa65d4f

      • invocation_state

        • scheduled

      • workflow_id

        • c51e8e37efa65d4f

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@pimarin