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mvdbeek / usegalaxy-tests

Run tests against usegalaxy.org
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Test toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1 #5

Closed natefoo closed 2 years ago

natefoo commented 2 years ago

This tool is already configured to run in Singularity.

Installed in galaxyproject/usegalaxy-tools#447.

natefoo commented 2 years ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1

mvdbeek commented 2 years ago

Results (powered by Planemo)

Summary

State Count
Total 33
Passed 16
Error 0
Failure 17
Skipped 0
Failed s *
❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #13)
**Problems**: * ``` 500 Server Error: Internal Server Error for url: https://usegalaxy.org/api/histories/f9ed30e8defc1cae/contents/bbd44e69cb8906b52737edec0d7b5017/display?raw=true ``` * ``` 500 Server Error: Internal Server Error for url: https://usegalaxy.org/api/histories/f9ed30e8defc1cae/contents/bbd44e69cb8906b55d68d51f66b31dc3/display?raw=true ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a AGATCGGAAGAGC --untrimmed-output=untrimmed_output.fq.gz --output=out1.fq.gz --error-rate=0.1 --times=1 --overlap=3 --action=trim bwa-mem-fastq1_fq_gz.fq.gz Processing reads on 6 cores in single-end mode ... Finished in 0.07 s (685 µs/read; 0.09 M reads/minute). === Summary === Total reads processed: 99 Reads with adapters: 2 (2.0%) == Read fate breakdown == Reads discarded as untrimmed: 97 (98.0%) Reads written (passing filters): 2 (2.0%) Total basepairs processed: 24,849 bp Total written (filtered): 496 bp (2.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 0.0% C: 50.0% G: 50.0% T: 0.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 2 1.5 0 2 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82414150, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` "untrimmed_file" ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #14)
    **Problems**: * ``` 'command_line' ```
  • ❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #17)
    **Problems**: * ``` 500 Server Error: Internal Server Error for url: https://usegalaxy.org/api/histories/f9ed30e8defc1cae/contents/bbd44e69cb8906b54859691d43363960/display?raw=true ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a CGTCCGAANTAG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=retain cutadapt_small_fastq.fq Processing reads on 6 cores in single-end mode ... Finished in 0.05 s (17795 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 3 Reads with adapters: 1 (33.3%) Reads written (passing filters): 3 (100.0%) Total basepairs processed: 102 bp Total written (filtered): 80 bp (78.4%) === Adapter 1 === Sequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-11 bp: 1 Bases preceding removed adapters: A: 0.0% C: 0.0% G: 0.0% T: 0.0% none/other: 100.0% Overview of removed sequences length count expect max.err error counts 34 1 0.0 1 1 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82414168, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "CGTCCGAANTAG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "retain", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #19)
    **Problems**: * ``` 500 Server Error: Internal Server Error for url: https://usegalaxy.org/api/histories/f9ed30e8defc1cae/contents/bbd44e69cb8906b5095affee7746ddd5/display?raw=true ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a CGTCCGAANTAG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=lowercase cutadapt_small_fastq.fq Processing reads on 6 cores in single-end mode ... Finished in 0.05 s (15558 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 3 Reads with adapters: 1 (33.3%) Reads written (passing filters): 3 (100.0%) Total basepairs processed: 102 bp Total written (filtered): 102 bp (100.0%) === Adapter 1 === Sequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-11 bp: 1 Bases preceding removed adapters: A: 0.0% C: 0.0% G: 0.0% T: 0.0% none/other: 100.0% Overview of removed sequences length count expect max.err error counts 34 1 0.0 1 1 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82414168, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "CGTCCGAANTAG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "lowercase", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #3)
    **Problems**: * ``` 'command_line' ```
  • ❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #21)
    **Problems**: * ``` 500 Server Error: Internal Server Error for url: https://usegalaxy.org/api/histories/f9ed30e8defc1cae/contents/bbd44e69cb8906b55f3c5cb058e65dc5/display?raw=true ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a TAAACAGATTAGT --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --revcomp cutadapt_small_fastq.fq Processing reads on 6 cores in single-end mode ... Finished in 0.05 s (16225 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 3 Reads with adapters: 1 (33.3%) Reverse-complemented: 0 (0.0%) Reads written (passing filters): 3 (100.0%) Total basepairs processed: 102 bp Total written (filtered): 97 bp (95.1%) === Adapter 1 === Sequence: TAAACAGATTAGT; Type: regular 3'; Length: 13; Trimmed: 1 times; Reverse-complemented: 0 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 0.0% C: 0.0% G: 0.0% T: 100.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 5 1 0.0 0 1 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82414173, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "TAAACAGATTAGT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "true", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #22)
    **Problems**: * ``` 'command_line' ```
  • ❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #23)
    **Problems**: * ``` 'command_line' ```
  • ❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #24)
    **Problems**: * ``` 'command_line' ```
  • ❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #25)
    **Problems**: * ``` 'command_line' ```
  • ❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #29)
    **Problems**: * ``` 'command_line' ```
  • ❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #30)
    **Problems**: * ``` 'command_line' ```
  • ❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #32)
    **Problems**: * ``` 500 Server Error: Internal Server Error for url: https://usegalaxy.org/api/histories/f9ed30e8defc1cae/contents/bbd44e69cb8906b58df200d35f819c9e/display?raw=true ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a AGATCGGAAGAGC;noindels -A AGATCGGAAGAGC;noindels --output=/corral4/main/jobs/039/500/39500616/outputs/galaxy_dataset_0b0afb4f-7ed9-465d-b422-dee7ab935459.dat --paired-output=/corral4/main/jobs/039/500/39500616/outputs/galaxy_dataset_2f221778-e5fe-4c5a-8d28-bf0d67ec49db.dat --error-rate=0.1 --times=1 --overlap=3 --action=trim --pair-filter=any Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz Processing reads on 6 cores in paired-end mode ... Finished in 0.06 s (576 µs/read; 0.10 M reads/minute). === Summary === Total read pairs processed: 99 Read 1 with adapter: 2 (2.0%) Read 2 with adapter: 4 (4.0%) Pairs written (passing filters): 99 (100.0%) Total basepairs processed: 49,698 bp Read 1: 24,849 bp Read 2: 24,849 bp Total written (filtered): 49,677 bp (100.0%) Read 1: 24,843 bp Read 2: 24,834 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 0.0% C: 50.0% G: 50.0% T: 0.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 2 1.5 0 2 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 0.0% C: 0.0% G: 50.0% T: 50.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 2 1.5 0 2 4 1 0.4 0 1 5 1 0.1 0 1 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 2, "input_1": {"values": [{"id": 1297650, "src": "hdca"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "true"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source2": {"__current_case__": 0, "adapter2": "AGATCGGAAGAGC", "adapter_name2": "", "adapter_source_list2": "user"}, "single_noindels": "true"}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": [], "quality_cutoff2": null}, "type": "paired_collection"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #33)
    **Problems**: * ``` 500 Server Error: Internal Server Error for url: https://usegalaxy.org/api/histories/f9ed30e8defc1cae/contents/bbd44e69cb8906b5b9acd9f3a4dff170/display?raw=true ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --output=/corral4/main/jobs/039/500/39500617/outputs/galaxy_dataset_54657fb0-abd4-4bca-92e0-eabe97d7ba7c.dat --paired-output=/corral4/main/jobs/039/500/39500617/outputs/galaxy_dataset_b8be6988-fff6-4d15-ba36-8ca760987220.dat --error-rate=0.1 --times=1 --overlap=3 --action=trim --pair-filter=any --quality-cutoff=5 Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz -Q=15,20 Processing reads on 6 cores in paired-end mode ... Finished in 0.05 s (542 µs/read; 0.11 M reads/minute). === Summary === Total read pairs processed: 99 Read 1 with adapter: 2 (2.0%) Read 2 with adapter: 2 (2.0%) Pairs written (passing filters): 99 (100.0%) Total basepairs processed: 49,698 bp Read 1: 24,849 bp Read 2: 24,849 bp Quality-trimmed: 747 bp (1.5%) Read 1: 0 bp Read 2: 747 bp Total written (filtered): 48,938 bp (98.5%) Read 1: 24,843 bp Read 2: 24,095 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 0.0% C: 50.0% G: 50.0% T: 0.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 2 1.5 0 2 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 0.0% C: 0.0% G: 100.0% T: 0.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 1 1.5 0 1 4 1 0.4 0 1 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 2, "input_1": {"values": [{"id": 1297652, "src": "hdca"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source2": {"__current_case__": 0, "adapter2": "AGATCGGAAGAGC", "adapter_name2": "", "adapter_source_list2": "user"}, "single_noindels": "false"}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": [], "quality_cutoff2": "15,20"}, "type": "paired_collection"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "5", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #6)
    **Problems**: * ``` 'command_line' ```
  • ❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #7)
    **Problems**: * ``` 500 Server Error: Internal Server Error for url: https://usegalaxy.org/api/histories/f9ed30e8defc1cae/contents/bbd44e69cb8906b542f6d0b6113aa73d/display?raw=true ``` * ``` 500 Server Error: Internal Server Error for url: https://usegalaxy.org/api/histories/f9ed30e8defc1cae/contents/bbd44e69cb8906b55dec41fc9b98dbda/display?raw=true ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 --json stats.json -a AAAGATG --rest-file=rest_output.fa --output=out1.fa --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_rest_fa.fa Processing reads on 6 cores in single-end mode ... Finished in 0.07 s (13356 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 5 Reads with adapters: 5 (100.0%) Reads written (passing filters): 5 (100.0%) Total basepairs processed: 97 bp Total written (filtered): 35 bp (36.1%) === Adapter 1 === Sequence: AAAGATG; Type: regular 3'; Length: 7; Trimmed: 5 times Minimum overlap: 3 No. of allowed errors: 1-7 bp: 0 Bases preceding removed adapters: A: 0.0% C: 0.0% G: 100.0% T: 0.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 7 1 0.0 0 1 12 1 0.0 0 1 14 2 0.0 0 2 15 1 0.0 0 1 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82414107, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AAAGATG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` ["rest_file", "json_stats"] ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #10)
    **Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1, exit_code: None, stderr: . ``` * ``` Output collection 'split_output': expected to have 3 elements, but it had 0. ``` **Command Line:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82414111, "src": "hda"}]}, "r1": {"adapters": [], "anywhere_adapters": [], "cut": "0", "front_adapters": [{"__index__": 0, "front_adapter_source": {"__current_case__": 0, "front_adapter": "^GTCGGTAA", "front_adapter_name": "A1", "front_adapter_source_list": "user"}, "single_noindels": "false"}, {"__index__": 1, "front_adapter_source": {"__current_case__": 0, "front_adapter": "^AGGTCACT", "front_adapter_name": "A2", "front_adapter_source_list": "user"}, "single_noindels": "false"}]}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` "multiple_output" ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |

Passed s *
✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #1)
**Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a AGATCGGAAGAGC --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_small_fastq.fq Processing reads on 6 cores in single-end mode ... Finished in 0.05 s (17418 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 3 Reads with adapters: 0 (0.0%) Reads written (passing filters): 3 (100.0%) Total basepairs processed: 102 bp Total written (filtered): 102 bp (100.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82414112, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #2)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a AGATCGGAAGAGC --output=out1.fq.gz --error-rate=0.1 --times=1 --overlap=3 --action=trim bwa-mem-fastq1_fq_gz.fq.gz Processing reads on 6 cores in single-end mode ... Finished in 0.06 s (583 µs/read; 0.10 M reads/minute). === Summary === Total reads processed: 99 Reads with adapters: 2 (2.0%) Reads written (passing filters): 99 (100.0%) Total basepairs processed: 24,849 bp Total written (filtered): 24,843 bp (100.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 0.0% C: 50.0% G: 50.0% T: 0.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 2 1.5 0 2 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82414115, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #11)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -g file:/corral4/main/objects/6/2/a/dataset_62a4f69b-f0e1-41b3-96e5-8a400d8988a8.dat --output=split/{name}.fastq.gz --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_in_split_fastq_gz.fq.gz Processing reads on 6 cores in single-end mode ... Finished in 0.09 s (8218 µs/read; 0.01 M reads/minute). === Summary === Total reads processed: 11 Reads with adapters: 10 (90.9%) Reads written (passing filters): 11 (100.0%) Total basepairs processed: 1,210 bp Total written (filtered): 1,130 bp (93.4%) === Adapter A2 === Sequence: AGGTCACT; Type: anchored 5'; Length: 8; Trimmed: 5 times No. of allowed errors: 0 Overview of removed sequences length count expect max.err error counts 8 5 0.0 0 5 === Adapter A1 === Sequence: GTCGGTAA; Type: anchored 5'; Length: 8; Trimmed: 5 times No. of allowed errors: 0 Overview of removed sequences length count expect max.err error counts 8 5 0.0 0 5 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82414109, "src": "hda"}]}, "r1": {"adapters": [], "anywhere_adapters": [], "cut": "0", "front_adapters": [{"__index__": 0, "front_adapter_source": {"__current_case__": 2, "front_adapter_file": {"values": [{"id": 82414116, "src": "hda"}]}, "front_adapter_source_list": "file"}, "single_noindels": "false"}]}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` "multiple_output" ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #12)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a AAAT --untrimmed-output=untrimmed_output.fq --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_small_fastq.fq Processing reads on 6 cores in single-end mode ... Finished in 0.04 s (14824 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 3 Reads with adapters: 1 (33.3%) == Read fate breakdown == Reads discarded as untrimmed: 2 (66.7%) Reads written (passing filters): 1 (33.3%) Total basepairs processed: 102 bp Total written (filtered): 30 bp (29.4%) === Adapter 1 === Sequence: AAAT; Type: regular 3'; Length: 4; Trimmed: 1 times Minimum overlap: 3 No. of allowed errors: 1-4 bp: 0 Bases preceding removed adapters: A: 0.0% C: 100.0% G: 0.0% T: 0.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 4 1 0.0 0 1 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82414154, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AAAT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` "untrimmed_file" ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #15)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a AGATCGGAAGAGC -u 5 --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_small_fastq.fq Processing reads on 6 cores in single-end mode ... Finished in 0.06 s (20588 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 3 Reads with adapters: 0 (0.0%) Reads written (passing filters): 3 (100.0%) Total basepairs processed: 102 bp Total written (filtered): 87 bp (85.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82414154, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "5", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #16)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a AGATCGGAAGAGC -u 5 --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --rename={id} barcode={cut_prefix} cutadapt_small_fastq.fq Processing reads on 6 cores in single-end mode ... Finished in 0.06 s (18753 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 3 Reads with adapters: 0 (0.0%) Reads written (passing filters): 3 (100.0%) Total basepairs processed: 102 bp Total written (filtered): 87 bp (85.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82414168, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "5", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": "{id} barcode={cut_prefix}", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #18)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a CGTCCGAANTAG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=mask cutadapt_small_fastq.fq Processing reads on 6 cores in single-end mode ... Finished in 0.04 s (14071 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 3 Reads with adapters: 1 (33.3%) Reads written (passing filters): 3 (100.0%) Total basepairs processed: 102 bp Total written (filtered): 102 bp (100.0%) === Adapter 1 === Sequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-11 bp: 1 Bases preceding removed adapters: A: 0.0% C: 0.0% G: 0.0% T: 0.0% none/other: 100.0% Overview of removed sequences length count expect max.err error counts 34 1 0.0 1 1 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82414173, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "CGTCCGAANTAG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "mask", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #20)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a CGTCCGAANTAG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=none cutadapt_small_fastq.fq Processing reads on 6 cores in single-end mode ... Finished in 0.06 s (19612 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 3 Reads with adapters: 1 (33.3%) Reads written (passing filters): 3 (100.0%) Total basepairs processed: 102 bp Total written (filtered): 102 bp (100.0%) === Adapter 1 === Sequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-11 bp: 1 Bases preceding removed adapters: A: 0.0% C: 0.0% G: 0.0% T: 0.0% none/other: 100.0% Overview of removed sequences length count expect max.err error counts 34 1 0.0 1 1 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82414173, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "CGTCCGAANTAG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "none", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #26)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a AGCCGCTANGACG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=10 cutadapt_small_fastq.fq Processing reads on 6 cores in single-end mode ... Finished in 0.10 s (34787 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 3 Reads with adapters: 1 (33.3%) Reads written (passing filters): 3 (100.0%) Total basepairs processed: 102 bp Total written (filtered): 20 bp (19.6%) === Adapter 1 === Sequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 0.0% C: 0.0% G: 0.0% T: 0.0% none/other: 100.0% Overview of removed sequences length count expect max.err error counts 34 1 0.0 1 1 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82414201, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGCCGCTANGACG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 0, "length": "10", "shorten_end": "3prime", "shorten_values": "True"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #27)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a AGCCGCTANGACG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=-10 cutadapt_small_fastq.fq Processing reads on 6 cores in single-end mode ... Finished in 0.04 s (14993 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 3 Reads with adapters: 1 (33.3%) Reads written (passing filters): 3 (100.0%) Total basepairs processed: 102 bp Total written (filtered): 20 bp (19.6%) === Adapter 1 === Sequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 0.0% C: 0.0% G: 0.0% T: 0.0% none/other: 100.0% Overview of removed sequences length count expect max.err error counts 34 1 0.0 1 1 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82414201, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGCCGCTANGACG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 0, "length": "10", "shorten_end": "5prime", "shorten_values": "True"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #28)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a AGCGGCTTAGACG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --max-expected-errors=10 cutadapt_small_fastq.fq Processing reads on 6 cores in single-end mode ... Finished in 0.05 s (16027 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 3 Reads with adapters: 0 (0.0%) == Read fate breakdown == Reads with too many exp. errors: 0 (0.0%) Reads written (passing filters): 3 (100.0%) Total basepairs processed: 102 bp Total written (filtered): 102 bp (100.0%) === Adapter 1 === Sequence: AGCGGCTTAGACG; Type: regular 3'; Length: 13; Trimmed: 0 times ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82414201, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGCGGCTTAGACG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "10", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #4)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --output=/corral4/main/jobs/039/500/39500551/outputs/galaxy_dataset_5b78f082-379b-4c9a-ae9d-b81ecb00789e.dat --paired-output=/corral4/main/jobs/039/500/39500551/outputs/galaxy_dataset_e49000c2-f7a2-47b6-85ff-8280ecefb317.dat --error-rate=0.1 --times=1 --overlap=3 --action=trim --pair-filter=any Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz Processing reads on 6 cores in paired-end mode ... Finished in 0.05 s (517 µs/read; 0.12 M reads/minute). === Summary === Total read pairs processed: 99 Read 1 with adapter: 2 (2.0%) Read 2 with adapter: 4 (4.0%) Pairs written (passing filters): 99 (100.0%) Total basepairs processed: 49,698 bp Read 1: 24,849 bp Read 2: 24,849 bp Total written (filtered): 49,677 bp (100.0%) Read 1: 24,843 bp Read 2: 24,834 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 0.0% C: 50.0% G: 50.0% T: 0.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 2 1.5 0 2 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 0.0% C: 0.0% G: 50.0% T: 50.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 2 1.5 0 2 4 1 0.4 0 1 5 1 0.1 0 1 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 2, "input_1": {"values": [{"id": 1297646, "src": "hdca"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source2": {"__current_case__": 0, "adapter2": "AGATCGGAAGAGC", "adapter_name2": "", "adapter_source_list2": "user"}, "single_noindels": "false"}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": [], "quality_cutoff2": null}, "type": "paired_collection"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #8)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a AGATCGGAAGAGC --output=out1.fq.gz --error-rate=0.1 --times=1 --overlap=3 --action=trim --nextseq-trim=20 bwa-mem-fastq1_fq_gz.fq.gz Processing reads on 6 cores in single-end mode ... Finished in 0.06 s (560 µs/read; 0.11 M reads/minute). === Summary === Total reads processed: 99 Reads with adapters: 4 (4.0%) Reads written (passing filters): 99 (100.0%) Total basepairs processed: 24,849 bp Quality-trimmed: 286 bp (1.2%) Total written (filtered): 24,550 bp (98.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 0.0% C: 75.0% G: 25.0% T: 0.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 3 1.5 0 3 4 1 0.4 0 1 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82414115, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "20", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #9)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82414112, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` ["report", "info_file"] ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |

natefoo commented 2 years ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1

Increased download attempts from 2 to 32, which is what I've been using when testing from the command line.

mvdbeek commented 2 years ago

Results (powered by Planemo)

Summary

State Count
Total 33
Passed 23
Error 0
Failure 10
Skipped 0
Failed s *
❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #14)
**Problems**: * ``` 'command_line' ```
  • ❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #3)
    **Problems**: * ``` 'command_line' ```
  • ❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #22)
    **Problems**: * ``` 'command_line' ```
  • ❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #23)
    **Problems**: * ``` 'command_line' ```
  • ❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #24)
    **Problems**: * ``` 'command_line' ```
  • ❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #25)
    **Problems**: * ``` 'command_line' ```
  • ❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #29)
    **Problems**: * ``` 'command_line' ```
  • ❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #30)
    **Problems**: * ``` 'command_line' ```
  • ❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #6)
    **Problems**: * ``` 'command_line' ```
  • ❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #7)
    **Problems**: * ``` Output json_stats: different than expected, difference (using diff): ( /tmp/tmp5il6xfercutadapt_rest.json v. /tmp/tmpnujq0u4wcutadapt_rest.json ) --- local_file +++ history_data @@ -4,7 +4,7 @@ "cutadapt_version": "3.5", "python_version": "3.9.7", "command_line_arguments": [ - "-j=1", + "-j=6", "--json", "stats.json", "-a", @@ -17,7 +17,7 @@ "--action=trim", "cutadapt_rest_fa.fa" ], - "cores": 1, + "cores": 6, "input": { "path1": "cutadapt_rest_fa.fa", "path2": null, ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 --json stats.json -a AAAGATG --rest-file=rest_output.fa --output=out1.fa --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_rest_fa.fa Processing reads on 6 cores in single-end mode ... Finished in 0.10 s (20545 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 5 Reads with adapters: 5 (100.0%) Reads written (passing filters): 5 (100.0%) Total basepairs processed: 97 bp Total written (filtered): 35 bp (36.1%) === Adapter 1 === Sequence: AAAGATG; Type: regular 3'; Length: 7; Trimmed: 5 times Minimum overlap: 3 No. of allowed errors: 1-7 bp: 0 Bases preceding removed adapters: A: 0.0% C: 0.0% G: 100.0% T: 0.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 7 1 0.0 0 1 12 1 0.0 0 1 14 2 0.0 0 2 15 1 0.0 0 1 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82415310, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AAAGATG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` ["rest_file", "json_stats"] ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |

Passed s *
✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #1)
**Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=10 -a AGATCGGAAGAGC --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_small_fastq.fq Processing reads on 10 cores in single-end mode ... Finished in 1.14 s (379415 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 3 Reads with adapters: 0 (0.0%) Reads written (passing filters): 3 (100.0%) Total basepairs processed: 102 bp Total written (filtered): 102 bp (100.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82415315, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #2)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=10 -a AGATCGGAAGAGC --output=out1.fq.gz --error-rate=0.1 --times=1 --overlap=3 --action=trim bwa-mem-fastq1_fq_gz.fq.gz Processing reads on 10 cores in single-end mode ... Finished in 6.02 s (60818 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 99 Reads with adapters: 2 (2.0%) Reads written (passing filters): 99 (100.0%) Total basepairs processed: 24,849 bp Total written (filtered): 24,843 bp (100.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 0.0% C: 50.0% G: 50.0% T: 0.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 2 1.5 0 2 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82415314, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #11)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=10 -g file:/jetstream/scratch0/main/jobs/39501486/inputs/dataset_0e94daef-475e-4d53-a713-a1435abc1da8.dat --output=split/{name}.fastq.gz --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_in_split_fastq_gz.fq.gz Processing reads on 10 cores in single-end mode ... Finished in 7.78 s (706942 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 11 Reads with adapters: 10 (90.9%) Reads written (passing filters): 11 (100.0%) Total basepairs processed: 1,210 bp Total written (filtered): 1,130 bp (93.4%) === Adapter A2 === Sequence: AGGTCACT; Type: anchored 5'; Length: 8; Trimmed: 5 times No. of allowed errors: 0 Overview of removed sequences length count expect max.err error counts 8 5 0.0 0 5 === Adapter A1 === Sequence: GTCGGTAA; Type: anchored 5'; Length: 8; Trimmed: 5 times No. of allowed errors: 0 Overview of removed sequences length count expect max.err error counts 8 5 0.0 0 5 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82415311, "src": "hda"}]}, "r1": {"adapters": [], "anywhere_adapters": [], "cut": "0", "front_adapters": [{"__index__": 0, "front_adapter_source": {"__current_case__": 2, "front_adapter_file": {"values": [{"id": 82415316, "src": "hda"}]}, "front_adapter_source_list": "file"}, "single_noindels": "false"}]}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` "multiple_output" ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #12)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a AAAT --untrimmed-output=untrimmed_output.fq --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_small_fastq.fq Processing reads on 6 cores in single-end mode ... Finished in 0.05 s (18025 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 3 Reads with adapters: 1 (33.3%) == Read fate breakdown == Reads discarded as untrimmed: 2 (66.7%) Reads written (passing filters): 1 (33.3%) Total basepairs processed: 102 bp Total written (filtered): 30 bp (29.4%) === Adapter 1 === Sequence: AAAT; Type: regular 3'; Length: 4; Trimmed: 1 times Minimum overlap: 3 No. of allowed errors: 1-4 bp: 0 Bases preceding removed adapters: A: 0.0% C: 100.0% G: 0.0% T: 0.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 4 1 0.0 0 1 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82415347, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AAAT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` "untrimmed_file" ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #13)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a AGATCGGAAGAGC --untrimmed-output=untrimmed_output.fq.gz --output=out1.fq.gz --error-rate=0.1 --times=1 --overlap=3 --action=trim bwa-mem-fastq1_fq_gz.fq.gz Processing reads on 6 cores in single-end mode ... Finished in 0.10 s (974 µs/read; 0.06 M reads/minute). === Summary === Total reads processed: 99 Reads with adapters: 2 (2.0%) == Read fate breakdown == Reads discarded as untrimmed: 97 (98.0%) Reads written (passing filters): 2 (2.0%) Total basepairs processed: 24,849 bp Total written (filtered): 496 bp (2.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 0.0% C: 50.0% G: 50.0% T: 0.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 2 1.5 0 2 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82415407, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` "untrimmed_file" ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #15)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=10 -a AGATCGGAAGAGC -u 5 --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_small_fastq.fq Processing reads on 10 cores in single-end mode ... Finished in 2.89 s (962239 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 3 Reads with adapters: 0 (0.0%) Reads written (passing filters): 3 (100.0%) Total basepairs processed: 102 bp Total written (filtered): 87 bp (85.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82415538, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "5", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #16)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=10 -a AGATCGGAAGAGC -u 5 --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --rename={id} barcode={cut_prefix} cutadapt_small_fastq.fq Processing reads on 10 cores in single-end mode ... Finished in 9.52 s (3172845 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 3 Reads with adapters: 0 (0.0%) Reads written (passing filters): 3 (100.0%) Total basepairs processed: 102 bp Total written (filtered): 87 bp (85.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82415538, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "5", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": "{id} barcode={cut_prefix}", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #17)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a CGTCCGAANTAG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=retain cutadapt_small_fastq.fq Processing reads on 6 cores in single-end mode ... Finished in 0.07 s (22246 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 3 Reads with adapters: 1 (33.3%) Reads written (passing filters): 3 (100.0%) Total basepairs processed: 102 bp Total written (filtered): 80 bp (78.4%) === Adapter 1 === Sequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-11 bp: 1 Bases preceding removed adapters: A: 0.0% C: 0.0% G: 0.0% T: 0.0% none/other: 100.0% Overview of removed sequences length count expect max.err error counts 34 1 0.0 1 1 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82415548, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "CGTCCGAANTAG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "retain", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #18)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a CGTCCGAANTAG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=mask cutadapt_small_fastq.fq Processing reads on 6 cores in single-end mode ... Finished in 0.05 s (18062 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 3 Reads with adapters: 1 (33.3%) Reads written (passing filters): 3 (100.0%) Total basepairs processed: 102 bp Total written (filtered): 102 bp (100.0%) === Adapter 1 === Sequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-11 bp: 1 Bases preceding removed adapters: A: 0.0% C: 0.0% G: 0.0% T: 0.0% none/other: 100.0% Overview of removed sequences length count expect max.err error counts 34 1 0.0 1 1 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82415569, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "CGTCCGAANTAG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "mask", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #19)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a CGTCCGAANTAG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=lowercase cutadapt_small_fastq.fq Processing reads on 6 cores in single-end mode ... Finished in 0.08 s (26085 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 3 Reads with adapters: 1 (33.3%) Reads written (passing filters): 3 (100.0%) Total basepairs processed: 102 bp Total written (filtered): 102 bp (100.0%) === Adapter 1 === Sequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-11 bp: 1 Bases preceding removed adapters: A: 0.0% C: 0.0% G: 0.0% T: 0.0% none/other: 100.0% Overview of removed sequences length count expect max.err error counts 34 1 0.0 1 1 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82415569, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "CGTCCGAANTAG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "lowercase", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #20)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a CGTCCGAANTAG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=none cutadapt_small_fastq.fq Processing reads on 6 cores in single-end mode ... Finished in 0.06 s (18497 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 3 Reads with adapters: 1 (33.3%) Reads written (passing filters): 3 (100.0%) Total basepairs processed: 102 bp Total written (filtered): 102 bp (100.0%) === Adapter 1 === Sequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-11 bp: 1 Bases preceding removed adapters: A: 0.0% C: 0.0% G: 0.0% T: 0.0% none/other: 100.0% Overview of removed sequences length count expect max.err error counts 34 1 0.0 1 1 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82415607, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "CGTCCGAANTAG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "none", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #21)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a TAAACAGATTAGT --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --revcomp cutadapt_small_fastq.fq Processing reads on 6 cores in single-end mode ... Finished in 0.05 s (16905 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 3 Reads with adapters: 1 (33.3%) Reverse-complemented: 0 (0.0%) Reads written (passing filters): 3 (100.0%) Total basepairs processed: 102 bp Total written (filtered): 97 bp (95.1%) === Adapter 1 === Sequence: TAAACAGATTAGT; Type: regular 3'; Length: 13; Trimmed: 1 times; Reverse-complemented: 0 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 0.0% C: 0.0% G: 0.0% T: 100.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 5 1 0.0 0 1 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82415607, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "TAAACAGATTAGT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "true", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #26)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=10 -a AGCCGCTANGACG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=10 cutadapt_small_fastq.fq Processing reads on 10 cores in single-end mode ... Finished in 1.40 s (467154 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 3 Reads with adapters: 1 (33.3%) Reads written (passing filters): 3 (100.0%) Total basepairs processed: 102 bp Total written (filtered): 20 bp (19.6%) === Adapter 1 === Sequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 0.0% C: 0.0% G: 0.0% T: 0.0% none/other: 100.0% Overview of removed sequences length count expect max.err error counts 34 1 0.0 1 1 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82415804, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGCCGCTANGACG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 0, "length": "10", "shorten_end": "3prime", "shorten_values": "True"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #27)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=10 -a AGCCGCTANGACG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=-10 cutadapt_small_fastq.fq Processing reads on 10 cores in single-end mode ... Finished in 5.11 s (1704897 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 3 Reads with adapters: 1 (33.3%) Reads written (passing filters): 3 (100.0%) Total basepairs processed: 102 bp Total written (filtered): 20 bp (19.6%) === Adapter 1 === Sequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 0.0% C: 0.0% G: 0.0% T: 0.0% none/other: 100.0% Overview of removed sequences length count expect max.err error counts 34 1 0.0 1 1 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82415888, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGCCGCTANGACG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 0, "length": "10", "shorten_end": "5prime", "shorten_values": "True"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #28)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a AGCGGCTTAGACG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --max-expected-errors=10 cutadapt_small_fastq.fq Processing reads on 6 cores in single-end mode ... Finished in 0.08 s (28167 µs/read; 0.00 M reads/minute). === Summary === Total reads processed: 3 Reads with adapters: 0 (0.0%) == Read fate breakdown == Reads with too many exp. errors: 0 (0.0%) Reads written (passing filters): 3 (100.0%) Total basepairs processed: 102 bp Total written (filtered): 102 bp (100.0%) === Adapter 1 === Sequence: AGCGGCTTAGACG; Type: regular 3'; Length: 13; Trimmed: 0 times ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82415900, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGCGGCTTAGACG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "10", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #4)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=10 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --output=/jetstream/scratch0/main/jobs/39501485/outputs/dataset_2eb82c17-e5fd-4786-8aaa-817dca189e10.dat --paired-output=/jetstream/scratch0/main/jobs/39501485/outputs/dataset_d2e7c738-bd09-48d7-927a-6093d81dea6f.dat --error-rate=0.1 --times=1 --overlap=3 --action=trim --pair-filter=any Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz Processing reads on 10 cores in paired-end mode ... Finished in 3.05 s (30846 µs/read; 0.00 M reads/minute). === Summary === Total read pairs processed: 99 Read 1 with adapter: 2 (2.0%) Read 2 with adapter: 4 (4.0%) Pairs written (passing filters): 99 (100.0%) Total basepairs processed: 49,698 bp Read 1: 24,849 bp Read 2: 24,849 bp Total written (filtered): 49,677 bp (100.0%) Read 1: 24,843 bp Read 2: 24,834 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 0.0% C: 50.0% G: 50.0% T: 0.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 2 1.5 0 2 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 0.0% C: 0.0% G: 50.0% T: 50.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 2 1.5 0 2 4 1 0.4 0 1 5 1 0.1 0 1 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 2, "input_1": {"values": [{"id": 1297774, "src": "hdca"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source2": {"__current_case__": 0, "adapter2": "AGATCGGAAGAGC", "adapter_name2": "", "adapter_source_list2": "user"}, "single_noindels": "false"}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": [], "quality_cutoff2": null}, "type": "paired_collection"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #32)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a AGATCGGAAGAGC;noindels -A AGATCGGAAGAGC;noindels --output=/corral4/main/jobs/039/501/39501903/outputs/galaxy_dataset_0ea0da83-76eb-4b1b-acf2-2bce3ef34418.dat --paired-output=/corral4/main/jobs/039/501/39501903/outputs/galaxy_dataset_605d6210-69b8-4b4d-ad27-bd06f083b9e1.dat --error-rate=0.1 --times=1 --overlap=3 --action=trim --pair-filter=any Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz Processing reads on 6 cores in paired-end mode ... Finished in 0.09 s (885 µs/read; 0.07 M reads/minute). === Summary === Total read pairs processed: 99 Read 1 with adapter: 2 (2.0%) Read 2 with adapter: 4 (4.0%) Pairs written (passing filters): 99 (100.0%) Total basepairs processed: 49,698 bp Read 1: 24,849 bp Read 2: 24,849 bp Total written (filtered): 49,677 bp (100.0%) Read 1: 24,843 bp Read 2: 24,834 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 0.0% C: 50.0% G: 50.0% T: 0.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 2 1.5 0 2 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 0.0% C: 0.0% G: 50.0% T: 50.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 2 1.5 0 2 4 1 0.4 0 1 5 1 0.1 0 1 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 2, "input_1": {"values": [{"id": 1297822, "src": "hdca"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "true"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source2": {"__current_case__": 0, "adapter2": "AGATCGGAAGAGC", "adapter_name2": "", "adapter_source_list2": "user"}, "single_noindels": "true"}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": [], "quality_cutoff2": null}, "type": "paired_collection"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #33)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --output=/corral4/main/jobs/039/501/39501922/outputs/galaxy_dataset_ee483ce3-e654-4f72-80c4-e51c64109d0c.dat --paired-output=/corral4/main/jobs/039/501/39501922/outputs/galaxy_dataset_f7968f4d-e42f-410b-9a3a-d0cefda338da.dat --error-rate=0.1 --times=1 --overlap=3 --action=trim --pair-filter=any --quality-cutoff=5 Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz -Q=15,20 Processing reads on 6 cores in paired-end mode ... Finished in 0.10 s (1029 µs/read; 0.06 M reads/minute). === Summary === Total read pairs processed: 99 Read 1 with adapter: 2 (2.0%) Read 2 with adapter: 2 (2.0%) Pairs written (passing filters): 99 (100.0%) Total basepairs processed: 49,698 bp Read 1: 24,849 bp Read 2: 24,849 bp Quality-trimmed: 747 bp (1.5%) Read 1: 0 bp Read 2: 747 bp Total written (filtered): 48,938 bp (98.5%) Read 1: 24,843 bp Read 2: 24,095 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 0.0% C: 50.0% G: 50.0% T: 0.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 2 1.5 0 2 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 0.0% C: 0.0% G: 100.0% T: 0.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 1 1.5 0 1 4 1 0.4 0 1 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 2, "input_1": {"values": [{"id": 1297824, "src": "hdca"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source2": {"__current_case__": 0, "adapter2": "AGATCGGAAGAGC", "adapter_name2": "", "adapter_source_list2": "user"}, "single_noindels": "false"}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": [], "quality_cutoff2": "15,20"}, "type": "paired_collection"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "5", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #8)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -a AGATCGGAAGAGC --output=out1.fq.gz --error-rate=0.1 --times=1 --overlap=3 --action=trim --nextseq-trim=20 bwa-mem-fastq1_fq_gz.fq.gz Processing reads on 6 cores in single-end mode ... Finished in 0.11 s (1068 µs/read; 0.06 M reads/minute). === Summary === Total reads processed: 99 Reads with adapters: 4 (4.0%) Reads written (passing filters): 99 (100.0%) Total basepairs processed: 24,849 bp Quality-trimmed: 286 bp (1.2%) Total written (filtered): 24,550 bp (98.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times Minimum overlap: 3 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 0.0% C: 75.0% G: 25.0% T: 0.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 3 1.5 0 3 4 1 0.4 0 1 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82415314, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "20", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` None ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #9)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82415315, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` ["report", "info_file"] ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test #10)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console This is cutadapt 3.5 with Python 3.9.7 Command line parameters: -j=6 -g A1=^GTCGGTAA -g A2=^AGGTCACT --output=split/{name}.fastq --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_in_split_fastq.fq Processing reads on 6 cores in single-end mode ... Finished in 0.05 s (4680 µs/read; 0.01 M reads/minute). === Summary === Total reads processed: 11 Reads with adapters: 10 (90.9%) Reads written (passing filters): 11 (100.0%) Total basepairs processed: 1,210 bp Total written (filtered): 1,130 bp (93.4%) === Adapter A1 === Sequence: GTCGGTAA; Type: anchored 5'; Length: 8; Trimmed: 5 times No. of allowed errors: 0 Overview of removed sequences length count expect max.err error counts 8 5 0.0 0 5 === Adapter A2 === Sequence: AGGTCACT; Type: anchored 5'; Length: 8; Trimmed: 5 times No. of allowed errors: 0 Overview of removed sequences length count expect max.err error counts 8 5 0.0 0 5 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | library | ` {"__current_case__": 0, "input_1": {"values": [{"id": 82415308, "src": "hda"}]}, "r1": {"adapters": [], "anywhere_adapters": [], "cut": "0", "front_adapters": [{"__index__": 0, "front_adapter_source": {"__current_case__": 0, "front_adapter": "^GTCGGTAA", "front_adapter_name": "A1", "front_adapter_source_list": "user"}, "single_noindels": "false"}, {"__index__": 1, "front_adapter_source": {"__current_case__": 0, "front_adapter": "^AGGTCACT", "front_adapter_name": "A2", "front_adapter_source_list": "user"}, "single_noindels": "false"}]}, "type": "single"} ` | | adapter\_options | ` {"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"} ` | | filter\_options | ` {"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"} ` | | read\_mod\_options | ` {"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "trim_n": "false", "zero_cap": "false"} ` | | output\_selector | ` "multiple_output" ` | | \_\_job\_resource | ` {"__current_case__": 0, "__job_resource__select": "no"} ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |

natefoo commented 2 years ago 
 Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/galaxy/tool_util/verify/script.py", line 297, in run_test
    register_job_data=register, publish_history=publish_history, **verify_kwds
  File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/galaxy/tool_util/verify/interactor.py", line 1134, in verify_tool
    raise e
  File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/galaxy/tool_util/verify/interactor.py", line 1127, in verify_tool
    job_stdio = _verify_outputs(testdef, test_history, jobs, data_list, data_collection_list, galaxy_interactor, quiet=quiet)
  File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/galaxy/tool_util/verify/interactor.py", line 1271, in _verify_outputs
    raw_data = job_stdio[what]
KeyError: 'command_line'

Maybe an issue with the galaxy-tool-util version? Because this doesn't happen locally. I'm declaring this working since it passes tests when I run those tests locally (against Main) from the command line.