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test against test.galaxyproject.org #2

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mvdbeek opened this issue May 6, 2021 · 33 comments
Open

test against test.galaxyproject.org #2

mvdbeek opened this issue May 6, 2021 · 33 comments

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@mvdbeek
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mvdbeek commented May 6, 2021

No description provided.

@mvdbeek
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mvdbeek commented May 6, 2021

/run-tool-test tool_id=addName

@mvdbeek
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mvdbeek commented May 6, 2021

/run-tool-test tool_id=addName server=https://test.galaxyproject.org

@mvdbeek
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mvdbeek commented May 6, 2021

/run-tool-test tool_id=cat1 server=https://test.galaxyproject.org

@mvdbeek
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mvdbeek commented May 6, 2021

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 1
Passed 1
Error 0
Failure 0
Skipped 0
Passed Tests
  • ✅ cat1 (Test tool test #1)

    Command Line:

    • python /cvmfs/test.galaxyproject.org/galaxy/tools/filters/catWrapper.py '/galaxy-repl/test/jobdir/001/401/1401075/outputs/galaxy_dataset_089c750a-8129-45ed-abe6-25102d9ce934.dat' '/galaxy-repl/test/object_store_cache/d/4/0/dataset_d40fa6a6-269e-45e8-933a-c7975d6d2c0b.dat' '/galaxy-repl/test/object_store_cache/2/b/e/dataset_2be0552c-0d45-4600-95b6-15fe409768f4.dat'

    Exit Code:

    • 0

    Job Parameters:

    • Job parameter Parameter value
      queries [{"__index__": 0, "input2": {"values": [{"id": 2058851, "src": "hda"}]}}]
      chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
      dbkey "?"
      __input_ext "bed"

@mvdbeek
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mvdbeek commented May 6, 2021

/run-tool-test tool_id=cat1

@mvdbeek
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mvdbeek commented May 6, 2021

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 1
Passed 1
Error 0
Failure 0
Skipped 0
Passed Tests
  • ✅ cat1 (Test tool test #1)

    Command Line:

    Exit Code:

    • 0

    Job Parameters:

    • Job parameter Parameter value
      queries [{"__index__": 0, "input2": {"values": [{"id": 69736907, "src": "hda"}]}}]
      chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
      dbkey "?"
      __input_ext "bed"

@mvdbeek
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mvdbeek commented May 6, 2021

/run-tool-test tool_id=cat1 server=https://test.galaxyproject.org

@mvdbeek
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mvdbeek commented May 6, 2021

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 1
Passed 1
Error 0
Failure 0
Skipped 0
Passed Tests
  • ✅ cat1 (Test tool test #1)

    Command Line:

    Exit Code:

    • 0

    Job Parameters:

    • Job parameter Parameter value
      queries [{"__index__": 0, "input2": {"values": [{"id": 2058854, "src": "hda"}]}}]
      chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
      dbkey "?"
      __input_ext "bed"

@natefoo
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natefoo commented May 6, 2021

/run-tool-test tool_id=cat1 server=https://test.galaxyproject.org

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@natefoo
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natefoo commented May 6, 2021

/run-tool-test tool_id=cat1 server=https://test.galaxyproject.org

@mvdbeek
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mvdbeek commented May 6, 2021

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 1
Passed 1
Error 0
Failure 0
Skipped 0
Passed Tests
  • ✅ cat1 (Test tool test #1)

    Command Line:

    Exit Code:

    • 0

    Job Parameters:

    • Job parameter Parameter value
      queries [{"__index__": 0, "input2": {"values": [{"id": 2058857, "src": "hda"}]}}]
      chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
      dbkey "?"
      __input_ext "bed"

@mvdbeek
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mvdbeek commented May 7, 2021

/run-tool-test tool_id=cat1 server=https://test.galaxyproject.org

3 similar comments
@mvdbeek
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mvdbeek commented May 7, 2021

/run-tool-test tool_id=cat1 server=https://test.galaxyproject.org

@mvdbeek
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mvdbeek commented May 7, 2021

/run-tool-test tool_id=cat1 server=https://test.galaxyproject.org

@mvdbeek
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mvdbeek commented May 7, 2021

/run-tool-test tool_id=cat1 server=https://test.galaxyproject.org

@mvdbeek
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mvdbeek commented May 7, 2021

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 1
Passed 1
Error 0
Failure 0
Skipped 0
Passed Tests
  • ✅ cat1 (Test tool test #1)

    Command Line:

    Exit Code:

    • 0

    Job Parameters:

    • Job parameter Parameter value
      queries [{"__index__": 0, "input2": {"values": [{"id": 2058871, "src": "hda"}]}}]
      chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
      dbkey "?"
      __input_ext "bed"

@mvdbeek
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mvdbeek commented May 7, 2021

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 1
Passed 1
Error 0
Failure 0
Skipped 0
Passed Tests
  • ✅ cat1 (Test tool test #1)

    Command Line:

    Exit Code:

    • 0

    Job Parameters:

    • Job parameter Parameter value
      queries [{"__index__": 0, "input2": {"values": [{"id": 2058873, "src": "hda"}]}}]
      chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
      dbkey "?"
      __input_ext "bed"

@mvdbeek
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mvdbeek commented May 7, 2021

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 1
Passed 1
Error 0
Failure 0
Skipped 0
Passed Tests
  • ✅ cat1 (Test tool test #1)

    Command Line:

    Exit Code:

    • 0

    Job Parameters:

    • Job parameter Parameter value
      queries [{"__index__": 0, "input2": {"values": [{"id": 2058877, "src": "hda"}]}}]
      chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
      dbkey "?"
      __input_ext "bed"

@mvdbeek
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mvdbeek commented May 7, 2021

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 1
Passed 1
Error 0
Failure 0
Skipped 0
Passed Tests
  • ✅ cat1 (Test tool test #1)

    Command Line:

    Exit Code:

    • 0

    Job Parameters:

    • Job parameter Parameter value
      queries [{"__index__": 0, "input2": {"values": [{"id": 2058875, "src": "hda"}]}}]
      chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
      dbkey "?"
      __input_ext "bed"

@natefoo
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natefoo commented May 7, 2021

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6 server=https://test.galaxyproject.org

Pre-Singularity Test

EDIT: bad choice since it's a multicore tool. I'm gonna have the job router send jobs from this account to a fast queue.

@natefoo
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natefoo commented May 7, 2021

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6 server=https://test.galaxyproject.org

Pre-Singularity test w/ test job prioritization

@mvdbeek
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mvdbeek commented May 7, 2021

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6 server=https://test.galaxyproject.org

@mvdbeek
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mvdbeek commented May 7, 2021

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 13
Passed 13
Error 0
Failure 0
Skipped 0
Passed Tests
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test tool test #1)

    Command Line:

    Exit Code:

    • 0

    Standard Output:

    • This is cutadapt 1.16 with Python 3.6.6
      Command line parameters: -j 1 -a AGATCGGAAGAGC --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 cutadapt_small_fastq.fq
      Running on 1 core
      Trimming 1 adapter with at most 10.0% errors in single-end mode ...
      Finished in 0.01 s (2309 us/read; 0.03 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": 2058943, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "false", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __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 test against test.galaxyproject.org #2)

    Command Line:

    Exit Code:

    • 0

    Standard Output:

    • This is cutadapt 1.16 with Python 3.6.6
      Command line parameters: -j 1 -a AGATCGGAAGAGC --output=out1.fq.gz --error-rate=0.1 --times=1 --overlap=3 bwa-mem-fastq1_fq_gz.fq.gz
      Running on 1 core
      Trimming 1 adapter with at most 10.0% errors in single-end mode ...
      Finished in 0.03 s (285 us/read; 0.21 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.
      
      No. of allowed errors:
      0-9 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": 2058944, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "false", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __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 Test racon 1.3.1.1 #11)

    Command Line:

    Exit Code:

    • 0

    Standard Output:

    • This is cutadapt 1.16 with Python 3.6.6
      Command line parameters: -j 1 -g file:/galaxy-repl/test/object_store_cache/e/9/5/dataset_e9563cb1-d5ab-42e4-9e0b-d2e280fbc17f.dat --output=split/{name}.fastq.gz --error-rate=0.1 --times=1 --overlap=3 cutadapt_in_split_fastq_gz.fq.gz
      Running on 1 core
      Trimming 2 adapters with at most 10.0% errors in single-end mode ...
      Finished in 0.76 s (68787 us/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:
      0-8 bp: 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:
      0-8 bp: 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": 2058942, "src": "hda"}]}, "r1": {"adapters": [], "anywhere_adapters": [], "cut": "0", "front_adapters": [{"__index__": 0, "front_adapter_source": {"__current_case__": 2, "front_adapter_file": {"values": [{"id": 2058947, "src": "hda"}]}, "front_adapter_source_list": "file"}}]}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "true", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __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 Test mafft 7.221.3 #12)

    Command Line:

    Exit Code:

    • 0

    Standard Output:

    • This is cutadapt 1.16 with Python 3.6.6
      Command line parameters: -a AAAT --untrimmed-output=untrimmed_output.fq --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 cutadapt_small_fastq.fq
      Running on 1 core
      Trimming 1 adapter with at most 10.0% errors in single-end mode ...
      Finished in 0.05 s (16097 us/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):             98 bp (96.1%)
      
      === Adapter 1 ===
      
      Sequence: AAAT; Type: regular 3'; Length: 4; Trimmed: 1 times.
      
      No. of allowed errors:
      0-4 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
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      library {"__current_case__": 0, "input_1": {"values": [{"id": 2058965, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AAAT", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      output_options {"info_file": "false", "multiple_output": "false", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "true", "wildcard_file": "false"}
      __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 Test ebi_metagenomics_run_downloader 0.1.0 #13)

    Command Line:

    Exit Code:

    • 0

    Standard Output:

    • This is cutadapt 1.16 with Python 3.6.6
      Command line parameters: -a AGATCGGAAGAGC --untrimmed-output=untrimmed_output.fq.gz --output=out1.fq.gz --error-rate=0.1 --times=1 --overlap=3 bwa-mem-fastq1_fq_gz.fq.gz
      Running on 1 core
      Trimming 1 adapter with at most 10.0% errors in single-end mode ...
      Finished in 0.17 s (1726 us/read; 0.03 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.
      
      No. of allowed errors:
      0-9 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": 2058966, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "false", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "true", "wildcard_file": "false"}
      __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 Test Prokka 1.14.6+galaxy1 #3)

    Command Line:

    Exit Code:

    • 0

    Standard Output:

    • This is cutadapt 1.16 with Python 3.6.6
      Command line parameters: -j 1 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --output=out1.fq.gz --paired-output=out2.fq.gz --error-rate=0.1 --times=1 --overlap=3 --pair-filter=any bwa-mem-fastq1_fq_gz.fq.gz bwa-mem-fastq2_fq_gz.fq.gz
      Running on 1 core
      Trimming 2 adapters with at most 10.0% errors in paired-end mode ...
      Finished in 0.05 s (466 us/read; 0.13 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.
      
      No. of allowed errors:
      0-9 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.
      
      No. of allowed errors:
      0-9 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__": 1, "input_1": {"values": [{"id": 2058944, "src": "hda"}]}, "input_2": {"values": [{"id": 2058948, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source2": {"__current_case__": 0, "adapter2": "AGATCGGAAGAGC", "adapter_name2": "", "adapter_source_list2": "user"}}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": []}, "type": "paired"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "false", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __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 Test roary 3.13.0+galaxy2 #4)

    Command Line:

    Exit Code:

    • 0

    Standard Output:

    • This is cutadapt 1.16 with Python 3.6.6
      Command line parameters: -j 1 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --output=out1.fq.gz --paired-output=out2.fq.gz --error-rate=0.1 --times=1 --overlap=3 --pair-filter=any Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz
      Running on 1 core
      Trimming 2 adapters with at most 10.0% errors in paired-end mode ...
      Finished in 0.05 s (459 us/read; 0.13 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.
      
      No. of allowed errors:
      0-9 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.
      
      No. of allowed errors:
      0-9 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": 15154, "src": "hdca"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source2": {"__current_case__": 0, "adapter2": "AGATCGGAAGAGC", "adapter_name2": "", "adapter_source_list2": "user"}}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": []}, "type": "paired_collection"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "false", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __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 Test trinotate 3.2.2+galaxy0 #6)

    Command Line:

    Exit Code:

    • 0

    Standard Output:

    • This is cutadapt 1.16 with Python 3.6.6
      Command line parameters: -j 1 -a TTAGACATATCTCCGTCG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --discard cutadapt_small_fastq.fq
      Running on 1 core
      Trimming 1 adapter with at most 10.0% errors in single-end mode ...
      Finished in 0.01 s (2138 us/read; 0.03 M reads/minute).
      
      === Summary ===
      
      Total reads processed:                       3
      Reads with adapters:                         2 (66.7%)
      Reads written (passing filters):             1 (33.3%)
      
      Total basepairs processed:           102 bp
      Total written (filtered):             34 bp (33.3%)
      
      === Adapter 1 ===
      
      Sequence: TTAGACATATCTCCGTCG; Type: regular 3'; Length: 18; Trimmed: 2 times.
      
      No. of allowed errors:
      0-9 bp: 0; 10-18 bp: 1
      
      Bases preceding removed adapters:
        A: 50.0%
        C: 50.0%
        G: 0.0%
        T: 0.0%
        none/other: 0.0%
      
      Overview of removed sequences
      length	count	expect	max.err	error counts
      10	1	0.0	1	0 1
      12	1	0.0	1	0 1
      
      

    Job Parameters:

    • Job parameter Parameter value
      library {"__current_case__": 0, "input_1": {"values": [{"id": 2058943, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "TTAGACATATCTCCGTCG", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "true", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "false", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __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 Test pangolin 3.1.17+galaxy1 #7)

    Command Line:

    Exit Code:

    • 0

    Standard Output:

    • This is cutadapt 1.16 with Python 3.6.6
      Command line parameters: -a AAAGATG --rest-file=rest_output.fa --output=out1.fa --error-rate=0.1 --times=1 --overlap=3 cutadapt_rest_fa.fa
      Running on 1 core
      Trimming 1 adapter with at most 10.0% errors in single-end mode ...
      Finished in 0.07 s (13563 us/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.
      
      No. of allowed errors:
      0-7 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": 2058938, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AAAGATG", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "false", "report": "false", "rest_file": "true", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __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 Test SEACR 1.3+galaxy1 on usegalaxy.org #8)

    Command Line:

    Exit Code:

    • 0

    Standard Output:

    • This is cutadapt 1.16 with Python 3.6.6
      Command line parameters: -j 1 -a AGATCGGAAGAGC --output=out1.fq.gz --error-rate=0.1 --times=1 --overlap=3 --nextseq-trim=20 bwa-mem-fastq1_fq_gz.fq.gz
      Running on 1 core
      Trimming 1 adapter with at most 10.0% errors in single-end mode ...
      Finished in 0.03 s (301 us/read; 0.20 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
      Total written (filtered):         24,550 bp (98.8%)
      
      === Adapter 1 ===
      
      Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times.
      
      No. of allowed errors:
      0-9 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": 2058944, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "20", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "false", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __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 Test gffread 2.2.1.3+galaxy0 #9)

    Command Line:

    Exit Code:

    • 0

    Job Parameters:

    • Job parameter Parameter value
      library {"__current_case__": 0, "input_1": {"values": [{"id": 2058943, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "true", "multiple_output": "false", "report": "true", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __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 Test trim_galore 0.6.7+galaxy0 #10)

    Command Line:

    Exit Code:

    • 0

    Standard Output:

    • This is cutadapt 1.16 with Python 3.6.6
      Command line parameters: -j 1 -g A1=^GTCGGTAA -g A2=^AGGTCACT --output=split/{name}.fastq --error-rate=0.1 --times=1 --overlap=3 cutadapt_in_split_fastq.fq
      Running on 1 core
      Trimming 2 adapters with at most 10.0% errors in single-end mode ...
      Finished in 0.01 s (1283 us/read; 0.05 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:
      0-8 bp: 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:
      0-8 bp: 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": 2058940, "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"}}, {"__index__": 1, "front_adapter_source": {"__current_case__": 0, "front_adapter": "^AGGTCACT", "front_adapter_name": "A2", "front_adapter_source_list": "user"}}]}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "true", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __job_resource {"__current_case__": 0, "__job_resource__select": "no"}
      chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
      dbkey "?"
      __input_ext "input"

@natefoo
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natefoo commented May 10, 2021

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6 server=https://test.galaxyproject.org

Now with Singularity™!

@mvdbeek
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Owner Author

mvdbeek commented May 10, 2021

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 13
Passed 1
Error 0
Failure 12
Skipped 0
Failed Tests
  • ❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test tool test #1)

    Problems:

    • Job in error state.
      
    • Job in error state.
      

    Command Line:

    Job Parameters:

    • Job parameter Parameter value
      library {"__current_case__": 0, "input_1": {"values": [{"id": 2059621, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "false", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __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 test against test.galaxyproject.org #2)

    Problems:

    • Job in error state.
      
    • Job in error state.
      

    Command Line:

    Job Parameters:

    • Job parameter Parameter value
      library {"__current_case__": 0, "input_1": {"values": [{"id": 2059620, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "false", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __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 Test racon 1.3.1.1 #11)

    Problems:

    • Job in error state.
      
    • Expected output collection [split_output] to have 3 elements, but it had 0.
      

    Command Line:

    Job Parameters:

    • Job parameter Parameter value
      library {"__current_case__": 0, "input_1": {"values": [{"id": 2059616, "src": "hda"}]}, "r1": {"adapters": [], "anywhere_adapters": [], "cut": "0", "front_adapters": [{"__index__": 0, "front_adapter_source": {"__current_case__": 2, "front_adapter_file": {"values": [{"id": 2059622, "src": "hda"}]}, "front_adapter_source_list": "file"}}]}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "true", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __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 Test mafft 7.221.3 #12)

    Problems:

    • Job in error state.
      
    • Job in error state.
      
    • Job in error state.
      

    Command Line:

    Job Parameters:

    • Job parameter Parameter value
      library {"__current_case__": 0, "input_1": {"values": [{"id": 2059632, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AAAT", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "false", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "true", "wildcard_file": "false"}
      __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 Test ebi_metagenomics_run_downloader 0.1.0 #13)

    Problems:

    • Job in error state.
      
    • Job in error state.
      
    • Job in error state.
      

    Command Line:

    Job Parameters:

    • Job parameter Parameter value
      library {"__current_case__": 0, "input_1": {"values": [{"id": 2059633, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "false", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "true", "wildcard_file": "false"}
      __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 Test Prokka 1.14.6+galaxy1 #3)

    Problems:

    • Job in error state.
      
    • Job in error state.
      
    • Job in error state.
      

    Command Line:

    Job Parameters:

    • Job parameter Parameter value
      library {"__current_case__": 1, "input_1": {"values": [{"id": 2059633, "src": "hda"}]}, "input_2": {"values": [{"id": 2059624, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source2": {"__current_case__": 0, "adapter2": "AGATCGGAAGAGC", "adapter_name2": "", "adapter_source_list2": "user"}}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": []}, "type": "paired"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "false", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __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 Test roary 3.13.0+galaxy2 #4)

    Problems:

    • Job in error state.
      
    • Job in error state.
      
    • Job in error state.
      

    Command Line:

    Job Parameters:

    • Job parameter Parameter value
      library {"__current_case__": 2, "input_1": {"values": [{"id": 15158, "src": "hdca"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source2": {"__current_case__": 0, "adapter2": "AGATCGGAAGAGC", "adapter_name2": "", "adapter_source_list2": "user"}}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": []}, "type": "paired_collection"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "false", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __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 Test trinotate 3.2.2+galaxy0 #6)

    Problems:

    • Job in error state.
      
    • Job in error state.
      

    Command Line:

    Job Parameters:

    • Job parameter Parameter value
      library {"__current_case__": 0, "input_1": {"values": [{"id": 2059632, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "TTAGACATATCTCCGTCG", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "true", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "false", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __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 Test pangolin 3.1.17+galaxy1 #7)

    Problems:

    • Job in error state.
      
    • Job in error state.
      
    • Job in error state.
      

    Command Line:

    Job Parameters:

    • Job parameter Parameter value
      library {"__current_case__": 0, "input_1": {"values": [{"id": 2059617, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AAAGATG", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "false", "report": "false", "rest_file": "true", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __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 Test SEACR 1.3+galaxy1 on usegalaxy.org #8)

    Problems:

    • Job in error state.
      
    • Job in error state.
      

    Command Line:

    Job Parameters:

    • Job parameter Parameter value
      library {"__current_case__": 0, "input_1": {"values": [{"id": 2059633, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "20", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "false", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __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 Test gffread 2.2.1.3+galaxy0 #9)

    Problems:

    • Job in error state.
      
    • Job in error state.
      
    • Job in error state.
      
    • Job in error state.
      

    Command Line:

    Job Parameters:

    • Job parameter Parameter value
      library {"__current_case__": 0, "input_1": {"values": [{"id": 2059621, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "true", "multiple_output": "false", "report": "true", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __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 Test trim_galore 0.6.7+galaxy0 #10)

    Problems:

    • Job in error state.
      
    • Expected output collection [split_output] to have 3 elements, but it had 0.
      

    Command Line:

    Job Parameters:

    • Job parameter Parameter value
      library {"__current_case__": 0, "input_1": {"values": [{"id": 2059614, "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"}}, {"__index__": 1, "front_adapter_source": {"__current_case__": 0, "front_adapter": "^AGGTCACT", "front_adapter_name": "A2", "front_adapter_source_list": "user"}}]}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "true", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __job_resource {"__current_case__": 0, "__job_resource__select": "no"}
      chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
      dbkey "?"
      __input_ext "input"
Passed Tests

@natefoo
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Collaborator

natefoo commented May 10, 2021

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6 server=https://test.galaxyproject.org

Singularity attempt 2 (had a typo in the job router config)

@mvdbeek
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mvdbeek commented May 10, 2021

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 13
Passed 13
Error 0
Failure 0
Skipped 0
Passed Tests
  • ✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test tool test #1)

    Command Line:

    Exit Code:

    • 0

    Standard Output:

    • This is cutadapt 1.16 with Python 3.6.5
      Command line parameters: -j 1 -a AGATCGGAAGAGC --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 cutadapt_small_fastq.fq
      Running on 1 core
      Trimming 1 adapter with at most 10.0% errors in single-end mode ...
      Finished in 0.00 s (1425 us/read; 0.04 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": 2059653, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "false", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __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 test against test.galaxyproject.org #2)

    Command Line:

    Exit Code:

    • 0

    Standard Output:

    • This is cutadapt 1.16 with Python 3.6.5
      Command line parameters: -j 1 -a AGATCGGAAGAGC --output=out1.fq.gz --error-rate=0.1 --times=1 --overlap=3 bwa-mem-fastq1_fq_gz.fq.gz
      Running on 1 core
      Trimming 1 adapter with at most 10.0% errors in single-end mode ...
      Finished in 0.02 s (184 us/read; 0.33 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.
      
      No. of allowed errors:
      0-9 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": 2059652, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "false", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __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 Test racon 1.3.1.1 #11)

    Command Line:

    Exit Code:

    • 0

    Standard Output:

    • This is cutadapt 1.16 with Python 3.6.5
      Command line parameters: -j 1 -g file:/galaxy-repl/test/object_store_cache/4/9/9/dataset_49994cf1-7503-4996-ae70-07e6899dd394.dat --output=split/{name}.fastq.gz --error-rate=0.1 --times=1 --overlap=3 cutadapt_in_split_fastq_gz.fq.gz
      Running on 1 core
      Trimming 2 adapters with at most 10.0% errors in single-end mode ...
      Finished in 0.02 s (1590 us/read; 0.04 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:
      0-8 bp: 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:
      0-8 bp: 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": 2059651, "src": "hda"}]}, "r1": {"adapters": [], "anywhere_adapters": [], "cut": "0", "front_adapters": [{"__index__": 0, "front_adapter_source": {"__current_case__": 2, "front_adapter_file": {"values": [{"id": 2059655, "src": "hda"}]}, "front_adapter_source_list": "file"}}]}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "true", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __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 Test mafft 7.221.3 #12)

    Command Line:

    Exit Code:

    • 0

    Standard Output:

    • This is cutadapt 1.16 with Python 3.6.5
      Command line parameters: -a AAAT --untrimmed-output=untrimmed_output.fq --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 cutadapt_small_fastq.fq
      Running on 1 core
      Trimming 1 adapter with at most 10.0% errors in single-end mode ...
      Finished in 0.01 s (3122 us/read; 0.02 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):             98 bp (96.1%)
      
      === Adapter 1 ===
      
      Sequence: AAAT; Type: regular 3'; Length: 4; Trimmed: 1 times.
      
      No. of allowed errors:
      0-4 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": 2059676, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AAAT", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "false", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "true", "wildcard_file": "false"}
      __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 Test ebi_metagenomics_run_downloader 0.1.0 #13)

    Command Line:

    Exit Code:

    • 0

    Standard Output:

    • This is cutadapt 1.16 with Python 3.6.5
      Command line parameters: -a AGATCGGAAGAGC --untrimmed-output=untrimmed_output.fq.gz --output=out1.fq.gz --error-rate=0.1 --times=1 --overlap=3 bwa-mem-fastq1_fq_gz.fq.gz
      Running on 1 core
      Trimming 1 adapter with at most 10.0% errors in single-end mode ...
      Finished in 0.03 s (340 us/read; 0.18 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.
      
      No. of allowed errors:
      0-9 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": 2059677, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "false", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "true", "wildcard_file": "false"}
      __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 Test Prokka 1.14.6+galaxy1 #3)

    Command Line:

    Exit Code:

    • 0

    Standard Output:

    • This is cutadapt 1.16 with Python 3.6.5
      Command line parameters: -j 1 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --output=out1.fq.gz --paired-output=out2.fq.gz --error-rate=0.1 --times=1 --overlap=3 --pair-filter=any bwa-mem-fastq1_fq_gz.fq.gz bwa-mem-fastq2_fq_gz.fq.gz
      Running on 1 core
      Trimming 2 adapters with at most 10.0% errors in paired-end mode ...
      Finished in 0.04 s (375 us/read; 0.16 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.
      
      No. of allowed errors:
      0-9 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.
      
      No. of allowed errors:
      0-9 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__": 1, "input_1": {"values": [{"id": 2059652, "src": "hda"}]}, "input_2": {"values": [{"id": 2059656, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source2": {"__current_case__": 0, "adapter2": "AGATCGGAAGAGC", "adapter_name2": "", "adapter_source_list2": "user"}}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": []}, "type": "paired"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "false", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __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 Test roary 3.13.0+galaxy2 #4)

    Command Line:

    Exit Code:

    • 0

    Standard Output:

    • This is cutadapt 1.16 with Python 3.6.5
      Command line parameters: -j 1 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --output=out1.fq.gz --paired-output=out2.fq.gz --error-rate=0.1 --times=1 --overlap=3 --pair-filter=any Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz
      Running on 1 core
      Trimming 2 adapters with at most 10.0% errors in paired-end mode ...
      Finished in 0.08 s (831 us/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.
      
      No. of allowed errors:
      0-9 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.
      
      No. of allowed errors:
      0-9 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": 15161, "src": "hdca"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source2": {"__current_case__": 0, "adapter2": "AGATCGGAAGAGC", "adapter_name2": "", "adapter_source_list2": "user"}}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": []}, "type": "paired_collection"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "false", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __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 Test trinotate 3.2.2+galaxy0 #6)

    Command Line:

    Exit Code:

    • 0

    Standard Output:

    • This is cutadapt 1.16 with Python 3.6.5
      Command line parameters: -j 1 -a TTAGACATATCTCCGTCG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --discard cutadapt_small_fastq.fq
      Running on 1 core
      Trimming 1 adapter with at most 10.0% errors in single-end mode ...
      Finished in 4.74 s (1579158 us/read; 0.00 M reads/minute).
      
      === Summary ===
      
      Total reads processed:                       3
      Reads with adapters:                         2 (66.7%)
      Reads written (passing filters):             1 (33.3%)
      
      Total basepairs processed:           102 bp
      Total written (filtered):             34 bp (33.3%)
      
      === Adapter 1 ===
      
      Sequence: TTAGACATATCTCCGTCG; Type: regular 3'; Length: 18; Trimmed: 2 times.
      
      No. of allowed errors:
      0-9 bp: 0; 10-18 bp: 1
      
      Bases preceding removed adapters:
        A: 50.0%
        C: 50.0%
        G: 0.0%
        T: 0.0%
        none/other: 0.0%
      
      Overview of removed sequences
      length	count	expect	max.err	error counts
      10	1	0.0	1	0 1
      12	1	0.0	1	0 1
      
      

    Job Parameters:

    • Job parameter Parameter value
      library {"__current_case__": 0, "input_1": {"values": [{"id": 2059653, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "TTAGACATATCTCCGTCG", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "true", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "false", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __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 Test pangolin 3.1.17+galaxy1 #7)

    Command Line:

    Exit Code:

    • 0

    Standard Output:

    • This is cutadapt 1.16 with Python 3.6.5
      Command line parameters: -a AAAGATG --rest-file=rest_output.fa --output=out1.fa --error-rate=0.1 --times=1 --overlap=3 cutadapt_rest_fa.fa
      Running on 1 core
      Trimming 1 adapter with at most 10.0% errors in single-end mode ...
      Finished in 0.01 s (1470 us/read; 0.04 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.
      
      No. of allowed errors:
      0-7 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": 2059647, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AAAGATG", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "false", "report": "false", "rest_file": "true", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __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 Test SEACR 1.3+galaxy1 on usegalaxy.org #8)

    Command Line:

    Exit Code:

    • 0

    Standard Output:

    • This is cutadapt 1.16 with Python 3.6.5
      Command line parameters: -j 1 -a AGATCGGAAGAGC --output=out1.fq.gz --error-rate=0.1 --times=1 --overlap=3 --nextseq-trim=20 bwa-mem-fastq1_fq_gz.fq.gz
      Running on 1 core
      Trimming 1 adapter with at most 10.0% errors in single-end mode ...
      Finished in 0.03 s (332 us/read; 0.18 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
      Total written (filtered):         24,550 bp (98.8%)
      
      === Adapter 1 ===
      
      Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times.
      
      No. of allowed errors:
      0-9 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": 2059652, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "20", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "false", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __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 Test gffread 2.2.1.3+galaxy0 #9)

    Command Line:

    Exit Code:

    • 0

    Job Parameters:

    • Job parameter Parameter value
      library {"__current_case__": 0, "input_1": {"values": [{"id": 2059653, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "true", "multiple_output": "false", "report": "true", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __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 Test trim_galore 0.6.7+galaxy0 #10)

    Command Line:

    Exit Code:

    • 0

    Standard Output:

    • This is cutadapt 1.16 with Python 3.6.5
      Command line parameters: -j 1 -g A1=^GTCGGTAA -g A2=^AGGTCACT --output=split/{name}.fastq --error-rate=0.1 --times=1 --overlap=3 cutadapt_in_split_fastq.fq
      Running on 1 core
      Trimming 2 adapters with at most 10.0% errors in single-end mode ...
      Finished in 0.01 s (589 us/read; 0.10 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:
      0-8 bp: 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:
      0-8 bp: 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": 2059650, "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"}}, {"__index__": 1, "front_adapter_source": {"__current_case__": 0, "front_adapter": "^AGGTCACT", "front_adapter_name": "A2", "front_adapter_source_list": "user"}}]}, "type": "single"}
      adapter_options {"count": "1", "error_rate": "0.1", "mask_adapter": "false", "match_read_wildcards": " ", "no_indels": "false", "no_trim": "false", "overlap": "3"}
      filter_options {"discard": "false", "discard_untrimmed": "false", "max": "0", "max_n": "", "min": "0", "pair_filter": "any"}
      read_mod_options {"length": "0", "length_tag": "", "nextseq_trim": "0", "prefix": "", "quality_cutoff": "0", "strip_suffix": "", "suffix": "", "trim_n": "false"}
      output_options {"info_file": "false", "multiple_output": "true", "report": "false", "rest_file": "false", "too_long_file": "false", "too_short_file": "false", "untrimmed_file": "false", "wildcard_file": "false"}
      __job_resource {"__current_case__": 0, "__job_resource__select": "no"}
      chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
      dbkey "?"
      __input_ext "input"

@natefoo
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natefoo commented May 10, 2021

/run-tool-test tool_id=bowtie2 server=https://test.galaxyproject.org

Singularity enabled

@mvdbeek
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mvdbeek commented May 10, 2021

Test Results (powered by Planemo)

Test Summary

Test State Count
Total 10
Passed 10
Error 0
Failure 0
Skipped 0
Passed Tests
  • ✅ bowtie2 (Test tool test #1)

    Command Line:

    Exit Code:

    • 0

    Standard Error:

    • Building a SMALL index
      perl: warning: Setting locale failed.
      perl: warning: Please check that your locale settings:
      	LANGUAGE = (unset),
      	LC_ALL = (unset),
      	LANG = "en_US.UTF-8"
          are supported and installed on your system.
      perl: warning: Falling back to the standard locale ("C").
      100 reads; of these:
        100 (100.00%) were paired; of these:
          97 (97.00%) aligned concordantly 0 times
          3 (3.00%) aligned concordantly exactly 1 time
          0 (0.00%) aligned concordantly >1 times
          ----
          97 pairs aligned concordantly 0 times; of these:
            8 (8.25%) aligned discordantly 1 time
          ----
          89 pairs aligned 0 times concordantly or discordantly; of these:
            178 mates make up the pairs; of these:
              153 (85.96%) aligned 0 times
              25 (14.04%) aligned exactly 1 time
              0 (0.00%) aligned >1 times
      23.50% overall alignment rate
      

    Standard Output:

    • Settings:
        Output files: "genome.*.bt2"
        Line rate: 6 (line is 64 bytes)
        Lines per side: 1 (side is 64 bytes)
        Offset rate: 4 (one in 16)
        FTable chars: 10
        Strings: unpacked
        Max bucket size: default
        Max bucket size, sqrt multiplier: default
        Max bucket size, len divisor: 4
        Difference-cover sample period: 1024
        Endianness: little
        Actual local endianness: little
        Sanity checking: disabled
        Assertions: disabled
        Random seed: 0
        Sizeofs: void*:8, int:4, long:8, size_t:8
      Input files DNA, FASTA:
        /galaxy-repl/test/object_store_cache/6/6/2/dataset_66233eb3-9662-4e74-a14e-bafc9c647fb6.dat
      Reading reference sizes
        Time reading reference sizes: 00:00:00
      Calculating joined length
      Writing header
      Reserving space for joined string
      Joining reference sequences
        Time to join reference sequences: 00:00:00
      bmax according to bmaxDivN setting: 4142
      Using parameters --bmax 3107 --dcv 1024
        Doing ahead-of-time memory usage test
        Passed!  Constructing with these parameters: --bmax 3107 --dcv 1024
      Constructing suffix-array element generator
      Building DifferenceCoverSample
        Building sPrime
        Building sPrimeOrder
        V-Sorting samples
        V-Sorting samples time: 00:00:00
        Allocating rank array
        Ranking v-sort output
        Ranking v-sort output time: 00:00:00
        Invoking Larsson-Sadakane on ranks
        Invoking Larsson-Sadakane on ranks time: 00:00:00
        Sanity-checking and returning
      Building samples
      Reserving space for 12 sample suffixes
      Generating random suffixes
      QSorting 12 sample offsets, eliminating duplicates
      QSorting sample offsets, eliminating duplicates time: 00:00:00
      Multikey QSorting 12 samples
        (Using difference cover)
        Multikey QSorting samples time: 00:00:00
      Calculating bucket sizes
      Splitting and merging
        Splitting and merging time: 00:00:00
      Avg bucket size: 16568 (target: 3106)
      Converting suffix-array elements to index image
      Allocating ftab, absorbFtab
      Entering Ebwt loop
      Getting block 1 of 1
        No samples; assembling all-inclusive block
        Sorting block of length 16568 for bucket 1
        (Using difference cover)
        Sorting block time: 00:00:00
      Returning block of 16569 for bucket 1
      Exited Ebwt loop
      fchr[A]: 0
      fchr[C]: 5124
      fchr[G]: 10305
      fchr[T]: 12474
      fchr[$]: 16568
      Exiting Ebwt::buildToDisk()
      Returning from initFromVector
      Wrote 4200050 bytes to primary EBWT file: genome.1.bt2
      Wrote 4148 bytes to secondary EBWT file: genome.2.bt2
      Re-opening _in1 and _in2 as input streams
      Returning from Ebwt constructor
      Headers:
          len: 16568
          bwtLen: 16569
          sz: 4142
          bwtSz: 4143
          lineRate: 6
          offRate: 4
          offMask: 0xfffffff0
          ftabChars: 10
          eftabLen: 20
          eftabSz: 80
          ftabLen: 1048577
          ftabSz: 4194308
          offsLen: 1036
          offsSz: 4144
          lineSz: 64
          sideSz: 64
          sideBwtSz: 48
          sideBwtLen: 192
          numSides: 87
          numLines: 87
          ebwtTotLen: 5568
          ebwtTotSz: 5568
          color: 0
          reverse: 0
      Total time for call to driver() for forward index: 00:00:00
      Reading reference sizes
        Time reading reference sizes: 00:00:00
      Calculating joined length
      Writing header
      Reserving space for joined string
      Joining reference sequences
        Time to join reference sequences: 00:00:00
        Time to reverse reference sequence: 00:00:00
      bmax according to bmaxDivN setting: 4142
      Using parameters --bmax 3107 --dcv 1024
        Doing ahead-of-time memory usage test
        Passed!  Constructing with these parameters: --bmax 3107 --dcv 1024
      Constructing suffix-array element generator
      Building DifferenceCoverSample
        Building sPrime
        Building sPrimeOrder
        V-Sorting samples
        V-Sorting samples time: 00:00:00
        Allocating rank array
        Ranking v-sort output
        Ranking v-sort output time: 00:00:00
        Invoking Larsson-Sadakane on ranks
        Invoking Larsson-Sadakane on ranks time: 00:00:00
        Sanity-checking and returning
      Building samples
      Reserving space for 12 sample suffixes
      Generating random suffixes
      QSorting 12 sample offsets, eliminating duplicates
      QSorting sample offsets, eliminating duplicates time: 00:00:00
      Multikey QSorting 12 samples
        (Using difference cover)
        Multikey QSorting samples time: 00:00:00
      Calculating bucket sizes
      Splitting and merging
        Splitting and merging time: 00:00:00
      Avg bucket size: 16568 (target: 3106)
      Converting suffix-array elements to index image
      Allocating ftab, absorbFtab
      Entering Ebwt loop
      Getting block 1 of 1
        No samples; assembling all-inclusive block
        Sorting block of length 16568 for bucket 1
        (Using difference cover)
        Sorting block time: 00:00:00
      Returning block of 16569 for bucket 1
      Exited Ebwt loop
      fchr[A]: 0
      fchr[C]: 5124
      fchr[G]: 10305
      fchr[T]: 12474
      fchr[$]: 16568
      Exiting Ebwt::buildToDisk()
      Returning from initFromVector
      Wrote 4200050 bytes to primary EBWT file: genome.rev.1.bt2
      Wrote 4148 bytes to secondary EBWT file: genome.rev.2.bt2
      Re-opening _in1 and _in2 as input streams
      Returning from Ebwt constructor
      Headers:
          len: 16568
          bwtLen: 16569
          sz: 4142
          bwtSz: 4143
          lineRate: 6
          offRate: 4
          offMask: 0xfffffff0
          ftabChars: 10
          eftabLen: 20
          eftabSz: 80
          ftabLen: 1048577
          ftabSz: 4194308
          offsLen: 1036
          offsSz: 4144
          lineSz: 64
          sideSz: 64
          sideBwtSz: 48
          sideBwtLen: 192
          numSides: 87
          numLines: 87
          ebwtTotLen: 5568
          ebwtTotSz: 5568
          color: 0
          reverse: 1
      Total time for backward call to driver() for mirror index: 00:00:00
      

    Job Parameters:

    • Job parameter Parameter value
      library {"__current_case__": 1, "aligned_file": "false", "input_1": {"values": [{"id": 2059702, "src": "hda"}]}, "input_2": {"values": [{"id": 2059710, "src": "hda"}]}, "paired_options": {"__current_case__": 1, "paired_options_selector": "no"}, "type": "paired", "unaligned_file": "false"}
      reference_genome {"__current_case__": 1, "own_file": {"values": [{"id": 2059719, "src": "hda"}]}, "source": "history"}
      rg {"__current_case__": 3, "rg_selector": "do_not_set"}
      analysis_type {"__current_case__": 0, "analysis_type_selector": "simple", "presets": "no_presets"}
      sam_options {"__current_case__": 1, "sam_options_selector": "no"}
      save_mapping_stats "false"
      chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
      dbkey "?"
      __input_ext "input"
  • ✅ bowtie2 (Test test against test.galaxyproject.org #2)

    Command Line:

    Exit Code:

    • 0

    Standard Error:

    • Building a SMALL index
      perl: warning: Setting locale failed.
      perl: warning: Please check that your locale settings:
      	LANGUAGE = (unset),
      	LC_ALL = (unset),
      	LANG = "en_US.UTF-8"
          are supported and installed on your system.
      perl: warning: Falling back to the standard locale ("C").
      100 reads; of these:
        100 (100.00%) were paired; of these:
          97 (97.00%) aligned concordantly 0 times
          3 (3.00%) aligned concordantly exactly 1 time
          0 (0.00%) aligned concordantly >1 times
          ----
          97 pairs aligned concordantly 0 times; of these:
            8 (8.25%) aligned discordantly 1 time
          ----
          89 pairs aligned 0 times concordantly or discordantly; of these:
            178 mates make up the pairs; of these:
              153 (85.96%) aligned 0 times
              25 (14.04%) aligned exactly 1 time
              0 (0.00%) aligned >1 times
      23.50% overall alignment rate
      

    Standard Output:

    • Settings:
        Output files: "genome.*.bt2"
        Line rate: 6 (line is 64 bytes)
        Lines per side: 1 (side is 64 bytes)
        Offset rate: 4 (one in 16)
        FTable chars: 10
        Strings: unpacked
        Max bucket size: default
        Max bucket size, sqrt multiplier: default
        Max bucket size, len divisor: 4
        Difference-cover sample period: 1024
        Endianness: little
        Actual local endianness: little
        Sanity checking: disabled
        Assertions: disabled
        Random seed: 0
        Sizeofs: void*:8, int:4, long:8, size_t:8
      Input files DNA, FASTA:
        /galaxy-repl/test/object_store_cache/6/6/2/dataset_66233eb3-9662-4e74-a14e-bafc9c647fb6.dat
      Reading reference sizes
        Time reading reference sizes: 00:00:00
      Calculating joined length
      Writing header
      Reserving space for joined string
      Joining reference sequences
        Time to join reference sequences: 00:00:00
      bmax according to bmaxDivN setting: 4142
      Using parameters --bmax 3107 --dcv 1024
        Doing ahead-of-time memory usage test
        Passed!  Constructing with these parameters: --bmax 3107 --dcv 1024
      Constructing suffix-array element generator
      Building DifferenceCoverSample
        Building sPrime
        Building sPrimeOrder
        V-Sorting samples
        V-Sorting samples time: 00:00:00
        Allocating rank array
        Ranking v-sort output
        Ranking v-sort output time: 00:00:00
        Invoking Larsson-Sadakane on ranks
        Invoking Larsson-Sadakane on ranks time: 00:00:00
        Sanity-checking and returning
      Building samples
      Reserving space for 12 sample suffixes
      Generating random suffixes
      QSorting 12 sample offsets, eliminating duplicates
      QSorting sample offsets, eliminating duplicates time: 00:00:00
      Multikey QSorting 12 samples
        (Using difference cover)
        Multikey QSorting samples time: 00:00:00
      Calculating bucket sizes
      Splitting and merging
        Splitting and merging time: 00:00:00
      Avg bucket size: 16568 (target: 3106)
      Converting suffix-array elements to index image
      Allocating ftab, absorbFtab
      Entering Ebwt loop
      Getting block 1 of 1
        No samples; assembling all-inclusive block
        Sorting block of length 16568 for bucket 1
        (Using difference cover)
        Sorting block time: 00:00:00
      Returning block of 16569 for bucket 1
      Exited Ebwt loop
      fchr[A]: 0
      fchr[C]: 5124
      fchr[G]: 10305
      fchr[T]: 12474
      fchr[$]: 16568
      Exiting Ebwt::buildToDisk()
      Returning from initFromVector
      Wrote 4200050 bytes to primary EBWT file: genome.1.bt2
      Wrote 4148 bytes to secondary EBWT file: genome.2.bt2
      Re-opening _in1 and _in2 as input streams
      Returning from Ebwt constructor
      Headers:
          len: 16568
          bwtLen: 16569
          sz: 4142
          bwtSz: 4143
          lineRate: 6
          offRate: 4
          offMask: 0xfffffff0
          ftabChars: 10
          eftabLen: 20
          eftabSz: 80
          ftabLen: 1048577
          ftabSz: 4194308
          offsLen: 1036
          offsSz: 4144
          lineSz: 64
          sideSz: 64
          sideBwtSz: 48
          sideBwtLen: 192
          numSides: 87
          numLines: 87
          ebwtTotLen: 5568
          ebwtTotSz: 5568
          color: 0
          reverse: 0
      Total time for call to driver() for forward index: 00:00:00
      Reading reference sizes
        Time reading reference sizes: 00:00:00
      Calculating joined length
      Writing header
      Reserving space for joined string
      Joining reference sequences
        Time to join reference sequences: 00:00:00
        Time to reverse reference sequence: 00:00:00
      bmax according to bmaxDivN setting: 4142
      Using parameters --bmax 3107 --dcv 1024
        Doing ahead-of-time memory usage test
        Passed!  Constructing with these parameters: --bmax 3107 --dcv 1024
      Constructing suffix-array element generator
      Building DifferenceCoverSample
        Building sPrime
        Building sPrimeOrder
        V-Sorting samples
        V-Sorting samples time: 00:00:00
        Allocating rank array
        Ranking v-sort output
        Ranking v-sort output time: 00:00:00
        Invoking Larsson-Sadakane on ranks
        Invoking Larsson-Sadakane on ranks time: 00:00:00
        Sanity-checking and returning
      Building samples
      Reserving space for 12 sample suffixes
      Generating random suffixes
      QSorting 12 sample offsets, eliminating duplicates
      QSorting sample offsets, eliminating duplicates time: 00:00:00
      Multikey QSorting 12 samples
        (Using difference cover)
        Multikey QSorting samples time: 00:00:00
      Calculating bucket sizes
      Splitting and merging
        Splitting and merging time: 00:00:00
      Avg bucket size: 16568 (target: 3106)
      Converting suffix-array elements to index image
      Allocating ftab, absorbFtab
      Entering Ebwt loop
      Getting block 1 of 1
        No samples; assembling all-inclusive block
        Sorting block of length 16568 for bucket 1
        (Using difference cover)
        Sorting block time: 00:00:00
      Returning block of 16569 for bucket 1
      Exited Ebwt loop
      fchr[A]: 0
      fchr[C]: 5124
      fchr[G]: 10305
      fchr[T]: 12474
      fchr[$]: 16568
      Exiting Ebwt::buildToDisk()
      Returning from initFromVector
      Wrote 4200050 bytes to primary EBWT file: genome.rev.1.bt2
      Wrote 4148 bytes to secondary EBWT file: genome.rev.2.bt2
      Re-opening _in1 and _in2 as input streams
      Returning from Ebwt constructor
      Headers:
          len: 16568
          bwtLen: 16569
          sz: 4142
          bwtSz: 4143
          lineRate: 6
          offRate: 4
          offMask: 0xfffffff0
          ftabChars: 10
          eftabLen: 20
          eftabSz: 80
          ftabLen: 1048577
          ftabSz: 4194308
          offsLen: 1036
          offsSz: 4144
          lineSz: 64
          sideSz: 64
          sideBwtSz: 48
          sideBwtLen: 192
          numSides: 87
          numLines: 87
          ebwtTotLen: 5568
          ebwtTotSz: 5568
          color: 0
          reverse: 1
      Total time for backward call to driver() for mirror index: 00:00:00
      

    Job Parameters:

    • Job parameter Parameter value
      library {"__current_case__": 2, "aligned_file": "false", "input_1": {"values": [{"id": 15162, "src": "hdca"}]}, "paired_options": {"__current_case__": 1, "paired_options_selector": "no"}, "type": "paired_collection", "unaligned_file": "true"}
      reference_genome {"__current_case__": 1, "own_file": {"values": [{"id": 2059719, "src": "hda"}]}, "source": "history"}
      rg {"__current_case__": 3, "rg_selector": "do_not_set"}
      analysis_type {"__current_case__": 0, "analysis_type_selector": "simple", "presets": "no_presets"}
      sam_options {"__current_case__": 1, "sam_options_selector": "no"}
      save_mapping_stats "false"
      chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
      dbkey "?"
      __input_ext "input"
  • ✅ bowtie2 (Test Test Prokka 1.14.6+galaxy1 #3)

    Command Line:

    Exit Code:

    • 0

    Standard Error:

    • Building a SMALL index
      perl: warning: Setting locale failed.
      perl: warning: Please check that your locale settings:
      	LANGUAGE = (unset),
      	LC_ALL = (unset),
      	LANG = "en_US.UTF-8"
          are supported and installed on your system.
      perl: warning: Falling back to the standard locale ("C").
      100 reads; of these:
        100 (100.00%) were paired; of these:
          97 (97.00%) aligned concordantly 0 times
          3 (3.00%) aligned concordantly exactly 1 time
          0 (0.00%) aligned concordantly >1 times
          ----
          97 pairs aligned concordantly 0 times; of these:
            8 (8.25%) aligned discordantly 1 time
          ----
          89 pairs aligned 0 times concordantly or discordantly; of these:
            178 mates make up the pairs; of these:
              153 (85.96%) aligned 0 times
              25 (14.04%) aligned exactly 1 time
              0 (0.00%) aligned >1 times
      23.50% overall alignment rate
      

    Standard Output:

    • Settings:
        Output files: "genome.*.bt2"
        Line rate: 6 (line is 64 bytes)
        Lines per side: 1 (side is 64 bytes)
        Offset rate: 4 (one in 16)
        FTable chars: 10
        Strings: unpacked
        Max bucket size: default
        Max bucket size, sqrt multiplier: default
        Max bucket size, len divisor: 4
        Difference-cover sample period: 1024
        Endianness: little
        Actual local endianness: little
        Sanity checking: disabled
        Assertions: disabled
        Random seed: 0
        Sizeofs: void*:8, int:4, long:8, size_t:8
      Input files DNA, FASTA:
        /galaxy-repl/test/object_store_cache/6/6/2/dataset_66233eb3-9662-4e74-a14e-bafc9c647fb6.dat
      Reading reference sizes
        Time reading reference sizes: 00:00:00
      Calculating joined length
      Writing header
      Reserving space for joined string
      Joining reference sequences
        Time to join reference sequences: 00:00:00
      bmax according to bmaxDivN setting: 4142
      Using parameters --bmax 3107 --dcv 1024
        Doing ahead-of-time memory usage test
        Passed!  Constructing with these parameters: --bmax 3107 --dcv 1024
      Constructing suffix-array element generator
      Building DifferenceCoverSample
        Building sPrime
        Building sPrimeOrder
        V-Sorting samples
        V-Sorting samples time: 00:00:00
        Allocating rank array
        Ranking v-sort output
        Ranking v-sort output time: 00:00:00
        Invoking Larsson-Sadakane on ranks
        Invoking Larsson-Sadakane on ranks time: 00:00:00
        Sanity-checking and returning
      Building samples
      Reserving space for 12 sample suffixes
      Generating random suffixes
      QSorting 12 sample offsets, eliminating duplicates
      QSorting sample offsets, eliminating duplicates time: 00:00:00
      Multikey QSorting 12 samples
        (Using difference cover)
        Multikey QSorting samples time: 00:00:00
      Calculating bucket sizes
      Splitting and merging
        Splitting and merging time: 00:00:00
      Avg bucket size: 16568 (target: 3106)
      Converting suffix-array elements to index image
      Allocating ftab, absorbFtab
      Entering Ebwt loop
      Getting block 1 of 1
        No samples; assembling all-inclusive block
        Sorting block of length 16568 for bucket 1
        (Using difference cover)
        Sorting block time: 00:00:00
      Returning block of 16569 for bucket 1
      Exited Ebwt loop
      fchr[A]: 0
      fchr[C]: 5124
      fchr[G]: 10305
      fchr[T]: 12474
      fchr[$]: 16568
      Exiting Ebwt::buildToDisk()
      Returning from initFromVector
      Wrote 4200050 bytes to primary EBWT file: genome.1.bt2
      Wrote 4148 bytes to secondary EBWT file: genome.2.bt2
      Re-opening _in1 and _in2 as input streams
      Returning from Ebwt constructor
      Headers:
          len: 16568
          bwtLen: 16569
          sz: 4142
          bwtSz: 4143
          lineRate: 6
          offRate: 4
          offMask: 0xfffffff0
          ftabChars: 10
          eftabLen: 20
          eftabSz: 80
          ftabLen: 1048577
          ftabSz: 4194308
          offsLen: 1036
          offsSz: 4144
          lineSz: 64
          sideSz: 64
          sideBwtSz: 48
          sideBwtLen: 192
          numSides: 87
          numLines: 87
          ebwtTotLen: 5568
          ebwtTotSz: 5568
          color: 0
          reverse: 0
      Total time for call to driver() for forward index: 00:00:01
      Reading reference sizes
        Time reading reference sizes: 00:00:00
      Calculating joined length
      Writing header
      Reserving space for joined string
      Joining reference sequences
        Time to join reference sequences: 00:00:00
        Time to reverse reference sequence: 00:00:00
      bmax according to bmaxDivN setting: 4142
      Using parameters --bmax 3107 --dcv 1024
        Doing ahead-of-time memory usage test
        Passed!  Constructing with these parameters: --bmax 3107 --dcv 1024
      Constructing suffix-array element generator
      Building DifferenceCoverSample
        Building sPrime
        Building sPrimeOrder
        V-Sorting samples
        V-Sorting samples time: 00:00:00
        Allocating rank array
        Ranking v-sort output
        Ranking v-sort output time: 00:00:00
        Invoking Larsson-Sadakane on ranks
        Invoking Larsson-Sadakane on ranks time: 00:00:00
        Sanity-checking and returning
      Building samples
      Reserving space for 12 sample suffixes
      Generating random suffixes
      QSorting 12 sample offsets, eliminating duplicates
      QSorting sample offsets, eliminating duplicates time: 00:00:00
      Multikey QSorting 12 samples
        (Using difference cover)
        Multikey QSorting samples time: 00:00:00
      Calculating bucket sizes
      Splitting and merging
        Splitting and merging time: 00:00:00
      Avg bucket size: 16568 (target: 3106)
      Converting suffix-array elements to index image
      Allocating ftab, absorbFtab
      Entering Ebwt loop
      Getting block 1 of 1
        No samples; assembling all-inclusive block
        Sorting block of length 16568 for bucket 1
        (Using difference cover)
        Sorting block time: 00:00:00
      Returning block of 16569 for bucket 1
      Exited Ebwt loop
      fchr[A]: 0
      fchr[C]: 5124
      fchr[G]: 10305
      fchr[T]: 12474
      fchr[$]: 16568
      Exiting Ebwt::buildToDisk()
      Returning from initFromVector
      Wrote 4200050 bytes to primary EBWT file: genome.rev.1.bt2
      Wrote 4148 bytes to secondary EBWT file: genome.rev.2.bt2
      Re-opening _in1 and _in2 as input streams
      Returning from Ebwt constructor
      Headers:
          len: 16568
          bwtLen: 16569
          sz: 4142
          bwtSz: 4143
          lineRate: 6
          offRate: 4
          offMask: 0xfffffff0
          ftabChars: 10
          eftabLen: 20
          eftabSz: 80
          ftabLen: 1048577
          ftabSz: 4194308
          offsLen: 1036
          offsSz: 4144
          lineSz: 64
          sideSz: 64
          sideBwtSz: 48
          sideBwtLen: 192
          numSides: 87
          numLines: 87
          ebwtTotLen: 5568
          ebwtTotSz: 5568
          color: 0
          reverse: 1
      Total time for backward call to driver() for mirror index: 00:00:01
      

    Job Parameters:

    • Job parameter Parameter value
      library {"__current_case__": 1, "aligned_file": "false", "input_1": {"values": [{"id": 2059702, "src": "hda"}]}, "input_2": {"values": [{"id": 2059710, "src": "hda"}]}, "paired_options": {"__current_case__": 1, "paired_options_selector": "no"}, "type": "paired", "unaligned_file": "false"}
      reference_genome {"__current_case__": 1, "own_file": {"values": [{"id": 2059719, "src": "hda"}]}, "source": "history"}
      rg {"CN": "", "DS": "", "DT": "", "FO": null, "KS": "", "PG": "", "PI": "", "PL": "CAPILLARY", "PU": null, "__current_case__": 1, "read_group_id_conditional": {"ID": "rg1", "__current_case__": 1, "do_auto_name": "false"}, "read_group_lb_conditional": {"LB": null, "__current_case__": 1, "do_auto_name": "false"}, "read_group_sm_conditional": {"SM": "", "__current_case__": 1, "do_auto_name": "false"}, "rg_selector": "set"}
      analysis_type {"__current_case__": 0, "analysis_type_selector": "simple", "presets": "no_presets"}
      sam_options {"__current_case__": 1, "sam_options_selector": "no"}
      save_mapping_stats "false"
      chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
      dbkey "?"
      __input_ext "input"
  • ✅ bowtie2 (Test Test roary 3.13.0+galaxy2 #4)

    Command Line:

    Exit Code:

    • 0

    Standard Error:

    • Building a SMALL index
      

    Standard Output:

    • Settings:
        Output files: "genome.*.bt2"
        Line rate: 6 (line is 64 bytes)
        Lines per side: 1 (side is 64 bytes)
        Offset rate: 4 (one in 16)
        FTable chars: 10
        Strings: unpacked
        Max bucket size: default
        Max bucket size, sqrt multiplier: default
        Max bucket size, len divisor: 4
        Difference-cover sample period: 1024
        Endianness: little
        Actual local endianness: little
        Sanity checking: disabled
        Assertions: disabled
        Random seed: 0
        Sizeofs: void*:8, int:4, long:8, size_t:8
      Input files DNA, FASTA:
        /galaxy-repl/test/object_store_cache/6/6/2/dataset_66233eb3-9662-4e74-a14e-bafc9c647fb6.dat
      Reading reference sizes
        Time reading reference sizes: 00:00:00
      Calculating joined length
      Writing header
      Reserving space for joined string
      Joining reference sequences
        Time to join reference sequences: 00:00:00
      bmax according to bmaxDivN setting: 4142
      Using parameters --bmax 3107 --dcv 1024
        Doing ahead-of-time memory usage test
        Passed!  Constructing with these parameters: --bmax 3107 --dcv 1024
      Constructing suffix-array element generator
      Building DifferenceCoverSample
        Building sPrime
        Building sPrimeOrder
        V-Sorting samples
        V-Sorting samples time: 00:00:00
        Allocating rank array
        Ranking v-sort output
        Ranking v-sort output time: 00:00:00
        Invoking Larsson-Sadakane on ranks
        Invoking Larsson-Sadakane on ranks time: 00:00:00
        Sanity-checking and returning
      Building samples
      Reserving space for 12 sample suffixes
      Generating random suffixes
      QSorting 12 sample offsets, eliminating duplicates
      QSorting sample offsets, eliminating duplicates time: 00:00:00
      Multikey QSorting 12 samples
        (Using difference cover)
        Multikey QSorting samples time: 00:00:00
      Calculating bucket sizes
      Splitting and merging
        Splitting and merging time: 00:00:00
      Avg bucket size: 16568 (target: 3106)
      Converting suffix-array elements to index image
      Allocating ftab, absorbFtab
      Entering Ebwt loop
      Getting block 1 of 1
        No samples; assembling all-inclusive block
        Sorting block of length 16568 for bucket 1
        (Using difference cover)
        Sorting block time: 00:00:00
      Returning block of 16569 for bucket 1
      Exited Ebwt loop
      fchr[A]: 0
      fchr[C]: 5124
      fchr[G]: 10305
      fchr[T]: 12474
      fchr[$]: 16568
      Exiting Ebwt::buildToDisk()
      Returning from initFromVector
      Wrote 4200050 bytes to primary EBWT file: genome.1.bt2
      Wrote 4148 bytes to secondary EBWT file: genome.2.bt2
      Re-opening _in1 and _in2 as input streams
      Returning from Ebwt constructor
      Headers:
          len: 16568
          bwtLen: 16569
          sz: 4142
          bwtSz: 4143
          lineRate: 6
          offRate: 4
          offMask: 0xfffffff0
          ftabChars: 10
          eftabLen: 20
          eftabSz: 80
          ftabLen: 1048577
          ftabSz: 4194308
          offsLen: 1036
          offsSz: 4144
          lineSz: 64
          sideSz: 64
          sideBwtSz: 48
          sideBwtLen: 192
          numSides: 87
          numLines: 87
          ebwtTotLen: 5568
          ebwtTotSz: 5568
          color: 0
          reverse: 0
      Total time for call to driver() for forward index: 00:00:00
      Reading reference sizes
        Time reading reference sizes: 00:00:00
      Calculating joined length
      Writing header
      Reserving space for joined string
      Joining reference sequences
        Time to join reference sequences: 00:00:00
        Time to reverse reference sequence: 00:00:00
      bmax according to bmaxDivN setting: 4142
      Using parameters --bmax 3107 --dcv 1024
        Doing ahead-of-time memory usage test
        Passed!  Constructing with these parameters: --bmax 3107 --dcv 1024
      Constructing suffix-array element generator
      Building DifferenceCoverSample
        Building sPrime
        Building sPrimeOrder
        V-Sorting samples
        V-Sorting samples time: 00:00:00
        Allocating rank array
        Ranking v-sort output
        Ranking v-sort output time: 00:00:00
        Invoking Larsson-Sadakane on ranks
        Invoking Larsson-Sadakane on ranks time: 00:00:00
        Sanity-checking and returning
      Building samples
      Reserving space for 12 sample suffixes
      Generating random suffixes
      QSorting 12 sample offsets, eliminating duplicates
      QSorting sample offsets, eliminating duplicates time: 00:00:00
      Multikey QSorting 12 samples
        (Using difference cover)
        Multikey QSorting samples time: 00:00:00
      Calculating bucket sizes
      Splitting and merging
        Splitting and merging time: 00:00:00
      Avg bucket size: 16568 (target: 3106)
      Converting suffix-array elements to index image
      Allocating ftab, absorbFtab
      Entering Ebwt loop
      Getting block 1 of 1
        No samples; assembling all-inclusive block
        Sorting block of length 16568 for bucket 1
        (Using difference cover)
        Sorting block time: 00:00:00
      Returning block of 16569 for bucket 1
      Exited Ebwt loop
      fchr[A]: 0
      fchr[C]: 5124
      fchr[G]: 10305
      fchr[T]: 12474
      fchr[$]: 16568
      Exiting Ebwt::buildToDisk()
      Returning from initFromVector
      Wrote 4200050 bytes to primary EBWT file: genome.rev.1.bt2
      Wrote 4148 bytes to secondary EBWT file: genome.rev.2.bt2
      Re-opening _in1 and _in2 as input streams
      Returning from Ebwt constructor
      Headers:
          len: 16568
          bwtLen: 16569
          sz: 4142
          bwtSz: 4143
          lineRate: 6
          offRate: 4
          offMask: 0xfffffff0
          ftabChars: 10
          eftabLen: 20
          eftabSz: 80
          ftabLen: 1048577
          ftabSz: 4194308
          offsLen: 1036
          offsSz: 4144
          lineSz: 64
          sideSz: 64
          sideBwtSz: 48
          sideBwtLen: 192
          numSides: 87
          numLines: 87
          ebwtTotLen: 5568
          ebwtTotSz: 5568
          color: 0
          reverse: 1
      Total time for backward call to driver() for mirror index: 00:00:00
      

    Job Parameters:

    • Job parameter Parameter value
      library {"__current_case__": 1, "aligned_file": "false", "input_1": {"values": [{"id": 2059702, "src": "hda"}]}, "input_2": {"values": [{"id": 2059710, "src": "hda"}]}, "paired_options": {"__current_case__": 1, "paired_options_selector": "no"}, "type": "paired", "unaligned_file": "false"}
      reference_genome {"__current_case__": 1, "own_file": {"values": [{"id": 2059719, "src": "hda"}]}, "source": "history"}
      rg {"__current_case__": 3, "rg_selector": "do_not_set"}
      analysis_type {"__current_case__": 0, "analysis_type_selector": "simple", "presets": "no_presets"}
      sam_options {"__current_case__": 1, "sam_options_selector": "no"}
      save_mapping_stats "true"
      chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
      dbkey "?"
      __input_ext "input"
  • ✅ bowtie2 (Test Test toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1 #5)

    Command Line:

    Exit Code:

    • 0

    Standard Error:

    • Building a SMALL index
      perl: warning: Setting locale failed.
      perl: warning: Please check that your locale settings:
      	LANGUAGE = (unset),
      	LC_ALL = (unset),
      	LANG = "en_US.UTF-8"
          are supported and installed on your system.
      perl: warning: Falling back to the standard locale ("C").
      3 reads; of these:
        3 (100.00%) were paired; of these:
          2 (66.67%) aligned concordantly 0 times
          1 (33.33%) aligned concordantly exactly 1 time
          0 (0.00%) aligned concordantly >1 times
          ----
          2 pairs aligned concordantly 0 times; of these:
            0 (0.00%) aligned discordantly 1 time
          ----
          2 pairs aligned 0 times concordantly or discordantly; of these:
            4 mates make up the pairs; of these:
              3 (75.00%) aligned 0 times
              1 (25.00%) aligned exactly 1 time
              0 (0.00%) aligned >1 times
      50.00% overall alignment rate
      

    Standard Output:

    • Settings:
        Output files: "genome.*.bt2"
        Line rate: 6 (line is 64 bytes)
        Lines per side: 1 (side is 64 bytes)
        Offset rate: 4 (one in 16)
        FTable chars: 10
        Strings: unpacked
        Max bucket size: default
        Max bucket size, sqrt multiplier: default
        Max bucket size, len divisor: 4
        Difference-cover sample period: 1024
        Endianness: little
        Actual local endianness: little
        Sanity checking: disabled
        Assertions: disabled
        Random seed: 0
        Sizeofs: void*:8, int:4, long:8, size_t:8
      Input files DNA, FASTA:
        /galaxy-repl/test/object_store_cache/6/6/2/dataset_66233eb3-9662-4e74-a14e-bafc9c647fb6.dat
      Reading reference sizes
        Time reading reference sizes: 00:00:00
      Calculating joined length
      Writing header
      Reserving space for joined string
      Joining reference sequences
        Time to join reference sequences: 00:00:00
      bmax according to bmaxDivN setting: 4142
      Using parameters --bmax 3107 --dcv 1024
        Doing ahead-of-time memory usage test
        Passed!  Constructing with these parameters: --bmax 3107 --dcv 1024
      Constructing suffix-array element generator
      Building DifferenceCoverSample
        Building sPrime
        Building sPrimeOrder
        V-Sorting samples
        V-Sorting samples time: 00:00:00
        Allocating rank array
        Ranking v-sort output
        Ranking v-sort output time: 00:00:00
        Invoking Larsson-Sadakane on ranks
        Invoking Larsson-Sadakane on ranks time: 00:00:00
        Sanity-checking and returning
      Building samples
      Reserving space for 12 sample suffixes
      Generating random suffixes
      QSorting 12 sample offsets, eliminating duplicates
      QSorting sample offsets, eliminating duplicates time: 00:00:00
      Multikey QSorting 12 samples
        (Using difference cover)
        Multikey QSorting samples time: 00:00:00
      Calculating bucket sizes
      Splitting and merging
        Splitting and merging time: 00:00:00
      Avg bucket size: 16568 (target: 3106)
      Converting suffix-array elements to index image
      Allocating ftab, absorbFtab
      Entering Ebwt loop
      Getting block 1 of 1
        No samples; assembling all-inclusive block
        Sorting block of length 16568 for bucket 1
        (Using difference cover)
        Sorting block time: 00:00:00
      Returning block of 16569 for bucket 1
      Exited Ebwt loop
      fchr[A]: 0
      fchr[C]: 5124
      fchr[G]: 10305
      fchr[T]: 12474
      fchr[$]: 16568
      Exiting Ebwt::buildToDisk()
      Returning from initFromVector
      Wrote 4200050 bytes to primary EBWT file: genome.1.bt2
      Wrote 4148 bytes to secondary EBWT file: genome.2.bt2
      Re-opening _in1 and _in2 as input streams
      Returning from Ebwt constructor
      Headers:
          len: 16568
          bwtLen: 16569
          sz: 4142
          bwtSz: 4143
          lineRate: 6
          offRate: 4
          offMask: 0xfffffff0
          ftabChars: 10
          eftabLen: 20
          eftabSz: 80
          ftabLen: 1048577
          ftabSz: 4194308
          offsLen: 1036
          offsSz: 4144
          lineSz: 64
          sideSz: 64
          sideBwtSz: 48
          sideBwtLen: 192
          numSides: 87
          numLines: 87
          ebwtTotLen: 5568
          ebwtTotSz: 5568
          color: 0
          reverse: 0
      Total time for call to driver() for forward index: 00:00:00
      Reading reference sizes
        Time reading reference sizes: 00:00:00
      Calculating joined length
      Writing header
      Reserving space for joined string
      Joining reference sequences
        Time to join reference sequences: 00:00:00
        Time to reverse reference sequence: 00:00:00
      bmax according to bmaxDivN setting: 4142
      Using parameters --bmax 3107 --dcv 1024
        Doing ahead-of-time memory usage test
        Passed!  Constructing with these parameters: --bmax 3107 --dcv 1024
      Constructing suffix-array element generator
      Building DifferenceCoverSample
        Building sPrime
        Building sPrimeOrder
        V-Sorting samples
        V-Sorting samples time: 00:00:00
        Allocating rank array
        Ranking v-sort output
        Ranking v-sort output time: 00:00:00
        Invoking Larsson-Sadakane on ranks
        Invoking Larsson-Sadakane on ranks time: 00:00:00
        Sanity-checking and returning
      Building samples
      Reserving space for 12 sample suffixes
      Generating random suffixes
      QSorting 12 sample offsets, eliminating duplicates
      QSorting sample offsets, eliminating duplicates time: 00:00:00
      Multikey QSorting 12 samples
        (Using difference cover)
        Multikey QSorting samples time: 00:00:00
      Calculating bucket sizes
      Splitting and merging
        Splitting and merging time: 00:00:00
      Avg bucket size: 16568 (target: 3106)
      Converting suffix-array elements to index image
      Allocating ftab, absorbFtab
      Entering Ebwt loop
      Getting block 1 of 1
        No samples; assembling all-inclusive block
        Sorting block of length 16568 for bucket 1
        (Using difference cover)
        Sorting block time: 00:00:00
      Returning block of 16569 for bucket 1
      Exited Ebwt loop
      fchr[A]: 0
      fchr[C]: 5124
      fchr[G]: 10305
      fchr[T]: 12474
      fchr[$]: 16568
      Exiting Ebwt::buildToDisk()
      Returning from initFromVector
      Wrote 4200050 bytes to primary EBWT file: genome.rev.1.bt2
      Wrote 4148 bytes to secondary EBWT file: genome.rev.2.bt2
      Re-opening _in1 and _in2 as input streams
      Returning from Ebwt constructor
      Headers:
          len: 16568
          bwtLen: 16569
          sz: 4142
          bwtSz: 4143
          lineRate: 6
          offRate: 4
          offMask: 0xfffffff0
          ftabChars: 10
          eftabLen: 20
          eftabSz: 80
          ftabLen: 1048577
          ftabSz: 4194308
          offsLen: 1036
          offsSz: 4144
          lineSz: 64
          sideSz: 64
          sideBwtSz: 48
          sideBwtLen: 192
          numSides: 87
          numLines: 87
          ebwtTotLen: 5568
          ebwtTotSz: 5568
          color: 0
          reverse: 1
      Total time for backward call to driver() for mirror index: 00:00:00
      

    Job Parameters:

    • Job parameter Parameter value
      library {"__current_case__": 3, "aligned_file": "false", "input_1": {"values": [{"id": 2059695, "src": "hda"}]}, "paired_options": {"__current_case__": 1, "paired_options_selector": "no"}, "type": "paired_interleaved", "unaligned_file": "false"}
      reference_genome {"__current_case__": 1, "own_file": {"values": [{"id": 2059719, "src": "hda"}]}, "source": "history"}
      rg {"CN": "", "DS": "", "DT": "", "FO": null, "KS": "", "PG": "", "PI": "", "PL": "CAPILLARY", "PU": null, "__current_case__": 1, "read_group_id_conditional": {"ID": "rg1", "__current_case__": 1, "do_auto_name": "false"}, "read_group_lb_conditional": {"LB": null, "__current_case__": 1, "do_auto_name": "false"}, "read_group_sm_conditional": {"SM": "", "__current_case__": 1, "do_auto_name": "false"}, "rg_selector": "set"}
      analysis_type {"__current_case__": 0, "analysis_type_selector": "simple", "presets": "no_presets"}
      sam_options {"__current_case__": 1, "sam_options_selector": "no"}
      save_mapping_stats "false"
      chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
      dbkey "?"
      __input_ext "input"
  • ✅ bowtie2 (Test Test trinotate 3.2.2+galaxy0 #6)

    Command Line:

    Exit Code:

    • 0

    Standard Error:

    • Building a SMALL index
      perl: warning: Setting locale failed.
      perl: warning: Please check that your locale settings:
      	LANGUAGE = (unset),
      	LC_ALL = (unset),
      	LANG = "en_US.UTF-8"
          are supported and installed on your system.
      perl: warning: Falling back to the standard locale ("C").
      100 reads; of these:
        100 (100.00%) were paired; of these:
          97 (97.00%) aligned concordantly 0 times
          3 (3.00%) aligned concordantly exactly 1 time
          0 (0.00%) aligned concordantly >1 times
          ----
          97 pairs aligned concordantly 0 times; of these:
            8 (8.25%) aligned discordantly 1 time
          ----
          89 pairs aligned 0 times concordantly or discordantly; of these:
            178 mates make up the pairs; of these:
              153 (85.96%) aligned 0 times
              25 (14.04%) aligned exactly 1 time
              0 (0.00%) aligned >1 times
      23.50% overall alignment rate
      

    Standard Output:

    • Settings:
        Output files: "genome.*.bt2"
        Line rate: 6 (line is 64 bytes)
        Lines per side: 1 (side is 64 bytes)
        Offset rate: 4 (one in 16)
        FTable chars: 10
        Strings: unpacked
        Max bucket size: default
        Max bucket size, sqrt multiplier: default
        Max bucket size, len divisor: 4
        Difference-cover sample period: 1024
        Endianness: little
        Actual local endianness: little
        Sanity checking: disabled
        Assertions: disabled
        Random seed: 0
        Sizeofs: void*:8, int:4, long:8, size_t:8
      Input files DNA, FASTA:
        /galaxy-repl/test/object_store_cache/6/6/2/dataset_66233eb3-9662-4e74-a14e-bafc9c647fb6.dat
      Reading reference sizes
        Time reading reference sizes: 00:00:00
      Calculating joined length
      Writing header
      Reserving space for joined string
      Joining reference sequences
        Time to join reference sequences: 00:00:00
      bmax according to bmaxDivN setting: 4142
      Using parameters --bmax 3107 --dcv 1024
        Doing ahead-of-time memory usage test
        Passed!  Constructing with these parameters: --bmax 3107 --dcv 1024
      Constructing suffix-array element generator
      Building DifferenceCoverSample
        Building sPrime
        Building sPrimeOrder
        V-Sorting samples
        V-Sorting samples time: 00:00:00
        Allocating rank array
        Ranking v-sort output
        Ranking v-sort output time: 00:00:00
        Invoking Larsson-Sadakane on ranks
        Invoking Larsson-Sadakane on ranks time: 00:00:00
        Sanity-checking and returning
      Building samples
      Reserving space for 12 sample suffixes
      Generating random suffixes
      QSorting 12 sample offsets, eliminating duplicates
      QSorting sample offsets, eliminating duplicates time: 00:00:00
      Multikey QSorting 12 samples
        (Using difference cover)
        Multikey QSorting samples time: 00:00:00
      Calculating bucket sizes
      Splitting and merging
        Splitting and merging time: 00:00:00
      Avg bucket size: 16568 (target: 3106)
      Converting suffix-array elements to index image
      Allocating ftab, absorbFtab
      Entering Ebwt loop
      Getting block 1 of 1
        No samples; assembling all-inclusive block
        Sorting block of length 16568 for bucket 1
        (Using difference cover)
        Sorting block time: 00:00:00
      Returning block of 16569 for bucket 1
      Exited Ebwt loop
      fchr[A]: 0
      fchr[C]: 5124
      fchr[G]: 10305
      fchr[T]: 12474
      fchr[$]: 16568
      Exiting Ebwt::buildToDisk()
      Returning from initFromVector
      Wrote 4200050 bytes to primary EBWT file: genome.1.bt2
      Wrote 4148 bytes to secondary EBWT file: genome.2.bt2
      Re-opening _in1 and _in2 as input streams
      Returning from Ebwt constructor
      Headers:
          len: 16568
          bwtLen: 16569
          sz: 4142
          bwtSz: 4143
          lineRate: 6
          offRate: 4
          offMask: 0xfffffff0
          ftabChars: 10
          eftabLen: 20
          eftabSz: 80
          ftabLen: 1048577
          ftabSz: 4194308
          offsLen: 1036
          offsSz: 4144
          lineSz: 64
          sideSz: 64
          sideBwtSz: 48
          sideBwtLen: 192
          numSides: 87
          numLines: 87
          ebwtTotLen: 5568
          ebwtTotSz: 5568
          color: 0
          reverse: 0
      Total time for call to driver() for forward index: 00:00:00
      Reading reference sizes
        Time reading reference sizes: 00:00:00
      Calculating joined length
      Writing header
      Reserving space for joined string
      Joining reference sequences
        Time to join reference sequences: 00:00:00
        Time to reverse reference sequence: 00:00:00
      bmax according to bmaxDivN setting: 4142
      Using parameters --bmax 3107 --dcv 1024
        Doing ahead-of-time memory usage test
        Passed!  Constructing with these parameters: --bmax 3107 --dcv 1024
      Constructing suffix-array element generator
      Building DifferenceCoverSample
        Building sPrime
        Building sPrimeOrder
        V-Sorting samples
        V-Sorting samples time: 00:00:00
        Allocating rank array
        Ranking v-sort output
        Ranking v-sort output time: 00:00:00
        Invoking Larsson-Sadakane on ranks
        Invoking Larsson-Sadakane on ranks time: 00:00:00
        Sanity-checking and returning
      Building samples
      Reserving space for 12 sample suffixes
      Generating random suffixes
      QSorting 12 sample offsets, eliminating duplicates
      QSorting sample offsets, eliminating duplicates time: 00:00:00
      Multikey QSorting 12 samples
        (Using difference cover)
        Multikey QSorting samples time: 00:00:00
      Calculating bucket sizes
      Splitting and merging
        Splitting and merging time: 00:00:00
      Avg bucket size: 16568 (target: 3106)
      Converting suffix-array elements to index image
      Allocating ftab, absorbFtab
      Entering Ebwt loop
      Getting block 1 of 1
        No samples; assembling all-inclusive block
        Sorting block of length 16568 for bucket 1
        (Using difference cover)
        Sorting block time: 00:00:00
      Returning block of 16569 for bucket 1
      Exited Ebwt loop
      fchr[A]: 0
      fchr[C]: 5124
      fchr[G]: 10305
      fchr[T]: 12474
      fchr[$]: 16568
      Exiting Ebwt::buildToDisk()
      Returning from initFromVector
      Wrote 4200050 bytes to primary EBWT file: genome.rev.1.bt2
      Wrote 4148 bytes to secondary EBWT file: genome.rev.2.bt2
      Re-opening _in1 and _in2 as input streams
      Returning from Ebwt constructor
      Headers:
          len: 16568
          bwtLen: 16569
          sz: 4142
          bwtSz: 4143
          lineRate: 6
          offRate: 4
          offMask: 0xfffffff0
          ftabChars: 10
          eftabLen: 20
          eftabSz: 80
          ftabLen: 1048577
          ftabSz: 4194308
          offsLen: 1036
          offsSz: 4144
          lineSz: 64
          sideSz: 64
          sideBwtSz: 48
          sideBwtLen: 192
          numSides: 87
          numLines: 87
          ebwtTotLen: 5568
          ebwtTotSz: 5568
          color: 0
          reverse: 1
      Total time for backward call to driver() for mirror index: 00:00:00
      

    Job Parameters:

    • Job parameter Parameter value
      library {"__current_case__": 1, "aligned_file": "false", "input_1": {"values": [{"id": 2059696, "src": "hda"}]}, "input_2": {"values": [{"id": 2059706, "src": "hda"}]}, "paired_options": {"__current_case__": 1, "paired_options_selector": "no"}, "type": "paired", "unaligned_file": "false"}
      reference_genome {"__current_case__": 1, "own_file": {"values": [{"id": 2059719, "src": "hda"}]}, "source": "history"}
      rg {"__current_case__": 3, "rg_selector": "do_not_set"}
      analysis_type {"__current_case__": 0, "analysis_type_selector": "simple", "presets": "no_presets"}
      sam_options {"__current_case__": 1, "sam_options_selector": "no"}
      save_mapping_stats "false"
      chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
      dbkey "?"
      __input_ext "input"
  • ✅ bowtie2 (Test Test pangolin 3.1.17+galaxy1 #7)

    Command Line:

    Exit Code:

    • 0

    Standard Error:

    • Building a SMALL index
      perl: warning: Setting locale failed.
      perl: warning: Please check that your locale settings:
      	LANGUAGE = (unset),
      	LC_ALL = (unset),
      	LANG = "en_US.UTF-8"
          are supported and installed on your system.
      perl: warning: Falling back to the standard locale ("C").
      100 reads; of these:
        100 (100.00%) were paired; of these:
          97 (97.00%) aligned concordantly 0 times
          3 (3.00%) aligned concordantly exactly 1 time
          0 (0.00%) aligned concordantly >1 times
          ----
          97 pairs aligned concordantly 0 times; of these:
            8 (8.25%) aligned discordantly 1 time
          ----
          89 pairs aligned 0 times concordantly or discordantly; of these:
            178 mates make up the pairs; of these:
              153 (85.96%) aligned 0 times
              25 (14.04%) aligned exactly 1 time
              0 (0.00%) aligned >1 times
      23.50% overall alignment rate
      

    Standard Output:

    • Settings:
        Output files: "genome.*.bt2"
        Line rate: 6 (line is 64 bytes)
        Lines per side: 1 (side is 64 bytes)
        Offset rate: 4 (one in 16)
        FTable chars: 10
        Strings: unpacked
        Max bucket size: default
        Max bucket size, sqrt multiplier: default
        Max bucket size, len divisor: 4
        Difference-cover sample period: 1024
        Endianness: little
        Actual local endianness: little
        Sanity checking: disabled
        Assertions: disabled
        Random seed: 0
        Sizeofs: void*:8, int:4, long:8, size_t:8
      Input files DNA, FASTA:
        /galaxy-repl/test/object_store_cache/6/6/2/dataset_66233eb3-9662-4e74-a14e-bafc9c647fb6.dat
      Reading reference sizes
        Time reading reference sizes: 00:00:00
      Calculating joined length
      Writing header
      Reserving space for joined string
      Joining reference sequences
        Time to join reference sequences: 00:00:00
      bmax according to bmaxDivN setting: 4142
      Using parameters --bmax 3107 --dcv 1024
        Doing ahead-of-time memory usage test
        Passed!  Constructing with these parameters: --bmax 3107 --dcv 1024
      Constructing suffix-array element generator
      Building DifferenceCoverSample
        Building sPrime
        Building sPrimeOrder
        V-Sorting samples
        V-Sorting samples time: 00:00:00
        Allocating rank array
        Ranking v-sort output
        Ranking v-sort output time: 00:00:00
        Invoking Larsson-Sadakane on ranks
        Invoking Larsson-Sadakane on ranks time: 00:00:00
        Sanity-checking and returning
      Building samples
      Reserving space for 12 sample suffixes
      Generating random suffixes
      QSorting 12 sample offsets, eliminating duplicates
      QSorting sample offsets, eliminating duplicates time: 00:00:00
      Multikey QSorting 12 samples
        (Using difference cover)
        Multikey QSorting samples time: 00:00:00
      Calculating bucket sizes
      Splitting and merging
        Splitting and merging time: 00:00:00
      Avg bucket size: 16568 (target: 3106)
      Converting suffix-array elements to index image
      Allocating ftab, absorbFtab
      Entering Ebwt loop
      Getting block 1 of 1
        No samples; assembling all-inclusive block
        Sorting block of length 16568 for bucket 1
        (Using difference cover)
        Sorting block time: 00:00:00
      Returning block of 16569 for bucket 1
      Exited Ebwt loop
      fchr[A]: 0
      fchr[C]: 5124
      fchr[G]: 10305
      fchr[T]: 12474
      fchr[$]: 16568
      Exiting Ebwt::buildToDisk()
      Returning from initFromVector
      Wrote 4200050 bytes to primary EBWT file: genome.1.bt2
      Wrote 4148 bytes to secondary EBWT file: genome.2.bt2
      Re-opening _in1 and _in2 as input streams
      Returning from Ebwt constructor
      Headers:
          len: 16568
          bwtLen: 16569
          sz: 4142
          bwtSz: 4143
          lineRate: 6
          offRate: 4
          offMask: 0xfffffff0
          ftabChars: 10
          eftabLen: 20
          eftabSz: 80
          ftabLen: 1048577
          ftabSz: 4194308
          offsLen: 1036
          offsSz: 4144
          lineSz: 64
          sideSz: 64
          sideBwtSz: 48
          sideBwtLen: 192
          numSides: 87
          numLines: 87
          ebwtTotLen: 5568
          ebwtTotSz: 5568
          color: 0
          reverse: 0
      Total time for call to driver() for forward index: 00:00:00
      Reading reference sizes
        Time reading reference sizes: 00:00:00
      Calculating joined length
      Writing header
      Reserving space for joined string
      Joining reference sequences
        Time to join reference sequences: 00:00:00
        Time to reverse reference sequence: 00:00:00
      bmax according to bmaxDivN setting: 4142
      Using parameters --bmax 3107 --dcv 1024
        Doing ahead-of-time memory usage test
        Passed!  Constructing with these parameters: --bmax 3107 --dcv 1024
      Constructing suffix-array element generator
      Building DifferenceCoverSample
        Building sPrime
        Building sPrimeOrder
        V-Sorting samples
        V-Sorting samples time: 00:00:00
        Allocating rank array
        Ranking v-sort output
        Ranking v-sort output time: 00:00:00
        Invoking Larsson-Sadakane on ranks
        Invoking Larsson-Sadakane on ranks time: 00:00:00
        Sanity-checking and returning
      Building samples
      Reserving space for 12 sample suffixes
      Generating random suffixes
      QSorting 12 sample offsets, eliminating duplicates
      QSorting sample offsets, eliminating duplicates time: 00:00:00
      Multikey QSorting 12 samples
        (Using difference cover)
        Multikey QSorting samples time: 00:00:00
      Calculating bucket sizes
      Splitting and merging
        Splitting and merging time: 00:00:00
      Avg bucket size: 16568 (target: 3106)
      Converting suffix-array elements to index image
      Allocating ftab, absorbFtab
      Entering Ebwt loop
      Getting block 1 of 1
        No samples; assembling all-inclusive block
        Sorting block of length 16568 for bucket 1
        (Using difference cover)
        Sorting block time: 00:00:00
      Returning block of 16569 for bucket 1
      Exited Ebwt loop
      fchr[A]: 0
      fchr[C]: 5124
      fchr[G]: 10305
      fchr[T]: 12474
      fchr[$]: 16568
      Exiting Ebwt::buildToDisk()
      Returning from initFromVector
      Wrote 4200050 bytes to primary EBWT file: genome.rev.1.bt2
      Wrote 4148 bytes to secondary EBWT file: genome.rev.2.bt2
      Re-opening _in1 and _in2 as input streams
      Returning from Ebwt constructor
      Headers:
          len: 16568
          bwtLen: 16569
          sz: 4142
          bwtSz: 4143
          lineRate: 6
          offRate: 4
          offMask: 0xfffffff0
          ftabChars: 10
          eftabLen: 20
          eftabSz: 80
          ftabLen: 1048577
          ftabSz: 4194308
          offsLen: 1036
          offsSz: 4144
          lineSz: 64
          sideSz: 64
          sideBwtSz: 48
          sideBwtLen: 192
          numSides: 87
          numLines: 87
          ebwtTotLen: 5568
          ebwtTotSz: 5568
          color: 0
          reverse: 1
      Total time for backward call to driver() for mirror index: 00:00:00
      

    Job Parameters:

    • Job parameter Parameter value
      library {"__current_case__": 1, "aligned_file": "false", "input_1": {"values": [{"id": 2059694, "src": "hda"}]}, "input_2": {"values": [{"id": 2059704, "src": "hda"}]}, "paired_options": {"__current_case__": 1, "paired_options_selector": "no"}, "type": "paired", "unaligned_file": "false"}
      reference_genome {"__current_case__": 1, "own_file": {"values": [{"id": 2059719, "src": "hda"}]}, "source": "history"}
      rg {"__current_case__": 3, "rg_selector": "do_not_set"}
      analysis_type {"__current_case__": 0, "analysis_type_selector": "simple", "presets": "no_presets"}
      sam_options {"__current_case__": 1, "sam_options_selector": "no"}
      save_mapping_stats "false"
      chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
      dbkey "?"
      __input_ext "input"
  • ✅ bowtie2 (Test Test SEACR 1.3+galaxy1 on usegalaxy.org #8)

    Command Line:

    Exit Code:

    • 0

    Standard Error:

    • Building a SMALL index
      perl: warning: Setting locale failed.
      perl: warning: Please check that your locale settings:
      	LANGUAGE = (unset),
      	LC_ALL = (unset),
      	LANG = "en_US.UTF-8"
          are supported and installed on your system.
      perl: warning: Falling back to the standard locale ("C").
      100 reads; of these:
        100 (100.00%) were paired; of these:
          97 (97.00%) aligned concordantly 0 times
          3 (3.00%) aligned concordantly exactly 1 time
          0 (0.00%) aligned concordantly >1 times
          ----
          97 pairs aligned concordantly 0 times; of these:
            7 (7.22%) aligned discordantly 1 time
          ----
          90 pairs aligned 0 times concordantly or discordantly; of these:
            180 mates make up the pairs; of these:
              156 (86.67%) aligned 0 times
              24 (13.33%) aligned exactly 1 time
              0 (0.00%) aligned >1 times
      22.00% overall alignment rate
      

    Standard Output:

    • Settings:
        Output files: "genome.*.bt2"
        Line rate: 6 (line is 64 bytes)
        Lines per side: 1 (side is 64 bytes)
        Offset rate: 4 (one in 16)
        FTable chars: 10
        Strings: unpacked
        Max bucket size: default
        Max bucket size, sqrt multiplier: default
        Max bucket size, len divisor: 4
        Difference-cover sample period: 1024
        Endianness: little
        Actual local endianness: little
        Sanity checking: disabled
        Assertions: disabled
        Random seed: 0
        Sizeofs: void*:8, int:4, long:8, size_t:8
      Input files DNA, FASTA:
        /galaxy-repl/test/object_store_cache/6/6/2/dataset_66233eb3-9662-4e74-a14e-bafc9c647fb6.dat
      Reading reference sizes
        Time reading reference sizes: 00:00:00
      Calculating joined length
      Writing header
      Reserving space for joined string
      Joining reference sequences
        Time to join reference sequences: 00:00:00
      bmax according to bmaxDivN setting: 4142
      Using parameters --bmax 3107 --dcv 1024
        Doing ahead-of-time memory usage test
        Passed!  Constructing with these parameters: --bmax 3107 --dcv 1024
      Constructing suffix-array element generator
      Building DifferenceCoverSample
        Building sPrime
        Building sPrimeOrder
        V-Sorting samples
        V-Sorting samples time: 00:00:00
        Allocating rank array
        Ranking v-sort output
        Ranking v-sort output time: 00:00:00
        Invoking Larsson-Sadakane on ranks
        Invoking Larsson-Sadakane on ranks time: 00:00:00
        Sanity-checking and returning
      Building samples
      Reserving space for 12 sample suffixes
      Generating random suffixes
      QSorting 12 sample offsets, eliminating duplicates
      QSorting sample offsets, eliminating duplicates time: 00:00:00
      Multikey QSorting 12 samples
        (Using difference cover)
        Multikey QSorting samples time: 00:00:00
      Calculating bucket sizes
      Splitting and merging
        Splitting and merging time: 00:00:00
      Avg bucket size: 16568 (target: 3106)
      Converting suffix-array elements to index image
      Allocating ftab, absorbFtab
      Entering Ebwt loop
      Getting block 1 of 1
        No samples; assembling all-inclusive block
        Sorting block of length 16568 for bucket 1
        (Using difference cover)
        Sorting block time: 00:00:00
      Returning block of 16569 for bucket 1
      Exited Ebwt loop
      fchr[A]: 0
      fchr[C]: 5124
      fchr[G]: 10305
      fchr[T]: 12474
      fchr[$]: 16568
      Exiting Ebwt::buildToDisk()
      Returning from initFromVector
      Wrote 4200050 bytes to primary EBWT file: genome.1.bt2
      Wrote 4148 bytes to secondary EBWT file: genome.2.bt2
      Re-opening _in1 and _in2 as input streams
      Returning from Ebwt constructor
      Headers:
          len: 16568
          bwtLen: 16569
          sz: 4142
          bwtSz: 4143
          lineRate: 6
          offRate: 4
          offMask: 0xfffffff0
          ftabChars: 10
          eftabLen: 20
          eftabSz: 80
          ftabLen: 1048577
          ftabSz: 4194308
          offsLen: 1036
          offsSz: 4144
          lineSz: 64
          sideSz: 64
          sideBwtSz: 48
          sideBwtLen: 192
          numSides: 87
          numLines: 87
          ebwtTotLen: 5568
          ebwtTotSz: 5568
          color: 0
          reverse: 0
      Total time for call to driver() for forward index: 00:00:00
      Reading reference sizes
        Time reading reference sizes: 00:00:00
      Calculating joined length
      Writing header
      Reserving space for joined string
      Joining reference sequences
        Time to join reference sequences: 00:00:00
        Time to reverse reference sequence: 00:00:00
      bmax according to bmaxDivN setting: 4142
      Using parameters --bmax 3107 --dcv 1024
        Doing ahead-of-time memory usage test
        Passed!  Constructing with these parameters: --bmax 3107 --dcv 1024
      Constructing suffix-array element generator
      Building DifferenceCoverSample
        Building sPrime
        Building sPrimeOrder
        V-Sorting samples
        V-Sorting samples time: 00:00:00
        Allocating rank array
        Ranking v-sort output
        Ranking v-sort output time: 00:00:00
        Invoking Larsson-Sadakane on ranks
        Invoking Larsson-Sadakane on ranks time: 00:00:00
        Sanity-checking and returning
      Building samples
      Reserving space for 12 sample suffixes
      Generating random suffixes
      QSorting 12 sample offsets, eliminating duplicates
      QSorting sample offsets, eliminating duplicates time: 00:00:00
      Multikey QSorting 12 samples
        (Using difference cover)
        Multikey QSorting samples time: 00:00:00
      Calculating bucket sizes
      Splitting and merging
        Splitting and merging time: 00:00:00
      Avg bucket size: 16568 (target: 3106)
      Converting suffix-array elements to index image
      Allocating ftab, absorbFtab
      Entering Ebwt loop
      Getting block 1 of 1
        No samples; assembling all-inclusive block
        Sorting block of length 16568 for bucket 1
        (Using difference cover)
        Sorting block time: 00:00:00
      Returning block of 16569 for bucket 1
      Exited Ebwt loop
      fchr[A]: 0
      fchr[C]: 5124
      fchr[G]: 10305
      fchr[T]: 12474
      fchr[$]: 16568
      Exiting Ebwt::buildToDisk()
      Returning from initFromVector
      Wrote 4200050 bytes to primary EBWT file: genome.rev.1.bt2
      Wrote 4148 bytes to secondary EBWT file: genome.rev.2.bt2
      Re-opening _in1 and _in2 as input streams
      Returning from Ebwt constructor
      Headers:
          len: 16568
          bwtLen: 16569
          sz: 4142
          bwtSz: 4143
          lineRate: 6
          offRate: 4
          offMask: 0xfffffff0
          ftabChars: 10
          eftabLen: 20
          eftabSz: 80
          ftabLen: 1048577
          ftabSz: 4194308
          offsLen: 1036
          offsSz: 4144
          lineSz: 64
          sideSz: 64
          sideBwtSz: 48
          sideBwtLen: 192
          numSides: 87
          numLines: 87
          ebwtTotLen: 5568
          ebwtTotSz: 5568
          color: 0
          reverse: 1
      Total time for backward call to driver() for mirror index: 00:00:00
      

    Job Parameters:

    • Job parameter Parameter value
      library {"__current_case__": 1, "aligned_file": "false", "input_1": {"values": [{"id": 2059701, "src": "hda"}]}, "input_2": {"values": [{"id": 2059709, "src": "hda"}]}, "paired_options": {"__current_case__": 1, "paired_options_selector": "no"}, "type": "paired", "unaligned_file": "false"}
      reference_genome {"__current_case__": 1, "own_file": {"values": [{"id": 2059719, "src": "hda"}]}, "source": "history"}
      rg {"__current_case__": 3, "rg_selector": "do_not_set"}
      analysis_type {"__current_case__": 0, "analysis_type_selector": "simple", "presets": "no_presets"}
      sam_options {"__current_case__": 1, "sam_options_selector": "no"}
      save_mapping_stats "false"
      chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
      dbkey "?"
      __input_ext "input"
  • ✅ bowtie2 (Test Test gffread 2.2.1.3+galaxy0 #9)

    Command Line:

    Exit Code:

    • 0

    Standard Error:

    • Building a SMALL index
      perl: warning: Setting locale failed.
      perl: warning: Please check that your locale settings:
      	LANGUAGE = (unset),
      	LC_ALL = (unset),
      	LANG = "en_US.UTF-8"
          are supported and installed on your system.
      perl: warning: Falling back to the standard locale ("C").
      100 reads; of these:
        100 (100.00%) were paired; of these:
          97 (97.00%) aligned concordantly 0 times
          3 (3.00%) aligned concordantly exactly 1 time
          0 (0.00%) aligned concordantly >1 times
          ----
          97 pairs aligned concordantly 0 times; of these:
            7 (7.22%) aligned discordantly 1 time
          ----
          90 pairs aligned 0 times concordantly or discordantly; of these:
            180 mates make up the pairs; of these:
              156 (86.67%) aligned 0 times
              24 (13.33%) aligned exactly 1 time
              0 (0.00%) aligned >1 times
      22.00% overall alignment rate
      

    Standard Output:

    • Settings:
        Output files: "genome.*.bt2"
        Line rate: 6 (line is 64 bytes)
        Lines per side: 1 (side is 64 bytes)
        Offset rate: 4 (one in 16)
        FTable chars: 10
        Strings: unpacked
        Max bucket size: default
        Max bucket size, sqrt multiplier: default
        Max bucket size, len divisor: 4
        Difference-cover sample period: 1024
        Endianness: little
        Actual local endianness: little
        Sanity checking: disabled
        Assertions: disabled
        Random seed: 0
        Sizeofs: void*:8, int:4, long:8, size_t:8
      Input files DNA, FASTA:
        /galaxy-repl/test/object_store_cache/6/6/2/dataset_66233eb3-9662-4e74-a14e-bafc9c647fb6.dat
      Reading reference sizes
        Time reading reference sizes: 00:00:00
      Calculating joined length
      Writing header
      Reserving space for joined string
      Joining reference sequences
        Time to join reference sequences: 00:00:00
      bmax according to bmaxDivN setting: 4142
      Using parameters --bmax 3107 --dcv 1024
        Doing ahead-of-time memory usage test
        Passed!  Constructing with these parameters: --bmax 3107 --dcv 1024
      Constructing suffix-array element generator
      Building DifferenceCoverSample
        Building sPrime
        Building sPrimeOrder
        V-Sorting samples
        V-Sorting samples time: 00:00:00
        Allocating rank array
        Ranking v-sort output
        Ranking v-sort output time: 00:00:00
        Invoking Larsson-Sadakane on ranks
        Invoking Larsson-Sadakane on ranks time: 00:00:00
        Sanity-checking and returning
      Building samples
      Reserving space for 12 sample suffixes
      Generating random suffixes
      QSorting 12 sample offsets, eliminating duplicates
      QSorting sample offsets, eliminating duplicates time: 00:00:00
      Multikey QSorting 12 samples
        (Using difference cover)
        Multikey QSorting samples time: 00:00:00
      Calculating bucket sizes
      Splitting and merging
        Splitting and merging time: 00:00:00
      Avg bucket size: 16568 (target: 3106)
      Converting suffix-array elements to index image
      Allocating ftab, absorbFtab
      Entering Ebwt loop
      Getting block 1 of 1
        No samples; assembling all-inclusive block
        Sorting block of length 16568 for bucket 1
        (Using difference cover)
        Sorting block time: 00:00:00
      Returning block of 16569 for bucket 1
      Exited Ebwt loop
      fchr[A]: 0
      fchr[C]: 5124
      fchr[G]: 10305
      fchr[T]: 12474
      fchr[$]: 16568
      Exiting Ebwt::buildToDisk()
      Returning from initFromVector
      Wrote 4200050 bytes to primary EBWT file: genome.1.bt2
      Wrote 4148 bytes to secondary EBWT file: genome.2.bt2
      Re-opening _in1 and _in2 as input streams
      Returning from Ebwt constructor
      Headers:
          len: 16568
          bwtLen: 16569
          sz: 4142
          bwtSz: 4143
          lineRate: 6
          offRate: 4
          offMask: 0xfffffff0
          ftabChars: 10
          eftabLen: 20
          eftabSz: 80
          ftabLen: 1048577
          ftabSz: 4194308
          offsLen: 1036
          offsSz: 4144
          lineSz: 64
          sideSz: 64
          sideBwtSz: 48
          sideBwtLen: 192
          numSides: 87
          numLines: 87
          ebwtTotLen: 5568
          ebwtTotSz: 5568
          color: 0
          reverse: 0
      Total time for call to driver() for forward index: 00:00:00
      Reading reference sizes
        Time reading reference sizes: 00:00:00
      Calculating joined length
      Writing header
      Reserving space for joined string
      Joining reference sequences
        Time to join reference sequences: 00:00:00
        Time to reverse reference sequence: 00:00:00
      bmax according to bmaxDivN setting: 4142
      Using parameters --bmax 3107 --dcv 1024
        Doing ahead-of-time memory usage test
        Passed!  Constructing with these parameters: --bmax 3107 --dcv 1024
      Constructing suffix-array element generator
      Building DifferenceCoverSample
        Building sPrime
        Building sPrimeOrder
        V-Sorting samples
        V-Sorting samples time: 00:00:00
        Allocating rank array
        Ranking v-sort output
        Ranking v-sort output time: 00:00:00
        Invoking Larsson-Sadakane on ranks
        Invoking Larsson-Sadakane on ranks time: 00:00:00
        Sanity-checking and returning
      Building samples
      Reserving space for 12 sample suffixes
      Generating random suffixes
      QSorting 12 sample offsets, eliminating duplicates
      QSorting sample offsets, eliminating duplicates time: 00:00:00
      Multikey QSorting 12 samples
        (Using difference cover)
        Multikey QSorting samples time: 00:00:00
      Calculating bucket sizes
      Splitting and merging
        Splitting and merging time: 00:00:00
      Avg bucket size: 16568 (target: 3106)
      Converting suffix-array elements to index image
      Allocating ftab, absorbFtab
      Entering Ebwt loop
      Getting block 1 of 1
        No samples; assembling all-inclusive block
        Sorting block of length 16568 for bucket 1
        (Using difference cover)
        Sorting block time: 00:00:00
      Returning block of 16569 for bucket 1
      Exited Ebwt loop
      fchr[A]: 0
      fchr[C]: 5124
      fchr[G]: 10305
      fchr[T]: 12474
      fchr[$]: 16568
      Exiting Ebwt::buildToDisk()
      Returning from initFromVector
      Wrote 4200050 bytes to primary EBWT file: genome.rev.1.bt2
      Wrote 4148 bytes to secondary EBWT file: genome.rev.2.bt2
      Re-opening _in1 and _in2 as input streams
      Returning from Ebwt constructor
      Headers:
          len: 16568
          bwtLen: 16569
          sz: 4142
          bwtSz: 4143
          lineRate: 6
          offRate: 4
          offMask: 0xfffffff0
          ftabChars: 10
          eftabLen: 20
          eftabSz: 80
          ftabLen: 1048577
          ftabSz: 4194308
          offsLen: 1036
          offsSz: 4144
          lineSz: 64
          sideSz: 64
          sideBwtSz: 48
          sideBwtLen: 192
          numSides: 87
          numLines: 87
          ebwtTotLen: 5568
          ebwtTotSz: 5568
          color: 0
          reverse: 1
      Total time for backward call to driver() for mirror index: 00:00:01
      

    Job Parameters:

    • Job parameter Parameter value
      library {"__current_case__": 1, "aligned_file": "false", "input_1": {"values": [{"id": 2059701, "src": "hda"}]}, "input_2": {"values": [{"id": 2059709, "src": "hda"}]}, "paired_options": {"__current_case__": 1, "paired_options_selector": "no"}, "type": "paired", "unaligned_file": "false"}
      reference_genome {"__current_case__": 1, "own_file": {"values": [{"id": 2059719, "src": "hda"}]}, "source": "history"}
      rg {"__current_case__": 3, "rg_selector": "do_not_set"}
      analysis_type {"__current_case__": 0, "analysis_type_selector": "simple", "presets": "no_presets"}
      sam_options {"__current_case__": 0, "no_unal": "false", "omit_sec_seq": "false", "reorder": "true", "sam_no_qname_trunc": "false", "sam_opt": "false", "sam_options_selector": "yes", "soft_clipped_unmapped_tlen": "false", "xeq": "false"}
      save_mapping_stats "false"
      chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
      dbkey "?"
      __input_ext "input"
  • ✅ bowtie2 (Test Test trim_galore 0.6.7+galaxy0 #10)

    Command Line:

    Exit Code:

    • 0

    Standard Error:

    • Building a SMALL index
      perl: warning: Setting locale failed.
      perl: warning: Please check that your locale settings:
      	LANGUAGE = (unset),
      	LC_ALL = (unset),
      	LANG = "en_US.UTF-8"
          are supported and installed on your system.
      perl: warning: Falling back to the standard locale ("C").
      100 reads; of these:
        100 (100.00%) were paired; of these:
          97 (97.00%) aligned concordantly 0 times
          3 (3.00%) aligned concordantly exactly 1 time
          0 (0.00%) aligned concordantly >1 times
          ----
          97 pairs aligned concordantly 0 times; of these:
            7 (7.22%) aligned discordantly 1 time
          ----
          90 pairs aligned 0 times concordantly or discordantly; of these:
            180 mates make up the pairs; of these:
              156 (86.67%) aligned 0 times
              24 (13.33%) aligned exactly 1 time
              0 (0.00%) aligned >1 times
      22.00% overall alignment rate
      

    Standard Output:

    • Settings:
        Output files: "genome.*.bt2"
        Line rate: 6 (line is 64 bytes)
        Lines per side: 1 (side is 64 bytes)
        Offset rate: 4 (one in 16)
        FTable chars: 10
        Strings: unpacked
        Max bucket size: default
        Max bucket size, sqrt multiplier: default
        Max bucket size, len divisor: 4
        Difference-cover sample period: 1024
        Endianness: little
        Actual local endianness: little
        Sanity checking: disabled
        Assertions: disabled
        Random seed: 0
        Sizeofs: void*:8, int:4, long:8, size_t:8
      Input files DNA, FASTA:
        /galaxy-repl/test/object_store_cache/6/6/2/dataset_66233eb3-9662-4e74-a14e-bafc9c647fb6.dat
      Reading reference sizes
        Time reading reference sizes: 00:00:00
      Calculating joined length
      Writing header
      Reserving space for joined string
      Joining reference sequences
        Time to join reference sequences: 00:00:00
      bmax according to bmaxDivN setting: 4142
      Using parameters --bmax 3107 --dcv 1024
        Doing ahead-of-time memory usage test
        Passed!  Constructing with these parameters: --bmax 3107 --dcv 1024
      Constructing suffix-array element generator
      Building DifferenceCoverSample
        Building sPrime
        Building sPrimeOrder
        V-Sorting samples
        V-Sorting samples time: 00:00:00
        Allocating rank array
        Ranking v-sort output
        Ranking v-sort output time: 00:00:00
        Invoking Larsson-Sadakane on ranks
        Invoking Larsson-Sadakane on ranks time: 00:00:00
        Sanity-checking and returning
      Building samples
      Reserving space for 12 sample suffixes
      Generating random suffixes
      QSorting 12 sample offsets, eliminating duplicates
      QSorting sample offsets, eliminating duplicates time: 00:00:00
      Multikey QSorting 12 samples
        (Using difference cover)
        Multikey QSorting samples time: 00:00:00
      Calculating bucket sizes
      Splitting and merging
        Splitting and merging time: 00:00:00
      Avg bucket size: 16568 (target: 3106)
      Converting suffix-array elements to index image
      Allocating ftab, absorbFtab
      Entering Ebwt loop
      Getting block 1 of 1
        No samples; assembling all-inclusive block
        Sorting block of length 16568 for bucket 1
        (Using difference cover)
        Sorting block time: 00:00:00
      Returning block of 16569 for bucket 1
      Exited Ebwt loop
      fchr[A]: 0
      fchr[C]: 5124
      fchr[G]: 10305
      fchr[T]: 12474
      fchr[$]: 16568
      Exiting Ebwt::buildToDisk()
      Returning from initFromVector
      Wrote 4200050 bytes to primary EBWT file: genome.1.bt2
      Wrote 4148 bytes to secondary EBWT file: genome.2.bt2
      Re-opening _in1 and _in2 as input streams
      Returning from Ebwt constructor
      Headers:
          len: 16568
          bwtLen: 16569
          sz: 4142
          bwtSz: 4143
          lineRate: 6
          offRate: 4
          offMask: 0xfffffff0
          ftabChars: 10
          eftabLen: 20
          eftabSz: 80
          ftabLen: 1048577
          ftabSz: 4194308
          offsLen: 1036
          offsSz: 4144
          lineSz: 64
          sideSz: 64
          sideBwtSz: 48
          sideBwtLen: 192
          numSides: 87
          numLines: 87
          ebwtTotLen: 5568
          ebwtTotSz: 5568
          color: 0
          reverse: 0
      Total time for call to driver() for forward index: 00:00:00
      Reading reference sizes
        Time reading reference sizes: 00:00:00
      Calculating joined length
      Writing header
      Reserving space for joined string
      Joining reference sequences
        Time to join reference sequences: 00:00:00
        Time to reverse reference sequence: 00:00:00
      bmax according to bmaxDivN setting: 4142
      Using parameters --bmax 3107 --dcv 1024
        Doing ahead-of-time memory usage test
        Passed!  Constructing with these parameters: --bmax 3107 --dcv 1024
      Constructing suffix-array element generator
      Building DifferenceCoverSample
        Building sPrime
        Building sPrimeOrder
        V-Sorting samples
        V-Sorting samples time: 00:00:00
        Allocating rank array
        Ranking v-sort output
        Ranking v-sort output time: 00:00:00
        Invoking Larsson-Sadakane on ranks
        Invoking Larsson-Sadakane on ranks time: 00:00:00
        Sanity-checking and returning
      Building samples
      Reserving space for 12 sample suffixes
      Generating random suffixes
      QSorting 12 sample offsets, eliminating duplicates
      QSorting sample offsets, eliminating duplicates time: 00:00:00
      Multikey QSorting 12 samples
        (Using difference cover)
        Multikey QSorting samples time: 00:00:00
      Calculating bucket sizes
      Splitting and merging
        Splitting and merging time: 00:00:00
      Avg bucket size: 16568 (target: 3106)
      Converting suffix-array elements to index image
      Allocating ftab, absorbFtab
      Entering Ebwt loop
      Getting block 1 of 1
        No samples; assembling all-inclusive block
        Sorting block of length 16568 for bucket 1
        (Using difference cover)
        Sorting block time: 00:00:00
      Returning block of 16569 for bucket 1
      Exited Ebwt loop
      fchr[A]: 0
      fchr[C]: 5124
      fchr[G]: 10305
      fchr[T]: 12474
      fchr[$]: 16568
      Exiting Ebwt::buildToDisk()
      Returning from initFromVector
      Wrote 4200050 bytes to primary EBWT file: genome.rev.1.bt2
      Wrote 4148 bytes to secondary EBWT file: genome.rev.2.bt2
      Re-opening _in1 and _in2 as input streams
      Returning from Ebwt constructor
      Headers:
          len: 16568
          bwtLen: 16569
          sz: 4142
          bwtSz: 4143
          lineRate: 6
          offRate: 4
          offMask: 0xfffffff0
          ftabChars: 10
          eftabLen: 20
          eftabSz: 80
          ftabLen: 1048577
          ftabSz: 4194308
          offsLen: 1036
          offsSz: 4144
          lineSz: 64
          sideSz: 64
          sideBwtSz: 48
          sideBwtLen: 192
          numSides: 87
          numLines: 87
          ebwtTotLen: 5568
          ebwtTotSz: 5568
          color: 0
          reverse: 1
      Total time for backward call to driver() for mirror index: 00:00:00
      

    Job Parameters:

    • Job parameter Parameter value
      library {"__current_case__": 1, "aligned_file": "false", "input_1": {"values": [{"id": 2059701, "src": "hda"}]}, "input_2": {"values": [{"id": 2059709, "src": "hda"}]}, "paired_options": {"__current_case__": 1, "paired_options_selector": "no"}, "type": "paired", "unaligned_file": "false"}
      reference_genome {"__current_case__": 1, "own_file": {"values": [{"id": 2059719, "src": "hda"}]}, "source": "history"}
      rg {"__current_case__": 3, "rg_selector": "do_not_set"}
      analysis_type {"__current_case__": 0, "analysis_type_selector": "simple", "presets": "no_presets"}
      sam_options {"__current_case__": 0, "no_unal": "false", "omit_sec_seq": "false", "reorder": "false", "sam_no_qname_trunc": "false", "sam_opt": "true", "sam_options_selector": "yes", "soft_clipped_unmapped_tlen": "false", "xeq": "false"}
      save_mapping_stats "false"
      chromInfo "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
      dbkey "?"
      __input_ext "input"

@natefoo
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natefoo commented May 11, 2021

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0 server=https://test.galaxyproject.org

This should fail

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