Test pangolin 3.1.17+galaxy1

[natefoo]

Installed in galaxyproject/usegalaxy-tools#451

[natefoo]

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/3.1.17+galaxy1

[mvdbeek]

Results (powered by Planemo)

Summary

State	Count
Total	4
Passed	2
Error	2
Failure	0
Skipped	0

Errored s

• ❌ toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin (Test tool test #1)

  Execution Problem:

  • Input staging problem: Expecting value: line 1 column 1 (char 0)
    

• ❌ toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin (Test test against test.galaxyproject.org #2)

  Execution Problem:

  • Input staging problem: Expecting value: line 1 column 1 (char 0)
    

Passed s

• ✅ toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin (Test Test Prokka 1.14.6+galaxy1 #3)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • pangolearn already latest release (2021-12-06)
    constellations updated to v0.1.1
    pango-designation already latest release (v1.2.112)
    Job stats:
    job                     count    min threads    max threads
    --------------------  -------  -------------  -------------
    add_failed_seqs             1              1              1
    align_to_reference          1              1              1
    all                         1              1              1
    generate_report             1              1              1
    get_constellations          1              1              1
    hash_sequence_assign        1              1              1
    pangolearn                  1              1              1
    scorpio                     1              1              1
    total                       8              1              1
    
    

  Standard Output:

  • loading model 12/16/2021, 21:05:23
    processing block of 1 sequences 12/16/2021, 21:05:25
    complete 12/16/2021, 21:05:25
    �[32mOutput file written to: �[0m/corral4/main/jobs/039/705/39705554/working/report.csv
    �[32mOutput alignment written to: �[0m/corral4/main/jobs/039/705/39705554/working/sequences.aln.fasta
    �[32mAll dependencies satisfied.�[0m
    �[32mThe query file is:�[0m/corral4/main/objects/5/8/3/dataset_5830703f-01a1-498a-94be-9eb2a4309059.dat
    �[32m** Running sequence QC **�[0m
    �[32mNumber of sequences detected: �[0m1
    �[32mTotal passing QC: �[0m1
    �[32m
    Data files found:�[0m
    Trained model:	/usr/local/lib/python3.8/site-packages/pangoLEARN/data/decisionTree_v1.joblib
    Header file:	/usr/local/lib/python3.8/site-packages/pangoLEARN/data/decisionTreeHeaders_v1.joblib
    Designated hash:	/usr/local/lib/python3.8/site-packages/pangoLEARN/data/lineages.hash.csv
    

  Job Parameters:

  • Job parameter	Parameter value
    usher	"false"
    alignment	"true"
    max_ambig	"0.5"
    min_length	"10000"
    include_header	"false"
    db	{"__current_case__": 0, "source": "download"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

• ✅ toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin (Test Test roary 3.13.0+galaxy2 #4)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • pangolearn already latest release (2021-12-06)
    constellations updated to v0.1.1
    pango-designation already latest release (v1.2.112)
    Job stats:
    job                     count    min threads    max threads
    --------------------  -------  -------------  -------------
    add_failed_seqs             1              1              1
    align_to_reference          1              1              1
    all                         1              1              1
    generate_report             1              1              1
    get_constellations          1              1              1
    hash_sequence_assign        1              1              1
    pangolearn                  1              1              1
    scorpio                     1              1              1
    total                       8              1              1
    
    

  Standard Output:

  • loading model 12/16/2021, 21:04:27
    processing block of 6 sequences 12/16/2021, 21:04:28
    complete 12/16/2021, 21:04:28
    �[32mOutput file written to: �[0m/corral4/main/jobs/039/705/39705556/working/report.csv
    �[32mAll dependencies satisfied.�[0m
    �[32mThe query file is:�[0m/corral4/main/objects/4/d/f/dataset_4df88074-3eb4-49f9-91ee-ca8bdf5cdd5c.dat
    �[32m** Running sequence QC **�[0m
    �[32mNumber of sequences detected: �[0m34
    �[32mTotal passing QC: �[0m34
    �[32m
    Data files found:�[0m
    Trained model:	/usr/local/lib/python3.8/site-packages/pangoLEARN/data/decisionTree_v1.joblib
    Header file:	/usr/local/lib/python3.8/site-packages/pangoLEARN/data/decisionTreeHeaders_v1.joblib
    Designated hash:	/usr/local/lib/python3.8/site-packages/pangoLEARN/data/lineages.hash.csv
    

  Job Parameters:

  • Job parameter	Parameter value
    usher	"false"
    alignment	"false"
    max_ambig	"0.5"
    min_length	"10000"
    include_header	"true"
    db	{"__current_case__": 0, "source": "download"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

[natefoo]

Again all 4 passed when run from the command line. =/