test mothur_unique_seqs 1.39.5.0

[jennaj]

toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0

[jennaj]

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0

[mvdbeek]

Results (powered by Planemo)

Summary

State	Count
Total	3
Passed	2
Error	0
Failure	1
Skipped	0

Failed s

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

  Problems:

  • Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0, exit_code: 1, stderr: .
    

  • Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0, exit_code: 1, stderr: .
    

  • Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0, exit_code: 1, stderr: .
    

  • Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0, exit_code: 1, stderr: .
    

  Command Line:

  Exit Code:

  • 1

  Standard Output:

  • �[H�[J
    
    
    
    
    
    mothur v.1.39.5
    Last updated: 3/20/2017
    
    by
    Patrick D. Schloss
    
    Department of Microbiology & Immunology
    University of Michigan
    http://www.mothur.org
    
    When using, please cite:
    Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.
    
    Distributed under the GNU General Public License
    
    Type 'help()' for information on the commands that are available
    
    For questions and analysis support, please visit our forum at https://www.mothur.org/forum
    
    Type 'quit()' to exit program
    
    
    
    mothur > unique.seqs(name=names.dat,fasta=fasta.dat,format=name)
    Unable to open names.dat. Trying default /usr/local/bin/mothur/names.dat
    Unable to open /usr/local/bin/mothur/names.dat. Trying mothur's location /usr/local/bin/mothurnames.dat
    Unable to open /usr/local/bin/mothurnames.dat
    [ERROR]: did not complete unique.seqs.
    
    mothur > quit
    
    
    ************************************************************
    ************************************************************
    ************************************************************
    Detected 1 [ERROR] messages, please review.
    ************************************************************
    ************************************************************
    ************************************************************
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    names	None
    format	"name"
    savelog	true
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

Passed s

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

  Command Line:

  Exit Code:

  • 0

  Standard Output:

  • �[H�[J
    
    
    
    
    
    mothur v.1.39.5
    Last updated: 3/20/2017
    
    by
    Patrick D. Schloss
    
    Department of Microbiology & Immunology
    University of Michigan
    http://www.mothur.org
    
    When using, please cite:
    Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.
    
    Distributed under the GNU General Public License
    
    Type 'help()' for information on the commands that are available
    
    For questions and analysis support, please visit our forum at https://www.mothur.org/forum
    
    Type 'quit()' to exit program
    
    
    
    mothur > unique.seqs(name=names.dat,fasta=fasta.dat,format=name)
    98	96
    
    Output File Names: 
    fasta.names
    fasta.unique.dat
    
    
    mothur > quit
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    format	"name"
    savelog	true
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

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

  Command Line:

  Exit Code:

  • 0

  Standard Output:

  • �[H�[J
    
    
    
    
    
    mothur v.1.39.5
    Last updated: 3/20/2017
    
    by
    Patrick D. Schloss
    
    Department of Microbiology & Immunology
    University of Michigan
    http://www.mothur.org
    
    When using, please cite:
    Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.
    
    Distributed under the GNU General Public License
    
    Type 'help()' for information on the commands that are available
    
    For questions and analysis support, please visit our forum at https://www.mothur.org/forum
    
    Type 'quit()' to exit program
    
    
    
    mothur > unique.seqs(count=names.dat,fasta=fasta.dat,format=count)
    96	96
    
    Output File Names: 
    fasta.count_table
    fasta.unique.dat
    
    
    mothur > quit
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    format	"count"
    savelog	true
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

[jennaj]

Should be fixed now, rerunning just to triple check

[jennaj]

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0

[mvdbeek]

Results (powered by Planemo)

Summary

State	Count
Total	3
Passed	2
Error	0
Failure	1
Skipped	0

Failed s

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

  Problems:

  • Dataset metadata verification for [file_ext] failed, expected [fasta] but found [auto]. Dataset API value was [{'id': 'f9cad7b01a472135aa70a4b92cda7a42', 'name': 'Unique.seqs on data 419: fasta', 'history_id': '763b0b6ba8e54d88', 'hid': 423, 'history_content_type': 'dataset', 'deleted': False, 'visible': True, 'type_id': 'dataset-f9cad7b01a472135aa70a4b92cda7a42', 'type': 'file', 'create_time': '2023-06-17T00:18:50.624503', 'update_time': '2023-06-17T00:21:28.410431', 'url': '/api/histories/763b0b6ba8e54d88/contents/f9cad7b01a472135aa70a4b92cda7a42', 'tags': [], 'dataset_id': 'bbd44e69cb8906b5045cc6606d9ef7cf', 'state': 'ok', 'extension': 'auto', 'purged': False, 'validated_state_message': None, 'api_type': 'file', 'download_url': '/api/histories/763b0b6ba8e54d88/contents/f9cad7b01a472135aa70a4b92cda7a42/display', 'resubmitted': False, 'uuid': 'ded672a8-91ef-4635-b118-1cb0a8b95859', 'genome_build': '?', 'copied_from_ldda_id': None, 'metadata_dbkey': '?', 'hashes': [], 'sources': [], 'drs_id': 'hda-527053b5a6a6e756a05bff7677c5537a', 'rerunnable': True, 'model_class': 'HistoryDatasetAssociation', 'peek': None, 'misc_blurb': 'data', 'misc_info': '\x1b[H\x1b[J\n\n\n\n\n\nmothur v.1.39.5\nLast updated: 3/20/2017\n\nby\nPatrick D. Schloss\n\nDepartment of Microbiology & Immunology\nUniversity of Michigan\nhttp://www.mothur.org\n\nWhen using, please cite:\nSchloss, P.D., et al., Introducing mothur: Open-source, platform-in', 'meta_files': [], 'accessible': True, 'annotation': None, 'file_size': 66311, 'creating_job': 'bbd44e69cb8906b5341dabd9b8bce20b', 'validated_state': 'unknown', 'permissions': {'manage': ['3e58473f839aa905'], 'access': []}, 'created_from_basename': 'fasta*.unique.*', 'display_apps': [], 'file_ext': 'auto', 'data_type': 'galaxy.datatypes.data.Data', 'hda_ldda': 'hda', 'display_types': []}].
    

  Command Line:

  Exit Code:

  • 0

  Standard Output:

  • �[H�[J
    
    
    
    
    
    mothur v.1.39.5
    Last updated: 3/20/2017
    
    by
    Patrick D. Schloss
    
    Department of Microbiology & Immunology
    University of Michigan
    http://www.mothur.org
    
    When using, please cite:
    Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.
    
    Distributed under the GNU General Public License
    
    Type 'help()' for information on the commands that are available
    
    For questions and analysis support, please visit our forum at https://www.mothur.org/forum
    
    Type 'quit()' to exit program
    
    
    
    mothur > unique.seqs(fasta=fasta.dat,format=name)
    98	96
    
    Output File Names: 
    fasta.names
    fasta.unique.dat
    
    
    mothur > quit
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    names	None
    format	"name"
    savelog	true
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

Passed s

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

  Command Line:

  Exit Code:

  • 0

  Standard Output:

  • �[H�[J
    
    
    
    
    
    mothur v.1.39.5
    Last updated: 3/20/2017
    
    by
    Patrick D. Schloss
    
    Department of Microbiology & Immunology
    University of Michigan
    http://www.mothur.org
    
    When using, please cite:
    Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.
    
    Distributed under the GNU General Public License
    
    Type 'help()' for information on the commands that are available
    
    For questions and analysis support, please visit our forum at https://www.mothur.org/forum
    
    Type 'quit()' to exit program
    
    
    
    mothur > unique.seqs(name=names.dat,fasta=fasta.dat,format=name)
    98	96
    
    Output File Names: 
    fasta.names
    fasta.unique.dat
    
    
    mothur > quit
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    format	"name"
    savelog	true
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

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

  Command Line:

  Exit Code:

  • 0

  Standard Output:

  • �[H�[J
    
    
    
    
    
    mothur v.1.39.5
    Last updated: 3/20/2017
    
    by
    Patrick D. Schloss
    
    Department of Microbiology & Immunology
    University of Michigan
    http://www.mothur.org
    
    When using, please cite:
    Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.
    
    Distributed under the GNU General Public License
    
    Type 'help()' for information on the commands that are available
    
    For questions and analysis support, please visit our forum at https://www.mothur.org/forum
    
    Type 'quit()' to exit program
    
    
    
    mothur > unique.seqs(count=names.dat,fasta=fasta.dat,format=count)
    96	96
    
    Output File Names: 
    fasta.count_table
    fasta.unique.dat
    
    
    mothur > quit
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    format	"count"
    savelog	true
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"