Test mothur_align_seqs 1.39.5.0

[jennaj]

Report bug test to eliminate technical factors with using the silva reference

Tool ID: toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.39.5.0

MTS: https://toolshed.g2.bx.psu.edu/repository?repository_id=b8bfc4c6aa897f97

[jennaj]

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

[mvdbeek]

Results (powered by Planemo)

Summary

State	Count
Total	5
Passed	5
Error	0
Failure	0
Skipped	0

Passed s

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

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • TERM environment variable not set.
    

  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 > align.seqs(fasta=fasta.dat,reference=alignment.reference.dat,align=need 
    leman,ksize=8,processors=6)
    
    Using 6 processors.
    
    Reading in the alignment.reference.dat template sequences...	DONE.
    It took 0 to read  32 sequences.
    Aligning sequences from fasta.dat ...
    3
    4
    3
    4
    4
    4
    It took 0 secs to align 22 sequences.
    
    
    Output File Names: 
    fasta.align
    fasta.align.report
    
    
    mothur > quit
    

  Job Parameters:

  • Job parameter	Parameter value
    alignment	{"__current_case__": 1, "reference": {"values": [{"id": 93418225, "src": "hda"}]}, "source": "history"}
    search	{"__current_case__": 0, "ksize": "8", "method": "kmer"}
    align	"needleman"
    scoring	{"__current_case__": 1, "adjust": "no"}
    reverse	{"__current_case__": 1, "flip": "no"}
    savelog	"true"
    __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/iuc/mothur_align_seqs/mothur_align_seqs (Test test against test.galaxyproject.org #2)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • TERM environment variable not set.
    

  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 > align.seqs(fasta=fasta.dat,reference=alignment.reference.dat,align=need 
    leman,ksize=8,match=2,mismatch=-15,gapopen=-6,gapextend=-3,processors=6)
    
    Using 6 processors.
    
    Reading in the alignment.reference.dat template sequences...	DONE.
    It took 0 to read  32 sequences.
    Aligning sequences from fasta.dat ...
    4
    4
    3
    4
    3
    4
    It took 0 secs to align 22 sequences.
    
    
    Output File Names: 
    fasta.align
    fasta.align.report
    
    
    mothur > quit
    

  Job Parameters:

  • Job parameter	Parameter value
    alignment	{"__current_case__": 1, "reference": {"values": [{"id": 93418225, "src": "hda"}]}, "source": "history"}
    search	{"__current_case__": 0, "ksize": "8", "method": "kmer"}
    align	"needleman"
    scoring	{"__current_case__": 0, "adjust": "yes", "gapextend": "-3", "gapopen": "-6", "match": "2", "mismatch": "-15"}
    reverse	{"__current_case__": 1, "flip": "no"}
    savelog	"true"
    __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/iuc/mothur_align_seqs/mothur_align_seqs (Test Test Prokka 1.14.6+galaxy1 #3)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • TERM environment variable not set.
    

  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 > align.seqs(fasta=fasta.dat,reference=alignment.reference.dat,align=goto 
    h,search=suffix,match=2,mismatch=-15,gapopen=-6,gapextend=-3,processors=6)
    
    Using 6 processors.
    
    Reading in the alignment.reference.dat template sequences...	DONE.
    It took 0 to read  32 sequences.
    Aligning sequences from fasta.dat ...
    4
    3
    4
    3
    4
    4
    It took 0 secs to align 22 sequences.
    
    
    Output File Names: 
    fasta.align
    fasta.align.report
    
    
    mothur > quit
    

  Job Parameters:

  • Job parameter	Parameter value
    alignment	{"__current_case__": 1, "reference": {"values": [{"id": 93418225, "src": "hda"}]}, "source": "history"}
    search	{"__current_case__": 1, "method": "suffix"}
    align	"gotoh"
    scoring	{"__current_case__": 0, "adjust": "yes", "gapextend": "-3", "gapopen": "-6", "match": "2", "mismatch": "-15"}
    reverse	{"__current_case__": 1, "flip": "no"}
    savelog	"true"
    __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/iuc/mothur_align_seqs/mothur_align_seqs (Test Test roary 3.13.0+galaxy2 #4)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • TERM environment variable not set.
    

  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 > align.seqs(fasta=fasta.dat,reference=alignment.reference.dat,align=blas 
    t,search=blast,flip=true,threshold=0.5,processors=6)
    
    Using 6 processors.
    
    Reading in the alignment.reference.dat template sequences...	DONE.
    It took 0 to read  32 sequences.
    Aligning sequences from fasta.dat ...
    3
    3
    4
    4
    4
    4
    It took 1 secs to align 22 sequences.
    
    
    Output File Names: 
    fasta.align
    fasta.align.report
    
    
    mothur > quit
    

  Job Parameters:

  • Job parameter	Parameter value
    alignment	{"__current_case__": 1, "reference": {"values": [{"id": 93418225, "src": "hda"}]}, "source": "history"}
    search	{"__current_case__": 2, "method": "blast"}
    align	"blast"
    scoring	{"__current_case__": 1, "adjust": "no"}
    reverse	{"__current_case__": 0, "flip": "yes", "threshold": "0.5"}
    savelog	"true"
    __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/iuc/mothur_align_seqs/mothur_align_seqs (Test Test toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1 #5)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • TERM environment variable not set.
    

  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 > align.seqs(fasta=fasta.dat,reference=alignment.reference.dat,align=need 
    leman,ksize=8,flip=true,threshold=0.5,processors=6)
    
    Using 6 processors.
    
    Reading in the alignment.reference.dat template sequences...	DONE.
    It took 0 to read  32 sequences.
    Aligning sequences from fasta.dat ...
    16
    16
    16
    18
    16
    16
    [WARNING]: Some of your sequences generated alignments that eliminated too many bases, a list is provided in fasta.flip.accnos. If the reverse compliment proved to be better it was reported.
    It took 1 secs to align 98 sequences.
    
    
    Output File Names: 
    fasta.align
    fasta.align.report
    fasta.flip.accnos
    
    
    mothur > quit
    
    
    <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
    <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
    <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
    Detected 1 [WARNING] messages, please review.
    <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
    <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
    <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<^>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
    

  Job Parameters:

  • Job parameter	Parameter value
    alignment	{"__current_case__": 1, "reference": {"values": [{"id": 93418225, "src": "hda"}]}, "source": "history"}
    search	{"__current_case__": 0, "ksize": "8", "method": "kmer"}
    align	"needleman"
    scoring	{"__current_case__": 1, "adjust": "no"}
    reverse	{"__current_case__": 0, "flip": "yes", "threshold": "0.5"}
    savelog	"true"
    __job_resource	{"__current_case__": 0, "__job_resource__select": "no"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"