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mothur / mothur

Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Immunology at The University of Michigan. This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
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Problem with formatting of rarefaction output in Mothur 1.42.3 #654

Closed isabelschober closed 5 years ago

isabelschober commented 5 years ago

Hello, I'm experiencing an issue with the output of the rarefaction.single() command in the newest mothur release.

Only the first four columns of the table are filled correctly.

mothur_rarefaction1

The values that should be in the following columns are all in the last row of the file.

mothur_rarefaction2

When I run my analysis with the same commands in mothur 1.40.0 the output is formatted correctly.

Best, Isabel

isabelschober commented 5 years ago

I just noticed the output files of the collect.single() command have the same problem.

mothur-westcott commented 5 years ago

Thanks for reporting this. Could you post the commands you ran so I can troubleshoot the issue?

isabelschober commented 5 years ago

This is the workflow we use with our students

summary.seqs(fasta=SAMPLE.fasta) unique.seqs(fasta=current) summary.seqs(fasta=current, name=current) align.seqs(template=silva.bacteria.fasta, processors=2) summary.seqs(fasta=current, name=current) screen.seqs(fasta=current, name=current, start=6388, end=13855) summary.seqs(fasta=current, name=current) filter.seqs(fasta=current, vertical=T, trump=., processors=2) summary.seqs(fasta=current, name=current) unique.seqs(fasta=current, name=current) summary.seqs(fasta=current, name=current) dist.seqs(fasta=current, cutoff=0.10, processors=2) cluster(name=current, method=furthest) collect.single(label=unique-0.01-0.03-0.05) summary.single(calc=nseqs-sobs-ace-chao-simpson-shannon-shannoneven) rarefaction.single(freq=10) quit()

mothur-westcott commented 5 years ago

Mothur is not handling the multiple labels correctly in the output file. This will be fixed in our next version coming soon. As a workaround, you can run the labels individually.

mothur > collect.single(label=unique) mothur > collect.single(label=0.01) mothur > collect.single(label=0.03) mothur > collect.single(label=0.05) ...

Sorry for the inconvenience and thanks again for reporting this issue.