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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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set.dir(modifynames=F) not working #835

Open abissett opened 1 year ago

abissett commented 1 year ago

Hi I'm trying to use the modifynames=F flag to prevent sequences ID's from being modified. Despite using the flag with set.dir the ":" in the sequence names are being modified to "_". Any help appreciated.

Andrew

mothur-westcott commented 1 year ago

Could you give more information?

  1. What version of mothur are you using?

  2. List of the commands you ran or the logfile?

abissett commented 1 year ago

Sorry, I can't get it to work with any version or command combination, so didn't think to include an example.

I've tried various versions (e.g., 1.45.3 and 1.48.0). I've tried both interactively, as below, and in batch mode with, for example, mothur "#set.dir(modifynames=F), screen.seqs(fasta=141086COIL_JHGCF.fasta, maxambig=0)". Both with the same result.

The fasta prior to interaction with mothur shows:

head *.fasta

sample=141086COIL_JHGCF;_M05960:271:000000000-JHGCF:1:1105:12158:7182 1:N:0:ACTCGCTA+CGTCTAAT GGAACTGGTTGAACAGTTTATCCCCCGCTTTCATCGGCGGCCGGCAGTCCCGGACCATCGGTTGATATGGCGATCTTTGCGCTTCATCTGGCGGGTGCCTCCTCGATCCTTGG............

with ":" in the def line.

and after any mothur processes the ":" are replaced thus: head 141086COIL_JHGCF.good.fasta

sample=141086COIL_JHGCF;_M05960_271_000000000-JHGCF_1_1101_19200_11557 1:N:0:ACTCGCTA+CGTCTATT GGAACAGGATGAACAGTTTACCCCCCTCTTTCAGGAGTTTTAGCTCATTCAGGAGGTTCTGTTGATTTGGCAATTTTCAGTCTTCACTTATCAGGTGCTGCGTCA..............................

LOGFILE

Linux version

Using ReadLine,Boost,HDF5,GSL mothur v.1.48.0 Last updated: 5/20/22 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://forum.mothur.org

Type 'quit()' to exit program

[NOTE]: Setting random seed to 19760620.

Interactive Mode

mothur > set.dir(modifynames=F)

mothur > screen.seqs(fasta=141086COIL_JHGCF.fasta, maxambig=0)

Using 64 processors.

It took 1 secs to screen 51277 sequences, removed 0.

[NOTE]: no sequences were bad, removing 141086COIL_JHGCF.bad.accnos

Output File Names: 141086COIL_JHGCF.good.fasta

It took 1 secs to screen 51277 sequences.

mothur > quit() Logfile : mothur.1670819609.logfile

mothur-westcott commented 1 year ago

Thanks for reporting this issue and providing such a detailed report. I have flagged it as a bug and we will fix it in our next release.

abissett commented 1 year ago

Great, thanks