Huge logfile if samples contain illegal character

mothur bugs
1

I’m not sure that this is really a bug. But I had some samples slip through with dashes in the names (about ~40 samples out of 190). The logfile was 1.5gb because mothur printed this warning ~9M times. Can this warning just be printed once?

[WARNING]: group deep.water.wm2.Blitz-H2O-51 contains illegal characters in the name. Group names should not include :, -, or / characters.  The ':' character is a special character used in trees. Using ':' will result in your tree being unreadable by tree reading software.  The '-' character is a special character used by mothur to parse group names.  Using the '-' character will prevent you from selecting groups. The '/' character will created unreadable filenames when mothur includes the group in an output filename.
2

You can silence all output except commands and errors with quiet mode. The flag is -q or -quiet.

sarahwestcott$ ./mothur -q “#summary.seqs(fasta=final.fasta);”

The output looks like this:

mothur > summary.seqs(fasta=final.fasta)

mothur > quit()

Without quiet mode the output would look like:

mothur v.1.39.1
Last updated: 2/2/2017

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 > summary.seqs(fasta=final.fasta) Unable to open final.fasta. Trying default /Users/sarahwestcott/desktop/release/final.fasta

Using 1 processors.

Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 471 263 0 3 1
2.5%-tile: 1 471 271 0 4 95
25%-tile: 1 471 274 0 4 944
Median: 1 471 275 0 4 1887
75%-tile: 1 471 275 0 5 2830
97.5%-tile: 1 471 277 0 6 3678
Maximum: 3 471 281 0 8 3772
Mean: 1.01326 471 274.342 0 4.5008

of Seqs: 3772

Output File Names:
/Users/sarahwestcott/desktop/release/final.summary

It took 0 secs to summarize 3772 sequences.

mothur > quit()