bug in pre.cluster (v.1.39.0)

[m-bakker]

pre.cluster doesn't seem to handle multiple processors (called in an earlier command) if no group information is provided. Sometimes seems to require running the exact same command twice, with explicit option that 'processors=1', before it will work.

mothur log file copied below:

Linux version
Using ReadLine
Running 64Bit Version
mothur v.1.39.0
Last updated: 1/23/2017
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
Interactive Mode

mothur > set.dir(input=/Desktop/scratch, output=/Desktop/scratch)
Mothur's directories:
outputDir=/home/mbakker/Desktop/scratch/
inputDir=/home/mbakker/Desktop/scratch/

mothur > summary.seqs(fasta=test.fasta, name=test.names, processors=4)

Using 4 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 5 759 233 0 3 1
2.5%-tile: 5 759 253 0 4 251
25%-tile: 5 759 253 0 4 2501
Median: 5 759 253 0 5 5001
75%-tile: 5 759 253 0 5 7501
97.5%-tile: 5 759 254 0 8 9751
Maximum: 5 759 257 0 10 10000
Mean: 5 759 253.046 0 5.0171

of unique seqs: 5854

total # of seqs: 10000

Output File Names:
/home/mbakker/Desktop/scratch/test.summary

It took 0 secs to summarize 10000 sequences.

mothur > pre.cluster(fasta=test.fasta, name=test.names)

Using 4 processors.
When using running without group information mothur can only use 1 processor, continuing.
5854 1 5853
Total number of sequences before precluster was 5854.
pre.cluster removed 5853 sequences.

It took 1 secs to cluster 5854 sequences.

Output File Names:
/home/mbakker/Desktop/scratch/test.precluster.fasta
/home/mbakker/Desktop/scratch/test.precluster.names
/home/mbakker/Desktop/scratch/test.precluster.map

mothur > pre.cluster(fasta=test.fasta, name=test.names, processors=1)

Using 1 processors.
5854 1 5853
Total number of sequences before precluster was 5854.
pre.cluster removed 5853 sequences.

It took 1 secs to cluster 5854 sequences.

Output File Names:
/home/mbakker/Desktop/scratch/test.precluster.fasta
/home/mbakker/Desktop/scratch/test.precluster.names
/home/mbakker/Desktop/scratch/test.precluster.map

mothur > pre.cluster(fasta=test.fasta, name=test.names, processors=1)
Using 1 processors.
5854 4442 1412
Total number of sequences before precluster was 5854.
pre.cluster removed 1412 sequences.

It took 8 secs to cluster 5854 sequences.

Output File Names:
/home/mbakker/Desktop/scratch/test.precluster.fasta
/home/mbakker/Desktop/scratch/test.precluster.names
/home/mbakker/Desktop/scratch/test.precluster.map

mothur > quit()

[m-bakker]

Now on the first issuance of the command, I'm getting all sequences (erroneously) preclustered together. Upon re-issuance of the identical command, mothur crashes with 'Segmentation fault (core dumped)'

[mothur-westcott]

This is corrected with version 1.39.1