ghost
commented
7 years ago 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
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()