Hi,
I’m using the MiSEQ SOP as a reference. I’m also in script mode. https://www.mothur.org/wiki/MiSeq_SOP
The dist.seq and count.seqs commands works, but cluster quits. The code is below.
`$mothur \"#dist.seqs(fasta=/home/mpiuser/$run_directory/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.filter.fasta, cutoff=0.20, processors=$number_of_processors)\"`;
`$mothur \"#count.seqs(name=/home/mpiuser/$run_directory/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.filter.names)\"`;
`$mothur \"#cluster(column=/home/mpiuser/161219_ILM001_WaterSamples/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.filter.dist, count=/home/mpiuser/161219_ILM001_WaterSamples/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.filter.count_table)\"`;
The cluster command doesn’t spit out an output file. It runs for a while and then stops. Here’s the log file.
[mpiuser@cluster ~]$ tail -50 mothur.1488203392.logfile
Linux version
Using ReadLine
Running 64Bit Version
mothur v.1.35.1
Last updated: 03/31/2015
by
Patrick D. Schloss
Department of Microbiology & Immunology
University of Michigan
pschloss@umich.edu
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
Type 'quit()' to exit program
Script Mode
I also tried using cluster.split, but I’m getting errors.
`$mothur \"#cluster.split(fasta=/home/mpiuser/$run_directory/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.filter.fasta, count=/home/mpiuser/$run_directory/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.filter.count_table, taxonomy=/home/mpiuser/$run_directory/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.nr_v123.wang.pick.taxonomy, splitmethod=classify, taxlevel=4, cutoff=0.02, processors=$number_of_processors)\"`;
Clustering /home/mpiuser/161219_ILM001_WaterSamples/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.filter.fasta.1.dist
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix: |||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************
Clustering /home/mpiuser/161219_ILM001_WaterSamples/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.filter.fasta.12.dist
Cutoff was 0.025 changed cutoff to 0.02
********************#****#****#****#****#****#****#****#****#****#****#
Reading matrix: |||||||||||||||||||||||||||||||||||||||||||||||||||
***********************************************************************
Clustering /home/mpiuser/161219_ILM001_WaterSamples/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.filter.fasta.3.dist
Cutoff was 0.025 changed cutoff to 0.02
Cutoff was 0.025 changed cutoff to 0.02
[ERROR]: Could not open 31950.temp
I would like to get something clustered with either command. Does anyone have any ideas how I could improve this?
Thanks!