When I run cluster.split using agc or dgc, files are split and clustered correctly (I see *.uc and *.list files). When it comes to merging the respective list files, the resulting final list file is empty and the rest gets cleaned up. I have attached my logfile.
thank you, Mina
Linux version
Using ReadLine
Running 64Bit Version
mothur v.1.37.4
Last updated: 5/11/2016
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
mothur > cluster.split(fasta=pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta, count=pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.count_table, taxlevel=4, splitmethod=classify, taxonomy=pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.taxonomy, cutoff=0.1, processors=20, method=agc)
Using 20 processors.
Splitting the file…
It took 176 seconds to split the distance file.
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.2.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.12.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.40.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.40.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.2.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.12.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.40.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.44.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.2.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.12.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.40.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.31.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.2.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.12.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.40.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.36.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.2.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.12.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.40.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.38.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.2.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.12.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.40.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.46.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.2.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.12.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.40.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.45.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.17.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.2.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.12.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.40.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.42.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.33.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.12.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.2.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.12.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.40.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.32.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.2.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.12.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.40.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.30.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.26.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.2.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.12.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.40.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.27.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.18.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.2.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.12.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.40.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.16.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.2.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.12.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.40.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.35.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.10.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.2.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.12.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.40.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.28.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.2.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.12.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.40.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.47.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.29.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.2.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.12.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.40.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.37.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.2.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.12.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.40.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.43.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.2.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.12.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.40.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.41.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.2.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.12.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.40.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.39.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.2.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.12.temp
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.40.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.20.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.21.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.11.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.14.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.19.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.23.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.25.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.24.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.9.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.13.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.7.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.6.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.22.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.3.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.5.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.1.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.15.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.8.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.4.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.34.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.0.temp
Clustering pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta.2.temp
Cutoff was 0.105 changed cutoff to 0.105
It took 1163 seconds to cluster
Merging the clustered files…
It took 10 seconds to merge.
Output File Names:
pic.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.agc.unique_list.list
mothur > quit()