cluster command won't work in script mode

mothur bugs
1

When I run the cluster command in my perl script, mothur will try to run for a few minutes, then times out.

`$mothur \"#cluster(column=/home/neilsharma/$run_directory/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.filter.dist, count=/home/neilsharma/$run_directory/stability.trim.contigs.good.unique.good.filter.unique.precluster.count_table)\"`;

Linux version

Using ReadLine

Running 64Bit Version

mothur v.1.39.5
Last updated: 3/20/2017

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
Script Mode

Notice that it does start mothur, but doesn’t seem to find the command. (Hence why it’s not printed to the logfile)

I should also add that I’ve execute many prior commands in script mode, have double checked the syntax, but still can’t get it to execute.

2

Can someone confirm this? Just to be sure I’m not doing something incorrect on my end.

3

I copy/pasted your command and got it to work fine if I removed the ‘`’ characters which I am guessing were just for formatting for posting on this forum? When I say it worked fine I mean it tried to run, but failed because I don’t have the files listed in the command.

I tested this on the 64-bit windows build of mothur 1.39.5

Hope that helps some.

Richard

4

I use bash rather than perl, but this is working for me

mothur "#cluster(column=/home/neilsharma/$run_directory/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.filter.dist, count=/home/neilsharma/$run_directory/stability.trim.contigs.good.unique.good.filter.unique.precluster.count_table)";

Are you sure you have to escape the "?

5

Hi!

Thanks for the responses! I downgraded to version 1.39.3 and got the cluster command to start, but then it dies ~10minutes in without any error and moves on the next command in my script. What’s interesting is I got this command to work on a centos-release-6-6.el6.centos.12.2.x86_64. The system it’s failing on is Ubuntu 16.04.2, but it’s on a SSD drive. Would the SSD drive effect the ‘cluster command’?

logfile below

Linux version

Using ReadLine

Running 64Bit Version

mothur v.1.39.3
Last updated: 2/23/2017

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
Script Mode


mothur > cluster(column=/home/neilsharma/161219_ILM001_WaterSamples/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.filter.dist, count=/home/neilsharma/161219_ILM001_WaterSamples/stability.trim.contigs.good.unique.good.filter.unique.precluster.count_table)

Using 1 processors.
[NOTE]: Default clustering method has changed to opti. To use average neighbor, set method=average.
6

We haven’t heard any problems with people using 1.39.5 for clustering. How big is your distance matrix and what was the command you used to generate it?

7

Hey! So the mystery continues. Both distance files are 223G, but the cluster command fails on machine we provided nicer hardware.

# Works!
# CentOS6.6- 16gb RAM and 32gb swap
# v1.39.3
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.count_table)
223G 161219_ILM001_WaterSamples/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.filter.dist

# Doesn't work!
# Ubuntu 16.04.2- 72gb RAM and a 72gb swap
# cluster command dies ~ 10minutes in. v1.39.3
mothur > cluster(column=/home/neilsharma/161219_ILM001_WaterSamples/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.filter.dist, count=/home/neilsharma/161219_ILM001_WaterSamples/stability.trim.contigs.good.unique.good.filter.unique.precluster.count_table)
223G 161219_ILM001_WaterSamples/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.filter.dist
8

Can you use cutoff=0.03 in dist.seqs and then use the default method in cluster?