Windows version

Running 64Bit Version

mothur v.1.36.1
Last updated: 7/27/2015

by
Patrick D. Schloss

Department of Microbiology & Immunology
University of Michigan
[email protected]
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 > set.logfile(name=mothur.ipython.62853.logfile)

mothur > set.dir(tempdefault=C:\Users\Richard\Documents\Mothur\mothur\)
Mothur's directories:
tempDefault=C:\Users\Richard\Documents\Mothur\mothur\

mothur > set.current(processors=8, summary=BFWGZ.trim.contigs.good.unique.good.filter.unique.precluster.summary, name=BFWGZ.trim.contigs.good.names, group=BFWGZ.contigs.good.groups, fasta=BFWGZ.trim.contigs.good.unique.good.filter.unique.precluster.fasta, count=BFWGZ.trim.contigs.good.unique.good.filter.unique.precluster.count_table)

Using 8 processors.

Current files saved by mothur:
fasta=BFWGZ.trim.contigs.good.unique.good.filter.unique.precluster.fasta
group=BFWGZ.contigs.good.groups
name=BFWGZ.trim.contigs.good.names
count=BFWGZ.trim.contigs.good.unique.good.filter.unique.precluster.count_table
processors=8
summary=BFWGZ.trim.contigs.good.unique.good.filter.unique.precluster.summary

mothur > chimera.uchime(fasta=current, count=current, dereplicate=t, processors=1)
Using BFWGZ.trim.contigs.good.unique.good.filter.unique.precluster.count_table as input file for the count parameter.
Using BFWGZ.trim.contigs.good.unique.good.filter.unique.precluster.fasta as input file for the fasta parameter.

Using 1 processors.

uchime by Robert C. Edgar
http://drive5.com/uchime
This code is donated to the public domain.

Checking sequences from BFWGZ.trim.contigs.good.unique.good.filter.unique.precluster.fasta ...
[ERROR]: Could not open BFWGZ.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.chimerasBF04_DG_5_22

quitting command...
Removing group: BF04_DG_5_22 because all sequences have been removed.


Removing group: BF1_850 because all sequences have been removed.

Removing group: BF99_DNA_6_18 because all sequences have been removed.

Removing group: BF_1999_DNA because all sequences have been removed.

Removing group: BRINE_9_2014_S2 because all sequences have been removed.

Removing group: H2O_neg because all sequences have been removed.

Removing group: MW_Brine_MX3 because all sequences have been removed.

Removing group: WGZ1_CM_SH because all sequences have been removed.

Removing group: WGZneg_CM_SH because all sequences have been removed.

Removing group: WINO_pos because all sequences have been removed.

Removing group: control_neg_BRINE_SX because all sequences have been removed.

Removing group: kit_blank because all sequences have been removed.


mothur > quit()