Linux version Using ReadLine Running 64Bit Version mothur v.1.32.1 Last updated: 10/16/2013 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 Batch Mode mothur > system(/bin/echo "starting count.seqs `date`" >>/dev/stderr) mothur > count.seqs(name=FieldTwo-2012.trim.contigs.good.names, group=FieldTwo-2012.contigs.good.groups, processors=8) Unable to open FieldTwo-2012.trim.contigs.good.names Unable to open FieldTwo-2012.contigs.good.groups Using 8 processors. [ERROR]: did not complete count.seqs. mothur > system(/bin/echo "starting summary.seqs `date`" >>/dev/stderr) mothur > summary.seqs(count=FieldTwo2013.trim.contigs.good.count_table, fasta=FieldTwo2013.trim.contigs.good.unique.fasta, processors=8) Unable to open FieldTwo2013.trim.contigs.good.count_table Using 8 processors. [ERROR]: did not complete summary.seqs. mothur > system(/bin/ls -ltr > mothur-output-files-5.txt) mothur > system(/bin/echo "starting align.seqs `date`" >>/dev/stderr) mothur > align.seqs(fasta=FieldTwo2013.trim.contigs.good.unique.fasta, reference=silva.v4.fasta, processors=8) Using 8 processors. Reading in the silva.v4.fasta template sequences... DONE. It took 4 to read 14956 sequences. Aligning sequences from FieldTwo2013.trim.contigs.good.unique.fasta ... Some of you sequences generated alignments that eliminated too many bases, a list is provided in FieldTwo2013.trim.contigs.good.unique.flip.accnos. If you set the flip parameter to true mothur will try aligning the reverse compliment as well. It took 756 secs to align 2691335 sequences. Output File Names: FieldTwo2013.trim.contigs.good.unique.align FieldTwo2013.trim.contigs.good.unique.align.report FieldTwo2013.trim.contigs.good.unique.flip.accnos mothur > system(/bin/echo "starting summary.seqs `date`" >>/dev/stderr) mothur > summary.seqs(fasta=FieldTwo2013.trim.contigs.good.unique.align, count=FieldTwo2013.trim.contigs.good.count_table, processors=8) Unable to open FieldTwo2013.trim.contigs.good.count_table Using 8 processors. [ERROR]: did not complete summary.seqs. mothur > system(/bin/ls -ltr > mothur-output-files-6.txt) mothur > quit()