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 screen.seqs `date`" >>/dev/stderr) mothur > screen.seqs(fasta=FieldTwo2013.trim.contigs.good.unique.align, count=FieldTwo2013.trim.contigs.good.count_table, start=8, end=9582, maxhomop=8, processors=8) Using 8 processors. Output File Names: FieldTwo2013.trim.contigs.good.unique.good.align FieldTwo2013.trim.contigs.good.unique.bad.accnos FieldTwo2013.trim.contigs.good.good.count_table It took 360 secs to screen 2691335 sequences. mothur > system(/bin/echo "starting summary.seqs `date`" >>/dev/stderr) mothur > summary.seqs(fasta=FieldTwo2013.trim.contigs.good.unique.good.align, count=FieldTwo2013.trim.contigs.good.good.count_table, processors=8) Using 8 processors. Start End NBases Ambigs Polymer NumSeqs Minimum: 1 9582 232 0 3 1 2.5%-tile: 8 9582 251 0 4 162571 25%-tile: 8 9582 252 0 4 1625703 Median: 8 9582 252 0 4 3251406 75%-tile: 8 9582 252 0 5 4877108 97.5%-tile: 8 9582 253 0 8 6340240 Maximum: 8 9582 274 0 8 6502810 Mean: 7.99998 9582 252.063 0 4.74327 # of unique seqs: 2673918 total # of seqs: 6502810 Output File Names: FieldTwo2013.trim.contigs.good.unique.good.summary mothur > system(/bin/ls -ltr > mothur-output-files-7.txt) mothur > system(/bin/echo "starting filter.seqs `date`" >>/dev/stderr) mothur > filter.seqs(fasta=FieldTwo2013.trim.contigs.good.unique.good.align, vertical=T, trump=., processors=8) Using 8 processors. Creating Filter... Running Filter... Length of filtered alignment: 658 Number of columns removed: 8924 Length of the original alignment: 9582 Number of sequences used to construct filter: 2673918 Output File Names: FieldTwo2013.filter FieldTwo2013.trim.contigs.good.unique.good.filter.fasta mothur > system(/bin/ls -ltr > mothur-output-files-8.txt) mothur > quit()