Running 64Bit Version

mothur v.1.37.3
Last updated: 5/3/2016

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 soft
ware 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
Interactive Mode


mothur > align.seqs(fasta=stability.trim.contigs.unique.fasta, reference=silva.v3-v4.fasta)

Using 1 processors.

Reading in the silva.v3-v4.fasta template sequences...	DONE.
It took 53 to read  14956 sequences.
Aligning sequences from stability.trim.contigs.unique.fasta ...

quitting command...

mothur > align.seqs(fasta=stability.trim.contigs.unique.fasta, reference=silva.v3-v4.fasta, processors
=16)

Using 16 processors.

Reading in the silva.v3-v4.fasta template sequences...	DONE.
It took 53 to read  14956 sequences.
Aligning sequences from stability.trim.contigs.unique.fasta ...
Some of your sequences generated alignments that eliminated too many bases, a list is provided in stab
ility.trim.contigs.unique.flip.accnos. If you set the flip parameter to true mothur will try aligning
the reverse compliment as well.
It took 1039 secs to align 951024 sequences.


Output File Names:
stability.trim.contigs.unique.align
stability.trim.contigs.unique.align.report
stability.trim.contigs.unique.flip.accnos


mothur > summary.seqs(fasta=stability.trim.contigs.unique.align, count=stability.trim.contigs.count_ta
ble, processors=16)

Using 16 processors.

		Start	End	NBases	Ambigs	Polymer	NumSeqs
Minimum:	1	2	1	0	1	1
2.5%-tile:	2	17012	401	0	4	46720
25%-tile:	2	17012	421	0	4	467197
Median: 	2	17012	426	0	5	934393
75%-tile:	2	17012	426	0	5	1401589
97.5%-tile:	2	17012	426	5	6	1822065
Maximum:	17016	17016	440	85	153	1868784
Mean:	5.79787	17010.9	420.379	0.611389	4.97777
# of unique seqs:	951024
total # of seqs:	1868784

Output File Names:
stability.trim.contigs.unique.summary

It took 230 secs to summarize 1868784 sequences.

mothur > mothur > screen.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.con
tigs.good.count_table, summary=stability.trim.contigs.good.unique.summary, start=1968, end=11550, maxh
omop=8)

mothur > screen.seqs(fasta=stability.trim.contigs.unique.align, count=stability.trim.contigs.count_tab
le, summary=stability.trim.contigs.unique.summary, start=2, end=17012, maxhomop=8, processors=16)

Using 16 processors.

quitting command...

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mothur >
[ERROR]: You are missing (
Invalid.

mothur >
[ERROR]: You are missing (
Invalid.

mothur > screen.seqs(fasta=stability.trim.contigs.unique.align, count=stability.trim.contigs.count_tab
le, summary=stability.trim.contigs.unique.summary, start=2, end=17012, maxhomop=8, processors=8)

Using 8 processors.

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