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- Running 64Bit Version
- mothur v.1.37.3
- Last updated: 5/3/2016
- 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 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...
- quitting command...
- quitting command...
- quitting command...
- quitting command...
- quitting command...
- 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.
- quitting command...
- quitting command...
- quitting command...
- quitting command...
- quitting command...
- quitting command...
- quitting command...
- quitting command...
- quitting command...
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