When I run this:
pre.cluster(fasta = twist.good.unique.fasta, name = twist.good.names, group = twist.good.groups)
My output includes an updated count_table but no updated names file. I expected the names file to get updated, rather than the count_table.
How can I update my names file? I know that if I have a names file, I can use count.seqs
to produce an updated count_table file. I’m not sure how to get an updated names file from my count_table.
Thank you!
Additional excerpts from the logfile, demonstrating my difficulty (I used ** to highlight the problem areas):
mothur > pre.cluster(fasta = twist.good.unique.fasta, name = twist.good.names, group = twist.good.groups)
Output File Names:
twist.good.count_table
twist.good.unique.precluster.fasta
twist.good.unique.precluster.count_table
(plus the twist.good.unique.precluster.{sample}.{primer}.map files) [*I summarized this part*]
chimera.vsearch(fasta=twist.good.unique.precluster.fasta,
count=twist.good.unique.precluster.count_table, dereplicate='t', vsearch=r'~/bin/vsearch')
Output File Names:
twist.good.unique.precluster.denovo.vsearch.pick.count_table
twist.good.unique.precluster.denovo.vsearch.chimeras
twist.good.unique.precluster.denovo.vsearch.accnos
twist.good.unique.precluster.{sample}.{primer}.count_table files [*I summarized this part*]
twist.good.unique.precluster.{sample}.{primer}.fasta files [*I summarized this part*]
mothur > get.current()
Current files saved by mothur:
accnos=twist.good.unique.precluster.denovo.vsearch.accnos
fasta=twist.good.unique.precluster.fasta
group=twist.good.groups
**name=twist.good.count_table**
count=twist.good.unique.precluster.denovo.vsearch.pick.count_table
processors=72
summary=twist.good.unique.summary
mothur > cluster(count='current', method='unique', cutoff='unique')
Using twist.good.unique.precluster.denovo.vsearch.pick.count_table as input file for the count parameter.
Output File Names:
twist.good.unique.precluster.denovo.vsearch.pick.unique.list
mothur > remove.rare(list='current', count='current', nseqs=9, label='unique')
Using twist.good.unique.precluster.denovo.vsearch.pick.count_table as input file for the count parameter.
Using twist.good.unique.precluster.denovo.vsearch.pick.unique.list as input file for the list parameter.
Output File Names:
twist.good.unique.precluster.denovo.vsearch.pick.pick.count_table
twist.good.unique.precluster.denovo.vsearch.pick.unique.0.pick.list
mothur > summary.seqs(fasta='current', name='current')
**[ERROR]: Your count file contains 951427 unique sequences, but your fasta file contains 700123. File mismatch detected, quitting command.**
mothur > count.seqs(name='current', group='current')
Using twist.good.groups as input file for the group parameter.
**Using twist.good.count_table as input file for the name parameter.**
[ERROR]: Format_ is not in your groupfile, please correct.
(plus tons of other errors, because the name file it is using is not a name file, it's a count_table...)