Memory error with remove.seqs

Commands in mothur
1

I want to remove sequences found in my control groups (FACS15,FACS9,FACS14,TDnegC080816) from my fasta file.

I am using

unique.seqs(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.count_table)
get.groups(count=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.count_table, groups=FACS15-FACS9-FACS14-TDnegC080816)
list.seqs(count=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.count_table)
remove.seqs(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.count_table, list=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.accnos)

but Mothur returns an error on the remove.seqs command: std::bad_allocRAM used: 4.25529Gigabytes . Total Ram: 23.8707Gigabytes.

Is this typical? Do I need to be working with a computer with more memory or is there a better way to do what I’m trying to do?

Thanks!

2

You could use the remove.groups command.

remove.groups(count=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.count_table, fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta, groups=FACS15-FACS9-FACS14-TDnegC080816)

You can also add other file types to the remove.groups command in case you need to remove the samples from a files.

remove.groups(count=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.count_table, fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta, taxonomy=current, groups=FACS15-FACS9-FACS14-TDnegC080816)

The error you are getting is caused by a typo:

remove.seqs(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.count_table, list=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.accnos)

The parameter should be accnos.