Pick.pick output file

After command line remove.lineage, I want to proceed to get.groups step, but I can’t find *.pick.pick.count_table and *.pick.pick fasta in my output file. Are there any steps that I missed?

What files does mothur tell you were generated as part of remove.lineage? Those should be the inputs to get.groups.


The output file from remove.lineage is…

For get.groups command, it needs count=oncom.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.count_table and fasta=oncom.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta

Those two files I couldn’t find in my output file.

did you include oncom.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta and oncom.trim.contigs.good.unique.good.filter.unique.precluster.pick.count_table as parameter values when you ran remove.lineage?

Yes I did. I tried to repeat and resulted in the same output file :


I am encountering a similar issue; the only output that I receive from remove.lineage is a pick.taxonomy file, NOT the *pick.pick.count_table or the *pick.pick.fasta. Example below:

remove.lineage(fasta=pilot.trim.contigs.renamed.trim.unique.precluster.pick.fasta, count=pilot.trim.contigs.renamed.trim.unique.precluster.denovo.vsearch.pick.count_table,, taxon=unknown-Protista-Plantae)

Output File Names:

Are you using our current version?

Are all your reads removed? Or none of them?

Could you send your log, fasta, count and taxonomy files to

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