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.
Pat
The output file from remove.lineage is… oncom.trim.contigs.good.unique.good.filter.unique.precluster.pick.ezbiocloud_id_taxonomy.wang.pick.taxonomy
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 : oncom.trim.contigs.good.unique.good.filter.unique.precluster.pick.ezbiocloud_id_taxonomy.wang.pick.taxonomy
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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, taxonomy=pilot.trim.contigs.renamed.trim.unique.precluster.pick.UNITEv8_sh_dynamic.wang.taxonomy, taxon=unknown-Protista-Plantae)
Output File Names:
pilot.trim.contigs.renamed.trim.unique.precluster.pick.UNITEv8_sh_dynamic.wang.pick.taxonomy
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 mothur.bugs@gmail.com?
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