After using the command remove.lineage, I just got one output file. Technically, I should got three output files which contains …pick.pick.fasta. I am using the latest mothur version. What should I do? Thanks!!!
mothur > remove.lineage(fasta=stability.trim.contigs.good.unique.good.filter.uique.precluster.pick.fasta,count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.count_table,taxonomy=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.taxonomy, taxon=Chloroplast-Mitochondria-unknown-Archaea-Eukaryota)
[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.
Output File Names:
A/stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.taxonomy
Thanks for reporting this and sorry for the confusion. The files aren’t generated because no contaminants were present in your dataset. In our latest version, mothur scans the taxonomy file and generates an accnos file containing the names of the sequences from the taxonomies you want to remove. Mothur then runs remove.seqs to remove these reads from the associated files. If the accnos file is blank, meaning no contaminants were found, then remove.seqs is not run. I will add an output message to indicate that no contaminants were found to clear things up in future releases.