Im using classify.seqs and remove lineage on my pipeline. It has not happened before but recently I noticed that one of my batch scripts took a realy long time and failed because of the timeout from resource manager. The last line on the log file was –
[WARNING]: mothur reversed some your sequences for a better classification. If you would like to take a closer look, please check koos.final.ggV6.wang.flip.accnos for the list of the sequences.
It took 131 secs to classify 157208 sequences.
It seems mothur had written out the classify.seqs output files (from command classify.seqs(fasta=koos.final.fasta,template=ggV6.fasta, taxonomy=ggV6.tax, cutoff=80, processors=30, group=koos.final.groups))
- when I later did --remove.lineage(taxonomy=koos.final.ggV6.wang.taxonomy, name=koos.final.names, group=koos.final.groups, fasta=koos.final.fasta, taxon=k__Archaea;unclassified;-k__Bacteria;unclassified-unclassified;, dups=T)
It seemed ok I’m still worried that the taxonomy file might be corrupted etc. though it seems it was written out a-ok. But for some reason then the batch stalled.