classify.seqs hangs on output

mothur bugs
1

Hi,
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.
2

The warning about reversing sequences is nothing to be concerned about. Mothur reverses the sequences to find the best classification. Did you see the “Output File Names:…” line? If not, then it is likely something went wrong? Could you send your log file to mothur.bugs@gmail.com?

3

Yeah, I ain’t concerned about the warning just wanted to show where it hanged — after It took 131 secs to classify 157208 sequences. It just stood there.
No output files … line reached. I was able to use the outputfiles afterwards but I’m concerened they might be corrupt. I’ll mail the logs.

4

The output files are likely not complete. I would not use them. I would try rerunning the command.

5

I guess I discovered what caused the hangup - some of the sequences given to me had spaces in their sequence identifiers.
I seem to remember that this is something that mothur does not like?
Anyway after removing spaces from fasta sequence identifiers it ran without hangups.