I am using the windows executable version 1.33.3 to analyse Illumina MiSeq 150bp paired end data. This is the first time I have used the mothur pipeline, and I am following the MiSeqSOP.
Using both my data, and the example data, I am experiencing what I consider to be extremely long processing times with the summary.seqs command – still no summary after 1 hour using 1 processor (I have terminated processes after this time), when all other commands take <5 min to process.
Is there a problem here, or is the summary.seqs command expected to take a relatively long time?
Details: I have experienced these “hangs†when attempting the commands
mothur > summary.seqs(fasta=stability.trim.contigs.fasta)
and
mothur > summary.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count_table)
however I did not experience a hang when attempting
mothur > summary.seqs(count=stability.trim.contigs.good.count_table)
In the case of
mothur > summary.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count_table)
the file ‘stability.trim.contigs.good.unique.align’ is 108MB and the file ‘stability.trim.contigs.good.count_table’ is 77MB.
I see that in the MiSeqSOP there are processing times given for some of the commands in the example, but not for the summary.seqs commands. Perhaps this would be useful for inexperienced users attempting to diagnose if there is an issue.
EDIT: I am now sure the program must be "hanging" as I left the command to process overnight and it was still stuck on the "using n processors" line in the morning.
I have also been experiencing a similar hang with other commands (e.g. align.seqs) where the program gets stuck on the line “using n processors”, but if I close the program, re-open, and try again with the same command it will suddenly work; but I haven’t had this approach work for the summary.seqs command.