count.seqs ERROR

Hi all,

I’m going through MiSeq SOP protocol and got an ERROR message when I run count.seqs:

mothur > count.seqs(name=stability.trim.contigs.good.good.names, group=stability.contigs.good.good.groups, processors=16)

Using 16 processors.
[ERROR]: processes reported processing 1376092 sequences, but group file indicates you have 3130329 sequences. Either you have a file mismatch or a process failed to complete the task assigned to it.

I run the same command a few weeks ago using the same dataset and didn’t get any error. Now I’m going through the same steps again because I made a mistake in a previous step, but apparently this time I’m getting this error. So I don’t see how it can be due to “a file mismatch”. How could have “the process failed to complete the task assigned to it”?

Thanks in advance,


The error is occurring because some of the multiple processes failed. Have you tried rerunning the command?