Error wit count.seqs

Hi all
I have been using mothur version v.1.33.3 to process bacterial 16S rRNA sequences (generated by Miseq). I have followed the miseq sop and succeeded to go through all the steps except when I try count.seqs, mothur gives me an error. However, it still creates an output file. The error message is following:

[ERROR]: processes reported processing 1773630 sequences, but group file indicates you have 1778590 sequences. Could you have a file mismatch? It took 29 secs to create a table for 1773630 sequences.

I have tried many times with different data sets from the beginning but the same error always happens except when I processed only one sample instead of all my samples. Every time I had the same command, e.g.

Count.seqs(name=stability.trim.contigs.good.trim.names, group=stability.contigs.good.groups, processors=1)
With more than 1 processor count.seqs didn’t work at all.

I appreciate any advice. Thanks!

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Could you try it with our current version? How many processors are you running the command with? Could you be running out of memory and a process dying?

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I’ll try with the newest mothur version and let you know how it works.

Thanks,

Hanna

Hi again

The newest mothur version worked fine with count.seqs and there is no error anymore.

Thanks,

Hanna