pre.cluster in batch mode

Commands in mothur
1

sorry if this has already been discussed - can’t find any threads on this topic.

Hi Pat and Sarah,

I am using pre.cluster() in a batch file following unique.seqs. This is for de-noising MiSeq sequences. It seems that pre.cluster does not find the name file as I get the following warning: “This command can take a namefile and you did not provide one. The current namefile is MSB_index25_9864.chop.good.filter.names which seems to match MSB_index25_9864.chop.good.filter.unique.fasta.”

The .map file output by pre.cluster indicates that the name file was ignored.

thanks,

Giovanni Widmer

2

are you using name=current when you run pre.cluster?

3

I did not. I wasn’t aware there was such a thing…thanks for quick reply, much appreciated! Congrats on the 1000 citations : )