Errors in chimera.uchime

Commands in mothur
1

I ran chimera.uchime with a reference. After looking at some posts here, I saw that it is probably better to run using the count_table and fasta. However, I get the following error after running those:

Command:

chimera.uchime(count=C:\Users\gaugustus\Documents\201506MiSeqData\16SV13Demult\mothur\stability.trim.contigs.good.unique.good.filter.unique.precluster.count_table,fasta=C:\Users\gaugustus\Documents\201506MiSeqData\16SV13Demult\mothur\stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta, dereplicate=T, processors=8)

Error:

[ERROR]: C:\Users\gaugustus\Documents\201506MiSeqData\16SV13Demult\mothur\stability.trim.contigs.good.unique.good.filter.unique.precluster.uchime.accnos is blank.  Please correct.

I am unable to move on because this file is blank. What went wrong and how do I fix it?

Thank you.

2

You had no sequences that were found to be chimeric across all groups, but some may have been flagged within their samples. You can ignore this error message. Mothur checks for blank files upon opening them. With the dereplicate=t option, mothur creates a new count table and accnos file but should have silenced the error message on the accnos file. I will fix this for our next release. Sorry for the confusion.

3

Thank you for the quick reply.