[Error] stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta is blank. Please correct


I’m a new mothur user using the version 1.43.0 and I’m not sure it’s a bug but I always get this error message after phylogenetic command:

Blockquote mothur > dist.seqs(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta, output=lt, processors=8)
[ERROR]: stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta is blank. Please correct.
Using 8 processors.
Sequence Time Num_Dists_Below_Cutoff
Segmentation fault

I followed the steps on MiSeq_SOP wifi page and the same error message appears when I try it with example data from Schloss lab. And if I just skip phylogenetic steps and use analysis commands it says it’s unable to open stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.opti_mcc.shared.

I would like to upload a logfile so it might be easy to troubleshoot but I don’t know how to upload since it doesn’t allow me to upload other than jpg file.

Any idea why this happens? Thanks!

Hi there,

It should not be a bug. I am also a newbie to Mothur. I just followed the SOP for all steps, and I did not encounter this issue.
I am guessing that the issue exists in your stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta file. You can open this file and see if it is truly blank. If it is trult blank, then, I think that your command of get.groups(count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.count_table, fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta, groups=Mock) has some issues.

Or, maybe you skipped the Mock community steps? If so, you might need to change the file names accordingly to avoid the issue that you are facing.

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Could you send your logfile to mothur.bugs@gmail.com?