Error running filter.seqs


I am getting an error “[ERROR]: Could not open mothur.1562956773.logfile” after trying to run filter.seqs on my aligned sequences using mothur 1.41.1 on the command line.

I am testing my commands on a small set of 16S V4 amplified oral samples. I have also tested the same commands on a small set of 16S V4 amplifed gut samples which were sequenced using the same methods, and I was able to generate a “stability.trim.contigs.good.unique.good.filter.fasta” file without an error message.

I have included the output from my align seqs, summary seqs and screen.seqs from my analysis of the oral samples below:

mothur "#rename.file(input=silva.132.v4.fasta, new=silva.v4.fasta)"

mothur "#align.seqs(fasta=stability.trim.contigs.good.unique.fasta, reference=silva.v4.fasta flip=T,processors=8)"

[WARNING]: 201 of your sequences generated alignments that eliminated too many bases, a list is provided in stability.trim.contigs.good.unique.flip.accnos.

[NOTE]: 124 of your sequences were reversed to produce a better alignment.

Output File Names:



mothur "#summary.seqs(fasta=stability.trim.contigs.good.unique.align)"

                	Start   End     NBases  Ambigs  Polymer NumSeqs
Minimum:	13862   13882   2       0       1       1
2.5%-tile:      	13862   23444   252     0       3       3522
25%-tile:       	13862   23444   253     0       4       35218
Median:         	13862   23444   253     0       4       70436
75%-tile:       	13862   23444   253     0       5       105654
97.5%-tile:     	13862   23444   255     0       5       137350
Maximum:        23481   23491   282     0       10      140871
Mean:   	        13867   23443   252     0       4

mothur "#screen.seqs(fasta=stability.trim.contigs.good.unique.align,name=stability.trim.contigs.good.names,group=stability.contigs.good.groups,start=13862,end=23444,processors=8)"

[NOTE]: no sequences were bad, removing stability.trim.contigs.good.unique.bad.accnos

Output File Names:


mothur "#filter.seqs(fasta=stability.trim.contigs.good.unique.good.align,vertical=T,trump=.,processors=8)"

[ERROR]: Could not open mothur.1562956773.logfile

Using 8 processors.

Creating Filter...

It took 0 secs to create filter for 0 sequences.

Please let me know if you have any suggestions on how I should proceed!

Thank you in advance,


Hi Guillaume -

Would you mind updating your version of mothur to 1.42.3 and trying again? I think we may have fixed these bugs since releasing 1.41.1.



Thank you for the suggestion! I will rerun the commands on mothur 1.42.3 and let you know if I run into any further issues!