Classify.seqs cannot resolve path lead segmentation fault

I’m using command-line Mothur v.1.27.0 on Ubuntu 10.10.

Since I’ve updated my mothur version (from v.1.18), I keeping getting an error with the classify.seqs.

I use mothur in whatever working directory my files are in while I have all my reference databases for mothur in a directory in the home directory(/home/jamie/mothur), which I set as the default path during mothur installation.

When I run the command it is able to read in the template and taxonomy, however it can’t seem to resolve the correct path (which should be my current working directory). The .temp.taxonomy files appear in my working directory but are empty.

I also tried including the full paths for my input fasta, and databases but got the same error. Same thing for using just one processor.

Here is my mothur log:

mothur > classify.seqs(fasta=thr_top_tRNA_rrna.fasta, template=silva_bac_unal.fasta,, cutoff=80, processors=3)

Using 3 processors.
Unable to open silva_bac_unal.fasta. Trying default /home/jamie/mothur/silva_bac_unal.fasta
Unable to open Trying default /home/jamie/mothur/
Reading template taxonomy… DONE.
Reading template probabilities… DONE.
It took 0 seconds get probabilities.
Classifying sequences from thr_top_tRNA_rrna.fasta …
cannot resolve path for thr_top_tRNA_rrna./home/jamie/mothur/silva_bac_silva.taxonomy18888.temp
[ERROR]: Could not open thr_top_tRNA_rrna./home/jamie/mothur/silva_bac_silva.taxonomy18888.temp
cannot resolve path for thr_top_tRNA_rrna./home/jamie/mothur/silva_bac_silva.flip.accnos18888.temp
[ERROR]: Could not open thr_top_tRNA_rrna./home/jamie/mothur/silva_bac_silva.flip.accnos18888.temp
cannot resolve path for thr_top_tRNA_rrna./home/jamie/mothur/silva_bac_silva.taxonomy
[ERROR]: Could not open thr_top_tRNA_rrna./home/jamie/mothur/silva_bac_silva.taxonomy
cannot resolve path for thr_top_tRNA_rrna./home/jamie/mothur/silva_bac_silva.flip.accnos
[ERROR]: Could not open thr_top_tRNA_rrna./home/jamie/mothur/silva_bac_silva.flip.accnos
cannot resolve path for thr_top_tRNA_rrna./home/jamie/mothur/silva_bac_silva.taxonomy18889.temp
[ERROR]: Could not open thr_top_tRNA_rrna./home/jamie/mothur/silva_bac_silva.taxonomy18889.temp
cannot resolve path for thr_top_tRNA_rrna./home/jamie/mothur/silva_bac_silva.flip.accnos18889.temp
[ERROR]: Could not open thr_top_tRNA_rrna./home/jamie/mothur/silva_bac_silva.flip.accnos18889.temp
Segmentation fault

Thanks for reporting this bug. It looks like mothur is having a hard time resolving the path. I have fixed the issue and the change will be part of our next release. As a workaround, if you make your taxonomy file name have 3 parts mothur will be able to process it. ie. change to