Failed to run hmmeralign

[marinamashintsova]

Hi,
I run into this problem when running "run_pasta.py --input=filtered.faa --datatype=Protein":

PASTA failed because one of the programs it tried to run failed.
The invocation that failed was:
".../.conda/envs/pasta/bin/hmmeralign" ".../.conda/envs/pastajob/tempsgmw9sal/init_aln/temphmmeraligntkj6o3kq/input.fasta" ".../.conda/envs/pastajob/tempsgmw9sal/init_aln/query-11.fasta" ".../.conda/envs/pastajob/tempsgmw9sal/init_aln/temphmmeraligntkj6o3kq/input.aligned" "amino"

Any idea on how this can be fixed?

[melop]

I confirm the same issue on bioconda installation of sepp and pasta.

[melop]

PASTA failed because one of the programs it tried to run failed.
The invocation that failed was:
    "/public/software/conda_envs/sepp4.5.1/lib/python3.7/site-packages/bin/hmmeralign" "/fast3/group_crf/home/cuirf/OR_hunt/pipeline/trees/OR/testpasta/pastaout/pastajob/templj5_supd/init_aln/temphmmeralignq4xsw1nw/input.fasta" "/fast3/group_crf/home/cuirf/OR_hunt/pipeline/trees/OR/testpasta/pastaout/pastajob/templj5_supd/init_aln/query-3.fasta" "/fast3/group_crf/home/cuirf/OR_hunt/pipeline/trees/OR/testpasta/pastaout/pastajob/templj5_supd/init_aln/temphmmeralignq4xsw1nw/input.aligned" "amino"

It appears that the command line constructed by pasta to run hmmalign was incorrect? What is the problem?

[melop]

Ok I found out the reason. This is because due to some reason the conda installation has an "hmmeralign" binary executable in the conda envoriment's bin folder. Replacing this file with the resource/script/hmmeralign python script works.

[smirarab]

@melop thanks for the report and diagnosis. Do I have any idea how hmmeralign binary executable had gotten there? HMMER's file is called hmmalign not hmmeralign. I am wondering if this is a problem I need to fix on the PASTA side or if this was a fluke?

[Lee-lab888]

@melop thanks for the report and diagnosis. Do I have any idea how hmmeralign binary executable had gotten there? HMMER's file is called hmmalign not hmmeralign. I am wondering if this is a problem I need to fix on the PASTA side or if this was a fluke?

Hi,
I`ve installed sepp and pasta from bioconda (conda install sepp) and have been trying to execute run_upp.py under conda environment ("run_upp.py -s sequence.faa -m amino -M 300 -T 0.66"), but I also get the following error:
log.txt

Packages in environment:

Name Version

dendropy 5.0.1
clustalw 2.1
freetype 2.12.1
hmmer 3.4
mafft 7.526
pasta 1.9.2
python 3.10.15
sepp 4.5.5

Any idea on how this can be fixed?

Thanks!