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phylo42 / IPK

Inference of phylo-k-mers
MIT License
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phyml-mpi issue #2

Closed woodford87 closed 1 year ago

woodford87 commented 3 years ago

Hello,

I'm trying to run xpas for the first time and I am getting the following error:

Command line: /usr/lib/phyml/bin/phyml-mpi --ancestral --no_memory_check -i /home/luke/Documents/Interspecies/extended_trees/extended_align.phylip -u /home/luke/Documents/Interspecies/extended_trees/extended_tree.newick -m HKY85 -c 4 -b 0 -v 0.000000 -o r -a 1.000000 /usr/lib/phyml/bin/phyml-mpi: unrecognized option '--leave_duplicates' /usr/lib/phyml/bin/phyml-mpi: unrecognized option '--leave_duplicates' /usr/lib/phyml/bin/phyml-mpi: unrecognized option '--leave_duplicates' -f e --leave_duplicates /usr/lib/phyml/bin/phyml-mpi: unrecognized option '--leave_duplicates' /usr/lib/phyml/bin/phyml-mpi: unrecognized option '--leave_duplicates' /usr/lib/phyml/bin/phyml-mpi: unrecognized option '--leave_duplicates'

Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted.

mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was:

Process name: [[27310,1],2] Exit code: 1

This is my input:

python ./xpas.py build -s nucl -b '/usr/bin/phyml' -w '/path/Interspecies' -r '/path/Interspecies/Ref_Alignment.fasta' -t '/path/LWreference_tree-NewickExportALT.nwk.newick' -k 10 -m HKY85 --use-unrooted

Can anyone advise how to get around this issue?

Thanks

nromashchenko commented 3 years ago

Hello,

Thank you for reporting the issue.

/usr/lib/phyml/bin/phyml-mpi: unrecognized option '--leave_duplicates' /usr/lib/phyml/bin/phyml-mpi: unrecognized option '--leave_duplicates'

It must be on the phyml side. Could you please indicate which version of phyml you are using?

UPD: depending on this, you may want to either update phyml or try raxml-ng instead: python xpas.py build -s nucl -b 'path-to-raxml-ng' -w .. -t ... -r ...

woodford87 commented 3 years ago

Hi.

Thanks for replying! My Phyml version is the latest version (3:3.3.20170530+dfsg-2).

Thanks, I'll give raxml a try!

nromashchenko commented 3 years ago

My Phyml version is the latest version (3:3.3.20170530+dfsg-2).

this is one of the versions of 2017, and the latest one is 3.3.20200621. You can either download it yourself here or just install it with bioconda.

woodford87 commented 3 years ago

I can't seem to update the version on ubuntu beyond the 2017 version

nromashchenko commented 3 years ago

I can't seem to update the version on ubuntu beyond the 2017 version

Yes, this is why I suggest using conda, there are multiple newer versions of phyml redistributed by bioconda: https://anaconda.org/bioconda/phyml