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cpockrandt / PhyloCSFpp

PhyloCSF++ computes PhyloCSF tracks for whole-genome multiple sequence alignments, scores single MSA, annotates CDS features in GFF/GTF files with PhyloCSF and confidence scores.
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OpenBLAS Warning creating heavy logs #11

Open aathbt opened 2 years ago

aathbt commented 2 years ago

Hello,

I've installed PhyloCSF++ using conda in a newly created environment. I then launched it using 

phylocsf++ build-tracks --output-raw-phylo 1 \
--output-regions 1 --genome-length 143726002 --coding-exons ./model/coding_exons.txt \
--threads 24 --output coding_regions_test ./model/mwga /path/to/maf

It hasn't finished to run yet, but it has already produced a very heavy log file (several tens of GB) containing the same line, repeated over and over: OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.

Do you have any idea on what could cause this and how to solve it? Thanks in advance!

Antonin

cpockrandt commented 2 years ago

Hi Antonin,

thanks for finding and reporting this issue! It seems there was a dependency missing in conda. I added and tested it, as soon as this gets merged, it should work. In the meantime you can also use the static binaries on GitHub.