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konradjk / loftee

MIT License
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Failed to instantiate plugin LoF: Can't open /vep/loftee/splice_data/donor_motifs/ese.txt: No such file or directory at /home/.vep/Plugins/loftee_splice_utils.pl line 212 #63

Open Ninjahelicopter opened 4 years ago

Ninjahelicopter commented 4 years ago

I ran the command according to the protocol (VEP version99) and I got the error message with the LOF annotation doesnt work at all:

Failed to instantiate plugin LoF: Can't open /vep/loftee/splice_data/donor_motifs/ese.txt: No such file or directory at /home/.vep/Plugins/loftee_splice_utils.pl line 212

My command line is using the VEP example input file, the "loftee" directory is directly under the VEP one.

./vep -i examples/homo_sapiens_GRCh37.vcf --cache --offline --plugin LoF,loftee_path:loftee --dir_plugins loftee --force_overwrite

Could you please help me @konradjk ?

Or somebody else?

Thanks a lot.

hcurley2 commented 4 years ago

The file loftee_splice_utils.pl is looking for the ese.txt and other files in the vep/loftee/ directory which isn't where you have your loft data stored. As I am working on a HPC that I can't add files into the /vep/ folders. I edited the code on line 206 of loftee_splice_utils.pl so that it was now looking into the correct directory for the files.

Either edit that line with the correct path or move the ese.txt etc files into the /vep/ program folder (usually easier). Note, if you edit the line you also have to edit line 83 in LoF.pm for other files (me2x3acc1 etc) later.