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sigven / cpsr

Cancer Predisposition Sequencing Reporter (CPSR)
https://sigven.github.io/cpsr/
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Failed to instantiate plug in LoF #21

Closed ridwan-shaikh closed 4 years ago

ridwan-shaikh commented 4 years ago

Hi Sigven/Vlad,

@vladsaveliev I assume this is probably more directed towards you as this is probably and issue from using the conda version (note: this is a fresh install too). Running the example.vcf.gz on v0.5.1.2 gives the following error:

2019-10-30 11:51:56 - cpsr-vep - INFO - STEP 1: Basic variant annotation with Variant Effect Predictor (98, GENCODE release 19, grch37) including loss-of-function prediction
Possible precedence issue with control flow operator at /.conda/envs/pcgr/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
Smartmatch is experimental at /.conda/envs/pcgr/share/ensembl-vep-98.2-0/de_novo_donor.pl line 175.
Smartmatch is experimental at /.conda/envs/pcgr/share/ensembl-vep-98.2-0/de_novo_donor.pl line 214.
Smartmatch is experimental at /.conda/envs/pcgr/share/ensembl-vep-98.2-0/splice_site_scan.pl line 191.
Smartmatch is experimental at /.conda/envs/pcgr/share/ensembl-vep-98.2-0/splice_site_scan.pl line 194.
Smartmatch is experimental at /.conda/envs/pcgr/share/ensembl-vep-98.2-0/splice_site_scan.pl line 238.
Smartmatch is experimental at /.conda/envs/pcgr/share/ensembl-vep-98.2-0/splice_site_scan.pl line 241.
Use of uninitialized value in string eq at /.conda/envs/pcgr/share/ensembl-vep-98.2-0/LoF.pm line 343.
WARNING: Failed to instantiate plugin LoF: Can't open /.conda/envs/pcgr/share/loftee/splice_data/donor_motifs/ese.txt: No such file or directory at /.conda/envs/pcgr/share/ensembl-vep-98.2-0/loftee_splice_utils.pl line 212.

listing at the location: /.conda/envs/pcgr/share/loftee shows only the gzipped folder with no other files:

$ ll
total 1.6M
-rw-rw-r-- 2 user group 1.6M Oct 28 07:28 loftee_1.0.3.tgz

I have tried untaring the loftee in the share location and attempting to run again but that results in the following error:

WARNING: Failed to compile plugin LoF: Can't locate Bio/DB/BigWig.pm in @INC (you may need to install the Bio::DB::BigWig module)

I have also attempted to declare the PERL5LIB to the correct paths where BigWig.pm is stored in the conda environment but that also fails

2019-10-30 15:01:25 - cpsr-vep - INFO - STEP 1: Basic variant annotation with Variant Effect Predictor (98, GENCODE release 19, grch37) including loss-of-function prediction
Possible precedence issue with control flow operator at /.conda/envs/pcgr/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
WARNING: Failed to compile plugin LoF: Can't locate Bio/DB/BigWig.pm in @INC (you may need to install the Bio::DB::BigWig module) (@INC contains: .conda/envs/pcgr/share/loftee /.conda/envs/pcgr/share/ensembl-vep-98.2-0/modules /.conda/envs/pcgr/share/ensembl-vep-98.2-0 /.conda/envs/pcgr/share/ensembl-vep-98.2-0/Bio/EnsEMBL/IO/Parser/ /.conda/envs/pcgr/lib/site_perl/5.26.2/x86_64-linux-thread-multi /.conda/envs/pcgr/lib/site_perl/5.26.2 /.conda/envs/pcgr/lib/5.26.2/x86_64-linux-thread-multi /.conda/envs/pcgr/lib/5.26.2 .) at /.conda/envs/pcgr/share/loftee/gerp_dist.pl line 2.
BEGIN failed--compilation aborted at /.conda/envs/pcgr/share/loftee/gerp_dist.pl line 2.
Compilation failed in require at /.conda/envs/pcgr/share/loftee/LoF.pm line 27.
Compilation failed in require at (eval 39) line 2.
BEGIN failed--compilation aborted at (eval 39) line 2.
vladsavelyev commented 4 years ago

Hi Ridwan,

I'm actually having the same error (and VEP continues running so I didn't even pay attention before). Not really sure how loftee installation works; I basically just copied this line from the Dockerfile into the conda recipe and assumed it will work with this tgz archive somehow.

Let me investigate :)

vladsavelyev commented 4 years ago

Totally forgot to update on this issue. Perl-BigFile library is now on conda: https://github.com/bioconda/bioconda-recipes/pull/18392 Meaning that LofTee should work properly with the most recent version of PCGR/CPSR (this pull request have the fixes https://github.com/sigven/pcgr/pull/98). Works on my side. So updating conda packages should fix the issue:

conda install -c pcgr -c conda-forge -c bioconda "pcgr==0.8.4.4" "cpsr==0.5.2.2"
ridwan-shaikh commented 4 years ago

Thanks Vlad. Tried it this morning and it works perfectly.