konradjk/loftee

fail to run plugin LoF

ZhangXiujuan opened this issue · 0 comments

Hi,
There is a question :
I installed kent source tree and Bio::DB::BigFile for LoF.pm , but when I run vep command I got the following error:

Possible precedence issue with control flow operator at Bio/DB/IndexedBase.pm line 845.
Smartmatch is experimental at vep_cache/Plugins/de_novo_donor.pl line 214.
Smartmatch is experimental at vep_cache/Plugins/splice_site_scan.pl line 191.
Smartmatch is experimental at Plugins/splice_site_scan.pl line 194.
Smartmatch is experimental at Plugins/splice_site_scan.pl line 238.
Smartmatch is experimental at vep_cache/Plugins/splice_site_scan.pl line 241.

-------------------- EXCEPTION --------------------
MSG:
ERROR: Forked process(es) died: read-through of cross-process communication detected

STACK Bio::EnsEMBL::VEP::Runner::_forked_buffer_to_output miniconda3/share/ensembl-vep-97.3-0/modules/Bio/EnsEMBL/VEP/Runner.pm:556
STACK Bio::EnsEMBL::VEP::Runner::next_output_line miniconda3/share/ensembl-vep-97.3-0/modules/Bio/EnsEMBL/VEP/Runner.pm:361
STACK Bio::EnsEMBL::VEP::Runner::run miniconda3/share/ensembl-vep-97.3-0/modules/Bio/EnsEMBL/VEP/Runner.pm:202
STACK toplevel miniconda3/bin/vep:223
Date (localtime)    = Fri Aug 30 16:39:18 2019
Ensembl API version = 97
---------------------------------------------------

LoF command:

--plugin LoF,loftee_path:vep_cache/Plugins/,gerp_bigwig:vep_cache/loftee_file/gerp_conservation_scores.homo_sapiens.GRCh38.bw,conservation_file:vep_cache/loftee_file/loftee.sql,human_ancestor_fa:vep_cache/loftee_file/human_ancestor.fa.gz
--fork 8

I have moved all loftee files into Plugins/ .

Whether LoF.pm cannot be used with -- fork.

Can you help me solve these problems?
Thank you.