Entering edit mode
2.9 years ago
yysu
▴
20
Hi Team,
My VEP (version 105, installed by perl INSTALL.pl) works well. But I face some problems to use dbNSFP plugin (also installed by perl INSTALL.pl) with VEP tool.
My dbNSFP version 4.2a was installed by the following code without any warning message.
wget ftp://dbnsfp:dbnsfp@dbnsfp.softgenetics.com/dbNSFP4.2a.zip
unzip dbNSFP4.2a.zip
zcat dbNSFP4.2a_variant.chr1.gz | head -n1 > h
zgrep -h -v ^#chr dbNSFP4.2a_variant.chr* | awk '$8 != "." ' | sort -T /home/user/ensembl-vep/temp -k8,8 -k9,9n - | cat h - | bgzip -c > dbNSFP4.2a_grch37.gz
tabix -s 8 -b 9 -e 9 /home/user/ensembl-vep/dbNSFP4.2a_grch37.gz
My command line is
./vep -i S25-G1.hard-filtered.vcf -o dbNSFP.txt --cache --offline --force_overwrite --hgvs --tab --fasta /home/user/.vep/homo_sapiens/105_GRCh37 --plugin dbNSFP, /home/user/ensembl-vep/dbNSFP4.2a_grch37.gz, LRT_score
I got error
Use of uninitialized value in pattern match (m//) at /home/user/.vep/Plugins/dbNSFP.pm line 159.
Use of uninitialized value $file in pattern match (m//) at /home/user/.vep/Plugins/dbNSFP.pm line 174.
Use of uninitialized value $file in pattern match (m//) at /home/user/.vep/Plugins/dbNSFP.pm line 176.
Use of uninitialized value $file in pattern match (m//) at /home/user/.vep/Plugins/dbNSFP.pm line 178.
Use of uninitialized value $file in pattern match (m//) at /home/user/.vep/Plugins/dbNSFP.pm line 180.
Use of uninitialized value $file in concatenation (.) or string at /home/user/.vep/Plugins/dbNSFP.pm line 183.
WARNING: Failed to instantiate plugin dbNSFP: ERROR: Could not retrieve dbNSFP version from filename
Could someone tell me how to solve this issue?
Many thanks in advance!
Hi, any answer to this question? I have the same problem.
Hi, did you solve this error?
Best,
Paul.
Hi all,
I have the same problem seeing the same line ERRORS by using the version 4.1 of dbNSFP. Anyone can solved it?