[ensembl-dev] EnsEmbl/Utils/Sequence.pm line 90 error

namchul ghim chulghim at gmail.com
Fri Apr 10 07:26:22 BST 2015


I use ensembl v79.

command is the following :

/xx/perl520/bin/perl
/xxx/VEP/src/ensembl-tools/scripts/variant_effect_predictor/
variant_effect_predictor.pl -i
/xxxx/VEP/sample/FC613-3.GATKv3.3-0.Filtered.Varinats.vcf --cache --offline
--everything --force_overwrite --dir /xxx/VEP/cache/GRCh37 -o
/xxx/VEP/20150410_Exome/out.vcf --vcf --species homo_sapiens --xref_refseq
--regulatory --flag_pick  --buffer_size 5000 --fork 10 * --hgvs --force
--fasta
/xxx/VEP/cache/GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa*

error message
 :Use of uninitialized value in reverse at
/mnt/lustre/Tools/VEP/src/ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Utils/Sequence.pm
line 90.

This message happens in the following option:
  * --hgvs --force --fasta
/xxx/VEP/cache/GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa*

this command is good in cache of refseq version.


Why?
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