[ensembl-dev] Segmentation fault when running VEP

[Emma Sernstad]

Hi,

we are experiencing problems that are difficult to debug.
Namely we get this output almost right away:

perl
/mnt/hds/proj/bioinfo/develop/modules/ensembl-tools-release-82/scripts/variant_effect_predictor/
variant_effect_predictor.pl --dir_cache
/mnt/hds/proj/cust003/develop/modules/ensembl-tools-release-82/cache
--cache --force_overwrite --vcf --fork 4 --buffer_size 20000 --offline
--chr 21 --hgvs --symbol --numbers --sift p --polyphen p --humdiv --domains
--protein --ccds --uniprot --biotype --regulatory --tsl -i
/mnt/hds/proj/bioinfo/develop/cust000/337334/analysis/exomes/337334/bwa/gatk/337334_sorted_smd_rreal_brecal_gvcf_vrecal_vt_BOTH_21.vcf
-o
/mnt/hds/proj/bioinfo/develop/cust000/337334/analysis/exomes/337334/bwa/gatk/337334_sorted_smd_rreal_brecal_gvcf_vrecal_vt_vep_BOTH_21.vcf

2015-11-24 10:10:10 - Read existing cache info

2015-11-24 10:10:10 - Auto-detected FASTA file in cache directory

Segmentation fault

Do you think it might be a corrupt cache directory? Can it have anything to
do with the perl installation (v5.18.2)?

We are running on CentOS 6.6.

-- 
Emma Sernstad
Science for Life Laboratory, KISP
Tomtebodavägen 23A
SE-171 65 Solna, Sweden

Email: emma.sernstad at scilifelab.se
Phone: +46 (0)722503877(Mobile)
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