[ensembl-dev] Lock on index file

Konrad Karczewski konradk at broadinstitute.org
Tue Dec 9 18:40:00 GMT 2014

Hi dev team,

I'm confused by an error I've been occasionally getting recently. I've created a sequence index using a test VEP run (and verified it's written and gets read by a test run without a problem), and then submit ~a few hundred VEP jobs to a cluster. A small subset of them come up with this error:

Can't open sequence index file /humgen/atgu1/fs03/konradk/vep/gold//homo_sapiens/77_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.index: No locks available at /humgen/atgu1/fs03/konradk/ensembl-tools-release-77/scripts/variant_effect_predictor/Bio/DB/Fasta.pm line 527.

I would have thought if the index existed and was readable, it wouldn't try to write it, but asking for a lock seems to suggest it is: any ideas what may be causing this? This happens on at least on VEP versions 77 and 78.

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