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Kurt-Hetrick / CIDR_WES

CIDR's production pipeline for WES and other targeted DNA sequencing projects.
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disable autoindexing for select the vcfs for verifybamid steps #38

Closed Kurt-Hetrick closed 6 years ago

Kurt-Hetrick commented 6 years ago

so this happened.

ERROR MESSAGE: Timeout of 30000 milliseconds was reached while trying to acquire a lock on file /mnt/research/tools/PIPELINE_FILES/GRCh37_aux_files/Omni25_genotypes_1525_samples_v2.b37.PASS.ALL.sites.vcf.idx. Since the GATK uses non-blocking lock acquisition calls that are not supposed to wait, this implies a problem with the file locking support in your operating system.
ERROR ------------------------------------------------------------------------------------------

need to add this for the select verifybam id vcf steps.

--disable_auto_index_creation_and_locking_when_reading_rods

Kurt-Hetrick commented 6 years ago

done