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.
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