[19454] [2020-11-11 22:00:15.485] [GLnexus] [info] Loaded 10409 datasets with 10409 samples; 2336168480176 bytes in 15722891405 BCF records (83322179 duplicate) in 429273641 buckets. Bucket max 736880 bytes, 4797 records. 23199252 BCF records skipped due to caller-specific exceptions
[19454] [2020-11-11 22:00:15.678] [GLnexus] [info] Created sample set *@10409
[19454] [2020-11-11 22:00:15.678] [GLnexus] [info] Flushing database...
[19454] [2020-11-11 22:00:29.146] [GLnexus] [info] Bulk load complete!
[19454] [2020-11-11 22:00:29.154] [GLnexus] [warning] Processing full length of 86 contigs, as no --bed was provided. Providing a BED file with regions of interest, if applicable, can speed this up.
[19454] [2020-11-11 22:00:29.190] [GLnexus] [info] found sample set *@10409
[19454] [2020-11-11 22:00:29.190] [GLnexus] [info] discovering alleles in 86 range(s) on 2 threads
glnexus_cli: /hgsc_software/7.x/glnexus/src/GLnexus-1.2.6/external/src/rocksdb/table/block_based/block_based_table_reader.cc:4041: virtual uint64_t rocksdb::BlockBasedTable::ApproximateSize(const rocksdb::Slice&, const rocksdb::Slice&, rocksdb::TableReaderCaller): Assertion `end_offset >= start_offset' failed.
/var/spool/torque/mom_priv/jobs/2817137.sug-moab.SC: line 1: 19454 Aborted /hgsc_software/software/GLnexus/1.2.6/bin/glnexus_cli --config xAtlas --list filelist -m 40 -t 4 > merged.INDEL.bcf
This only occur when I tried to merge INDELs, and all the individual gvcf files (from exome sequencing) are sorted and indexed.
Hi, I got this error when I run GLnexus
This only occur when I tried to merge INDELs, and all the individual gvcf files (from exome sequencing) are sorted and indexed.
Just wondering what might cause this issue.
Thanks! Hurley