----------------------------------------------------------- --- Running Snowman SV and indel detection on 4 threads --- --- (inspect *.log for real-time progress updates) --- ----------------------------------------------------------- [M::bwa_idx_load_from_disk] read 0 ALT contigs --- Loaded non-read data. Starting detection pipeline Caught exception for ref_allele on 17:-,100-9,759(+) ...vcf - reading in the breakpoints file ...vcf sizeof empty VCFEntryPair 64 bytes ...read in 783,980 indels and 1,149,810 SVs ...vcf - deduplicating 1,149,810 events ...dedupe at 0 of 1,149,810 ...dedupe at 250,000 of 1,149,810 ...dedupe at 500,000 of 1,149,810 ...dedupe at 750,000 of 1,149,810 ...dedupe at 1,000,000 of 1,149,810 ...hashing 783,980 indels for dedupe ...done deduping indels ...vcf - deduplicated down to 921,896 break pairs Done with snowman real 804m20.459s user 3150m40.280s sys 28m24.436s [bam_sort_core] merging from 3 files... real 17m35.883s user 17m9.407s sys 0m20.626s real 0m51.742s user 0m47.855s sys 0m1.824s