-----------------------------------------------------------
--- 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