-----------------------------------------------------------
--- 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:-,100-16,682(-)
Caught exception for ref_allele on 17:-,100-164(+)
...vcf - reading in the breakpoints file
...vcf sizeof empty VCFEntryPair 64 bytes 
...read in 1,258,627 indels and 1,995,879 SVs 
...vcf - deduplicating 1,995,879 events
...dedupe at 0 of 1,995,879
...dedupe at 250,000 of 1,995,879
...dedupe at 500,000 of 1,995,879
...dedupe at 750,000 of 1,995,879
...dedupe at 1,000,000 of 1,995,879
...dedupe at 1,250,000 of 1,995,879
...dedupe at 1,500,000 of 1,995,879
...dedupe at 1,750,000 of 1,995,879
...hashing 1,258,627 indels for dedupe
...done deduping indels
...vcf - deduplicated down to 1,514,651 break pairs
Done with snowman

real	1966m43.159s
user	7603m52.477s
sys	41m4.401s
[bam_sort_core] merging from 3 files...

real	24m29.537s
user	23m45.433s
sys	0m31.408s

real	1m16.755s
user	1m4.799s
sys	0m3.331s