-----------------------------------------------------------
--- 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:-,100-2,304(-)
Caught exception for ref_allele on 17:-,100-164(+)
...vcf - reading in the breakpoints file
...vcf sizeof empty VCFEntryPair 64 bytes 
...read in 846,286 indels and 1,262,637 SVs 
...vcf - deduplicating 1,262,637 events
...dedupe at 0 of 1,262,637
...dedupe at 250,000 of 1,262,637
...dedupe at 500,000 of 1,262,637
...dedupe at 750,000 of 1,262,637
...dedupe at 1,000,000 of 1,262,637
...dedupe at 1,250,000 of 1,262,637
...hashing 846,286 indels for dedupe
...done deduping indels
...vcf - deduplicated down to 981,344 break pairs
Done with snowman

real	585m14.441s
user	2277m31.602s
sys	10m28.302s
[bam_sort_core] merging from 3 files...

real	13m59.204s
user	13m33.707s
sys	0m20.675s

real	0m46.126s
user	0m40.558s
sys	0m4.068s