-----------------------------------------------------------
--- 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:-,100-194(-)
Caught exception for ref_allele on 17:-,100-4,033(-)
Caught exception for ref_allele on 17:-,100-204(-)
...vcf - reading in the breakpoints file
...vcf sizeof empty VCFEntryPair 64 bytes 
...read in 868,231 indels and 1,484,609 SVs 
...vcf - deduplicating 1,484,609 events
...dedupe at 0 of 1,484,609
...dedupe at 250,000 of 1,484,609
...dedupe at 500,000 of 1,484,609
...dedupe at 750,000 of 1,484,609
...dedupe at 1,000,000 of 1,484,609
...dedupe at 1,250,000 of 1,484,609
...hashing 868,231 indels for dedupe
...done deduping indels
...vcf - deduplicated down to 1,167,032 break pairs
Done with snowman

real	2837m23.037s
user	11047m59.192s
sys	122m57.084s
[bam_sort_core] merging from 3 files...

real	23m42.240s
user	22m57.702s
sys	0m29.097s

real	1m11.034s
user	1m0.878s
sys	0m3.051s