cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr19_47340800-47341813.bed.gz -i HCC1395_BL.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_1.haplotyper.chr19_47340800-47341813.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr19:49139961, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.0s, output queue size 459
progress 10% @chr19:50629294, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.0s, output queue size 1056
progress 15% @chr19:52553107, elapsed 0.0s, est remaining 0.1s, peak mem 72MB, user 0.0s, sys 0.0s, output queue size 45
progress 20% @chr19:54813842, elapsed 0.0s, est remaining 0.1s, peak mem 72MB, user 0.1s, sys 0.0s, output queue size 427
progress 25% @chr19:56221575, elapsed 0.0s, est remaining 0.1s, peak mem 72MB, user 0.1s, sys 0.0s, output queue size 864
progress 30% @chr19:58212161, elapsed 0.0s, est remaining 0.1s, peak mem 72MB, user 0.1s, sys 0.0s, output queue size 1110
progress 35% @chr21:30425394, elapsed 0.1s, est remaining 0.2s, peak mem 96MB, user 0.6s, sys 0.1s, output queue size 22
progress 40% @chr21:36245048, elapsed 0.3s, est remaining 0.4s, peak mem 144MB, user 1.5s, sys 0.2s, output queue size 107
progress 45% @chr21:42383033, elapsed 0.8s, est remaining 1.0s, peak mem 266MB, user 6.9s, sys 0.3s, output queue size 113
progress 50% @chr21:45515658, elapsed 1.0s, est remaining 1.0s, peak mem 272MB, user 8.7s, sys 0.3s, output queue size 118
progress 55% @chr22:19450670, elapsed 1.1s, est remaining 0.9s, peak mem 272MB, user 9.4s, sys 0.3s, output queue size 156
progress 60% @chr22:22201834, elapsed 1.1s, est remaining 0.8s, peak mem 272MB, user 9.5s, sys 0.3s, output queue size 633
progress 65% @chr22:23877721, elapsed 1.1s, est remaining 0.6s, peak mem 272MB, user 9.5s, sys 0.4s, output queue size 850
progress 70% @chr22:29293284, elapsed 1.1s, est remaining 0.5s, peak mem 272MB, user 9.5s, sys 0.4s, output queue size 1360
progress 75% @chr22:31838685, elapsed 1.2s, est remaining 0.4s, peak mem 272MB, user 9.5s, sys 0.5s, output queue size 1899
progress 80% @chr22:37947281, elapsed 1.2s, est remaining 0.3s, peak mem 272MB, user 9.5s, sys 0.5s, output queue size 2462
progress 85% @chr22:41240874, elapsed 1.2s, est remaining 0.2s, peak mem 272MB, user 9.5s, sys 0.6s, output queue size 2982
progress 90% @chr22:46256561, elapsed 1.2s, est remaining 0.1s, peak mem 272MB, user 9.5s, sys 0.7s, output queue size 3593
progress 95% @chr22:50739271, elapsed 1.2s, est remaining 0.1s, peak mem 272MB, user 9.5s, sys 0.7s, output queue size 915
progress 100% @chr22:50704738, elapsed 1.2s, est remaining 0.0s, peak mem 272MB, user 9.6s, sys 0.8s, output queue size 1493
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 12 max 384
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71692763
output file size: 77724
reads: 1001089
contig: 9624 intervals 1921786 bases
"assemble": 315 calls 0.385 user 0.007 sys 0.688 real
"assemble_addRead": 315 calls 0.040 user 0.000 sys 0.035 real
"assemble_buildGraph": 650 calls 0.122 user 0.000 sys 0.337 real
"assemble_computecigar": 513 calls 0.276 user 0.006 sys 0.374 real
"assemble_kg_build_calcsize": 650 calls 0.073 user 0.000 sys 0.184 real
"assemble_kg_build_clear": 775 calls 0.006 user 0.001 sys 0.016 real
"assemble_kg_build_prepare": 1300 calls 0.135 user 0.003 sys 0.153 real
"assemble_kg_build_threading": 525 calls 0.048 user 0.000 sys 0.149 real
"assemble_kg_op1": 525 calls 0.020 user 0.001 sys 0.032 real
"assemble_kg_op2": 525 calls 0.000 user 0.000 sys 0.008 real
"assemble_kg_op3": 525 calls 0.004 user 0.000 sys 0.011 real
"assemble_sg_clean": 513 calls 0.036 user 0.000 sys 0.040 real
"assemble_sg_create": 513 calls 0.035 user 0.002 sys 0.053 real
"checkGraph": 315 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 315 calls 0.320 user 0.006 sys 0.394 real
active: 19646 calls 0.014 user 0.000 sys 0.014 real
advance: 10022 calls 2.053 user 0.127 sys 2.968 real
annotate: 358 calls 0.002 user 0.000 sys 0.026 real
assemble_region: 315 calls 0.747 user 0.013 sys 1.120 real
build_variants: 312 calls 0.000 user 0.002 sys 0.002 real
calc: 19646 calls 0.213 user 0.000 sys 0.294 real
calc_region: 312 calls 4.308 user 0.010 sys 4.630 real
call_region: 312 calls 0.004 user 0.000 sys 0.050 real
clip_region: 627 calls 0.013 user 0.009 sys 0.063 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.001 user 0.010 sys 1.312 real
fetch: 19646 calls 0.138 user 0.011 sys 0.142 real
fetch_db: 312 calls 0.030 user 0.000 sys 0.081 real
fetch_ref: 19961 calls 0.005 user 0.016 sys 0.084 real
fetch_region: 315 calls 0.025 user 0.000 sys 0.014 real
idle: 39 calls 0.010 user 0.051 sys 13.333 real
init: 1 calls 0.028 user 0.012 sys 0.042 real
pairhmm: 1803 calls 6.630 user 0.002 sys 6.976 real
realign: 598 calls 0.432 user 0.001 sys 0.519 real
region: 19646 calls 6.506 user 0.049 sys 6.517 real
tracker: 19646 calls 0.014 user 0.003 sys 0.024 real
trim_region: 315 calls 0.000 user 0.000 sys 0.004 real
overall: 285270016 mem 12.743 user 1.311 sys 2.426 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory