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% @chr19:49138205, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 424
progress 10% @chr19:50629294, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 1022
progress 15% @chr19:52553107, elapsed 0.0s, est remaining 0.1s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 1388
progress 20% @chr19:54803891, elapsed 0.0s, est remaining 0.1s, peak mem 75MB, user 0.0s, sys 0.1s, output queue size 66
progress 25% @chr19:55729831, elapsed 0.0s, est remaining 0.1s, peak mem 79MB, user 0.0s, sys 0.2s, output queue size 520
progress 30% @chr19:58260851, elapsed 0.0s, est remaining 0.1s, peak mem 81MB, user 0.0s, sys 0.2s, output queue size 749
progress 35% @chr21:29342399, elapsed 0.1s, est remaining 0.2s, peak mem 102MB, user 0.6s, sys 0.3s, output queue size 83
progress 40% @chr21:36460976, elapsed 0.3s, est remaining 0.5s, peak mem 153MB, user 1.8s, sys 0.3s, output queue size 106
progress 45% @chr21:42381982, elapsed 1.1s, est remaining 1.3s, peak mem 276MB, user 8.7s, sys 0.4s, output queue size 111
progress 50% @chr21:45525817, elapsed 1.3s, est remaining 1.3s, peak mem 279MB, user 10.9s, sys 0.5s, output queue size 116
progress 55% @chr22:19405786, elapsed 1.4s, est remaining 1.1s, peak mem 282MB, user 11.7s, sys 0.5s, output queue size 91
progress 60% @chr22:22244803, elapsed 1.4s, est remaining 0.9s, peak mem 282MB, user 11.8s, sys 0.6s, output queue size 574
progress 65% @chr22:23894772, elapsed 1.4s, est remaining 0.7s, peak mem 282MB, user 11.8s, sys 0.6s, output queue size 793
progress 70% @chr22:29286684, elapsed 1.4s, est remaining 0.6s, peak mem 282MB, user 11.8s, sys 0.6s, output queue size 1301
progress 75% @chr22:31836972, elapsed 1.4s, est remaining 0.5s, peak mem 282MB, user 11.8s, sys 0.7s, output queue size 1838
progress 80% @chr22:37947281, elapsed 1.4s, est remaining 0.4s, peak mem 282MB, user 11.8s, sys 0.7s, output queue size 2402
progress 85% @chr22:41240874, elapsed 1.4s, est remaining 0.3s, peak mem 282MB, user 11.8s, sys 0.8s, output queue size 2921
progress 90% @chr22:46256561, elapsed 1.4s, est remaining 0.2s, peak mem 282MB, user 11.8s, sys 0.8s, output queue size 3532
progress 95% @chr22:50720184, elapsed 1.5s, est remaining 0.1s, peak mem 282MB, user 11.9s, sys 0.8s, output queue size 4113
progress 100% @chrY:1403269, elapsed 1.5s, est remaining 0.0s, peak mem 282MB, user 11.9s, sys 0.9s, output queue size 4684
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 12 max 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71692767
output file size: 77724
reads: 1001089
contig: 9624 intervals 1921786 bases
"assemble": 315 calls 0.596 user 0.017 sys 0.839 real
"assemble_addRead": 315 calls 0.003 user 0.000 sys 0.033 real
"assemble_buildGraph": 650 calls 0.284 user 0.010 sys 0.419 real
"assemble_computecigar": 513 calls 0.306 user 0.014 sys 0.414 real
"assemble_kg_build_calcsize": 650 calls 0.137 user 0.000 sys 0.233 real
"assemble_kg_build_clear": 775 calls 0.021 user 0.003 sys 0.017 real
"assemble_kg_build_prepare": 1300 calls 0.115 user 0.003 sys 0.182 real
"assemble_kg_build_threading": 525 calls 0.148 user 0.008 sys 0.182 real
"assemble_kg_op1": 525 calls 0.003 user 0.000 sys 0.040 real
"assemble_kg_op2": 525 calls 0.003 user 0.000 sys 0.010 real
"assemble_kg_op3": 525 calls 0.022 user 0.000 sys 0.013 real
"assemble_sg_clean": 513 calls 0.046 user 0.000 sys 0.050 real
"assemble_sg_create": 513 calls 0.051 user 0.003 sys 0.064 real
"checkGraph": 315 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 315 calls 0.314 user 0.014 sys 0.438 real
active: 19646 calls 0.011 user 0.006 sys 0.017 real
advance: 10022 calls 3.218 user 0.110 sys 3.704 real
annotate: 358 calls 0.013 user 0.001 sys 0.029 real
assemble_region: 315 calls 0.917 user 0.031 sys 1.313 real
build_variants: 312 calls 0.000 user 0.000 sys 0.001 real
calc: 19646 calls 0.252 user 0.008 sys 0.427 real
calc_region: 312 calls 5.006 user 0.036 sys 5.429 real
call_region: 312 calls 0.023 user 0.001 sys 0.057 real
clip_region: 627 calls 0.085 user 0.000 sys 0.073 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.003 user 0.002 sys 1.541 real
fetch: 19646 calls 0.132 user 0.040 sys 0.156 real
fetch_db: 312 calls 0.025 user 0.001 sys 0.096 real
fetch_ref: 19961 calls 0.038 user 0.019 sys 0.085 real
fetch_region: 315 calls 0.000 user 0.000 sys 0.020 real
idle: 39 calls 0.012 user 0.022 sys 13.504 real
init: 1 calls 0.039 user 0.011 sys 0.052 real
pairhmm: 1803 calls 8.106 user 0.032 sys 8.849 real
realign: 598 calls 0.516 user 0.003 sys 0.627 real
region: 19646 calls 7.828 user 0.108 sys 7.886 real
tracker: 19646 calls 0.026 user 0.000 sys 0.028 real
trim_region: 315 calls 0.020 user 0.000 sys 0.005 real
overall: 296562688 mem 15.580 user 1.336 sys 2.672 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory