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% @chr19:49139668, elapsed 0.0s, est remaining 0.2s, peak mem 66MB, user 0.0s, sys 0.0s, output queue size 447
progress 10% @chr19:50632286, elapsed 0.0s, est remaining 0.2s, peak mem 66MB, user 0.1s, sys 0.0s, output queue size 682
progress 15% @chr19:52553107, elapsed 0.0s, est remaining 0.2s, peak mem 66MB, user 0.1s, sys 0.1s, output queue size 1047
progress 20% @chr19:54803891, elapsed 0.0s, est remaining 0.2s, peak mem 66MB, user 0.1s, sys 0.1s, output queue size 1434
progress 25% @chr19:56221575, elapsed 0.1s, est remaining 0.2s, peak mem 66MB, user 0.1s, sys 0.1s, output queue size 1871
progress 30% @chr19:58242206, elapsed 0.1s, est remaining 0.1s, peak mem 66MB, user 0.1s, sys 0.1s, output queue size 2112
progress 35% @chr21:30425394, elapsed 0.1s, est remaining 0.2s, peak mem 87MB, user 0.6s, sys 0.2s, output queue size 118
progress 40% @chr21:36460976, elapsed 0.3s, est remaining 0.4s, peak mem 132MB, user 1.6s, sys 0.3s, output queue size 105
progress 45% @chr21:41990895, elapsed 0.9s, est remaining 1.1s, peak mem 237MB, user 6.5s, sys 0.3s, output queue size 124
progress 50% @chr21:45515658, elapsed 1.1s, est remaining 1.1s, peak mem 240MB, user 8.6s, sys 0.4s, output queue size 115
progress 55% @chr22:19405786, elapsed 1.2s, est remaining 1.0s, peak mem 246MB, user 9.3s, sys 0.4s, output queue size 299
progress 60% @chr22:22201834, elapsed 1.2s, est remaining 0.8s, peak mem 246MB, user 9.3s, sys 0.4s, output queue size 779
progress 65% @chr22:23884623, elapsed 1.2s, est remaining 0.6s, peak mem 246MB, user 9.3s, sys 0.4s, output queue size 1001
progress 70% @chr22:29294124, elapsed 1.2s, est remaining 0.5s, peak mem 246MB, user 9.3s, sys 0.5s, output queue size 1508
progress 75% @chr22:31814992, elapsed 1.2s, est remaining 0.4s, peak mem 246MB, user 9.3s, sys 0.5s, output queue size 2047
progress 80% @chr22:37933039, elapsed 1.2s, est remaining 0.3s, peak mem 246MB, user 9.3s, sys 0.6s, output queue size 357
progress 85% @chr22:41256711, elapsed 1.3s, est remaining 0.2s, peak mem 246MB, user 9.3s, sys 0.7s, output queue size 878
progress 90% @chr22:46256561, elapsed 1.3s, est remaining 0.1s, peak mem 246MB, user 9.3s, sys 0.7s, output queue size 1487
progress 95% @chr22:50730721, elapsed 1.3s, est remaining 0.1s, peak mem 246MB, user 9.3s, sys 0.8s, output queue size 2064
progress 100% @chrY:13251005, elapsed 1.3s, est remaining 0.0s, peak mem 246MB, user 9.3s, sys 0.8s, output queue size 2640
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 12 max 384
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71692772
output file size: 77725
reads: 1001089
contig: 9624 intervals 1921786 bases
"assemble": 315 calls 0.525 user 0.021 sys 0.742 real
"assemble_addRead": 315 calls 0.022 user 0.000 sys 0.036 real
"assemble_buildGraph": 650 calls 0.146 user 0.005 sys 0.363 real
"assemble_computecigar": 513 calls 0.284 user 0.000 sys 0.399 real
"assemble_kg_build_calcsize": 650 calls 0.051 user 0.000 sys 0.196 real
"assemble_kg_build_clear": 775 calls 0.004 user 0.000 sys 0.017 real
"assemble_kg_build_prepare": 1300 calls 0.227 user 0.008 sys 0.171 real
"assemble_kg_build_threading": 525 calls 0.092 user 0.005 sys 0.162 real
"assemble_kg_op1": 525 calls 0.039 user 0.005 sys 0.035 real
"assemble_kg_op2": 525 calls 0.000 user 0.000 sys 0.009 real
"assemble_kg_op3": 525 calls 0.020 user 0.000 sys 0.012 real
"assemble_sg_clean": 513 calls 0.026 user 0.000 sys 0.043 real
"assemble_sg_create": 513 calls 0.061 user 0.003 sys 0.056 real
"checkGraph": 315 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 315 calls 0.306 user 0.014 sys 0.419 real
active: 19646 calls 0.000 user 0.000 sys 0.015 real
advance: 10022 calls 2.461 user 0.092 sys 3.197 real
annotate: 358 calls 0.008 user 0.000 sys 0.030 real
assemble_region: 315 calls 0.853 user 0.035 sys 1.201 real
build_variants: 312 calls 0.000 user 0.000 sys 0.002 real
calc: 19646 calls 0.150 user 0.000 sys 0.327 real
calc_region: 312 calls 3.616 user 0.014 sys 4.022 real
call_region: 312 calls 0.008 user 0.000 sys 0.056 real
clip_region: 627 calls 0.047 user 0.000 sys 0.070 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.002 user 0.001 sys 1.416 real
fetch: 19646 calls 0.177 user 0.009 sys 0.170 real
fetch_db: 312 calls 0.008 user 0.005 sys 0.085 real
fetch_ref: 19961 calls 0.010 user 0.004 sys 0.087 real
fetch_region: 315 calls 0.012 user 0.000 sys 0.014 real
idle: 39 calls 0.002 user 0.023 sys 14.075 real
init: 1 calls 0.032 user 0.028 sys 0.053 real
pairhmm: 1803 calls 6.777 user 0.009 sys 7.145 real
realign: 598 calls 0.405 user 0.000 sys 0.526 real
region: 19646 calls 5.982 user 0.081 sys 6.244 real
tracker: 19646 calls 0.017 user 0.002 sys 0.026 real
trim_region: 315 calls 0.009 user 0.000 sys 0.005 real
overall: 258084864 mem 13.146 user 1.511 sys 2.565 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory