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 0.4s, peak mem 70MB, user 0.0s, sys 0.1s, output queue size 181
progress 10% @chr19:50661965, elapsed 0.0s, est remaining 0.4s, peak mem 70MB, user 0.0s, sys 0.1s, output queue size 785
progress 15% @chr19:52582202, elapsed 0.1s, est remaining 0.3s, peak mem 70MB, user 0.0s, sys 0.1s, output queue size 1146
progress 20% @chr19:54805951, elapsed 0.1s, est remaining 0.3s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 1532
progress 25% @chr19:56221575, elapsed 0.1s, est remaining 0.2s, peak mem 73MB, user 0.0s, sys 0.2s, output queue size 1968
progress 30% @chr19:58242206, elapsed 0.1s, est remaining 0.2s, peak mem 73MB, user 0.0s, sys 0.2s, output queue size 2209
progress 35% @chr21:29342399, elapsed 0.2s, est remaining 0.3s, peak mem 97MB, user 0.6s, sys 0.3s, output queue size 83
progress 40% @chr21:36245048, elapsed 0.3s, est remaining 0.5s, peak mem 145MB, user 1.6s, sys 0.4s, output queue size 109
progress 45% @chr21:42389927, elapsed 0.9s, est remaining 1.2s, peak mem 241MB, user 7.2s, sys 0.5s, output queue size 113
progress 50% @chr21:45515658, elapsed 1.2s, est remaining 1.2s, peak mem 247MB, user 9.3s, sys 0.5s, output queue size 116
progress 55% @chr22:19444265, elapsed 1.4s, est remaining 1.1s, peak mem 249MB, user 10.0s, sys 0.6s, output queue size 288
progress 60% @chr22:22195903, elapsed 1.4s, est remaining 0.9s, peak mem 249MB, user 10.1s, sys 0.6s, output queue size 767
progress 65% @chr22:23982871, elapsed 1.4s, est remaining 0.7s, peak mem 249MB, user 10.1s, sys 0.6s, output queue size 1005
progress 70% @chr22:29288004, elapsed 1.4s, est remaining 0.6s, peak mem 249MB, user 10.1s, sys 0.6s, output queue size 1493
progress 75% @chr22:31843645, elapsed 1.4s, est remaining 0.5s, peak mem 249MB, user 10.1s, sys 0.6s, output queue size 2036
progress 80% @chr22:37945042, elapsed 1.4s, est remaining 0.4s, peak mem 249MB, user 10.1s, sys 0.6s, output queue size 2600
progress 85% @chr22:41251007, elapsed 1.4s, est remaining 0.3s, peak mem 249MB, user 10.2s, sys 0.7s, output queue size 3118
progress 90% @chr22:46256561, elapsed 1.5s, est remaining 0.2s, peak mem 249MB, user 10.2s, sys 0.7s, output queue size 3734
progress 95% @chr22:50720184, elapsed 1.5s, est remaining 0.1s, peak mem 249MB, user 10.2s, sys 0.7s, output queue size 676
progress 100% @chr22:49913604, elapsed 1.5s, est remaining 0.0s, peak mem 249MB, user 10.2s, sys 0.8s, output queue size 1254
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 12 max 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71692765
output file size: 77724
reads: 1001089
contig: 9624 intervals 1921786 bases
"assemble": 315 calls 0.638 user 0.029 sys 0.769 real
"assemble_addRead": 315 calls 0.001 user 0.000 sys 0.041 real
"assemble_buildGraph": 650 calls 0.297 user 0.003 sys 0.376 real
"assemble_computecigar": 513 calls 0.302 user 0.015 sys 0.381 real
"assemble_kg_build_calcsize": 650 calls 0.172 user 0.000 sys 0.208 real
"assemble_kg_build_clear": 775 calls 0.016 user 0.001 sys 0.017 real
"assemble_kg_build_prepare": 1300 calls 0.201 user 0.022 sys 0.177 real
"assemble_kg_build_threading": 525 calls 0.125 user 0.003 sys 0.164 real
"assemble_kg_op1": 525 calls 0.011 user 0.000 sys 0.037 real
"assemble_kg_op2": 525 calls 0.002 user 0.000 sys 0.009 real
"assemble_kg_op3": 525 calls 0.010 user 0.000 sys 0.012 real
"assemble_sg_clean": 513 calls 0.022 user 0.000 sys 0.044 real
"assemble_sg_create": 513 calls 0.055 user 0.002 sys 0.058 real
"checkGraph": 315 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 315 calls 0.308 user 0.015 sys 0.402 real
active: 19646 calls 0.010 user 0.000 sys 0.015 real
advance: 10022 calls 2.555 user 0.157 sys 3.277 real
annotate: 358 calls 0.020 user 0.000 sys 0.028 real
assemble_region: 315 calls 0.948 user 0.045 sys 1.215 real
build_variants: 312 calls 0.000 user 0.000 sys 0.001 real
calc: 19646 calls 0.243 user 0.000 sys 0.377 real
calc_region: 312 calls 3.812 user 0.046 sys 4.164 real
call_region: 312 calls 0.040 user 0.000 sys 0.054 real
clip_region: 627 calls 0.040 user 0.000 sys 0.070 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.004 user 0.001 sys 1.572 real
fetch: 19646 calls 0.204 user 0.006 sys 0.166 real
fetch_db: 312 calls 0.022 user 0.001 sys 0.086 real
fetch_ref: 19961 calls 0.014 user 0.009 sys 0.080 real
fetch_region: 315 calls 0.010 user 0.000 sys 0.016 real
idle: 39 calls 0.002 user 0.007 sys 13.745 real
init: 1 calls 0.055 user 0.008 sys 0.064 real
pairhmm: 1803 calls 7.115 user 0.024 sys 7.832 real
realign: 598 calls 0.435 user 0.002 sys 0.537 real
region: 19646 calls 6.519 user 0.123 sys 6.673 real
tracker: 19646 calls 0.011 user 0.000 sys 0.028 real
trim_region: 315 calls 0.011 user 0.000 sys 0.005 real
overall: 261939200 mem 13.815 user 1.372 sys 2.734 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory