cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta --interval_padding 100 -i HCC1395_BL.recal.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed --algo TNhaplotyper2 --tumor_sample HCC1395_BL --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon.hotspot_protected.raw.vcf.gz HCC1395_BL.tnseq_tumor_only.vcf.gz --algo OrientationBias --tumor_sample HCC1395_BL HCC1395_BL.tnseq_tumor_only.orientation_data.tsv --algo ContaminationModel --tumor_sample HCC1395_BL --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments HCC1395_BL.tnseq_tumor_only.segments HCC1395_BL.tnseq_tumor_only.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr21:14516792, elapsed 0.1s, est remaining 1.1s, peak mem 129MB, user 0.3s, sys 0.0s, output queue size 54
progress 10% @chr21:25698577, elapsed 0.1s, est remaining 0.8s, peak mem 141MB, user 0.7s, sys 0.1s, output queue size 106
progress 15% @chr21:29034737, elapsed 0.1s, est remaining 0.7s, peak mem 150MB, user 1.1s, sys 0.1s, output queue size 44
progress 20% @chr21:30718483, elapsed 0.2s, est remaining 0.6s, peak mem 150MB, user 1.4s, sys 0.1s, output queue size 16
progress 25% @chr21:31684949, elapsed 0.2s, est remaining 0.6s, peak mem 153MB, user 1.8s, sys 0.1s, output queue size 64
progress 30% @chr21:33352658, elapsed 0.2s, est remaining 0.5s, peak mem 156MB, user 2.2s, sys 0.1s, output queue size 74
progress 35% @chr21:33914350, elapsed 0.3s, est remaining 0.5s, peak mem 162MB, user 2.7s, sys 0.1s, output queue size 74
progress 40% @chr21:36244948, elapsed 0.3s, est remaining 0.5s, peak mem 210MB, user 3.1s, sys 0.1s, output queue size 169
progress 45% @chr21:37267138, elapsed 0.5s, est remaining 0.6s, peak mem 216MB, user 3.6s, sys 0.1s, output queue size 281
progress 50% @chr21:39274274, elapsed 0.5s, est remaining 0.5s, peak mem 228MB, user 4.4s, sys 0.2s, output queue size 262
progress 55% @chr21:41406644, elapsed 0.6s, est remaining 0.5s, peak mem 237MB, user 4.8s, sys 0.2s, output queue size 369
progress 60% @chr21:41511073, elapsed 0.9s, est remaining 0.6s, peak mem 352MB, user 7.3s, sys 0.3s, output queue size 21
progress 65% @chr21:42363155, elapsed 1.0s, est remaining 0.5s, peak mem 355MB, user 8.3s, sys 0.3s, output queue size 100
progress 70% @chr21:43065103, elapsed 1.0s, est remaining 0.4s, peak mem 357MB, user 8.9s, sys 0.3s, output queue size 216
progress 75% @chr21:44126800, elapsed 1.1s, est remaining 0.4s, peak mem 361MB, user 9.3s, sys 0.3s, output queue size 327
progress 80% @chr21:44436962, elapsed 1.1s, est remaining 0.3s, peak mem 363MB, user 9.9s, sys 0.3s, output queue size 429
progress 85% @chr21:45220736, elapsed 1.2s, est remaining 0.2s, peak mem 366MB, user 10.5s, sys 0.3s, output queue size 503
progress 90% @chr21:46001861, elapsed 1.3s, est remaining 0.1s, peak mem 366MB, user 11.1s, sys 0.3s, output queue size 613
progress 95% @chr21:46317912, elapsed 1.3s, est remaining 0.1s, peak mem 366MB, user 12.0s, sys 0.4s, output queue size 74
progress 100% @chr21:46661700, elapsed 1.4s, est remaining 0.0s, peak mem 366MB, user 12.6s, sys 0.4s, output queue size 2
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
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: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 111697681
output file size: 58752
reads: 1322929
contig: 1979 intervals 801713 bases
"assemble": 392 calls 0.835 user 0.023 sys 0.841 real
"assemble_addRead": 392 calls 0.010 user 0.000 sys 0.016 real
"assemble_buildGraph": 837 calls 0.395 user 0.000 sys 0.382 real
"assemble_computecigar": 610 calls 0.065 user 0.001 sys 0.081 real
"assemble_kg_build_calcsize": 837 calls 0.165 user 0.000 sys 0.204 real
"assemble_kg_build_clear": 1061 calls 0.041 user 0.000 sys 0.018 real
"assemble_kg_build_prepare": 1674 calls 0.212 user 0.023 sys 0.183 real
"assemble_kg_build_threading": 613 calls 0.203 user 0.000 sys 0.169 real
"assemble_kg_op1": 613 calls 0.067 user 0.000 sys 0.108 real
"assemble_kg_op2": 613 calls 0.004 user 0.000 sys 0.005 real
"assemble_kg_op3": 613 calls 0.000 user 0.000 sys 0.008 real
"assemble_sg_clean": 610 calls 0.027 user 0.000 sys 0.034 real
"assemble_sg_create": 610 calls 0.076 user 0.000 sys 0.059 real
"checkGraph": 392 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 392 calls 0.065 user 0.001 sys 0.085 real
advance: 2074 calls 3.904 user 0.203 sys 4.638 real
assemble_region: 392 calls 0.909 user 0.024 sys 0.946 real
build_pileup: 1955 calls 0.049 user 0.009 sys 0.030 real
build_stats: 1978 calls 0.964 user 0.024 sys 0.988 real
build_variants: 232 calls 0.000 user 0.000 sys 0.001 real
calc: 3859 calls 0.387 user 0.004 sys 0.458 real
calc_region: 232 calls 3.108 user 0.024 sys 3.234 real
call_region: 232 calls 0.035 user 0.000 sys 0.058 real
clip_region: 624 calls 0.081 user 0.000 sys 0.058 real
done: 1 calls 0.300 user 0.000 sys 0.309 real
execute: 1 calls 0.002 user 0.001 sys 1.389 real
fetch: 8147 calls 0.725 user 0.020 sys 0.707 real
fetch_ref: 8593 calls 0.035 user 0.000 sys 0.036 real
fetch_region: 392 calls 0.020 user 0.000 sys 0.017 real
fetch_vcf: 2074 calls 0.803 user 0.000 sys 0.595 real
idle: 37 calls 0.038 user 0.000 sys 12.792 real
init: 1 calls 0.047 user 0.009 sys 0.055 real
pairhmm: 1073 calls 5.147 user 0.030 sys 5.301 real
realign: 232 calls 0.573 user 0.004 sys 0.615 real
region: 4053 calls 4.075 user 0.048 sys 4.228 real
tracker: 4053 calls 0.010 user 0.000 sys 0.011 real
trim_region: 392 calls 0.000 user 0.000 sys 0.002 real
overall: 384225280 mem 16.457 user 0.469 sys 2.868 real