cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta -i HCC1395_BL.recalibrated.bam -i HCC1395_tumor.recalibrated.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21_padded100bp.bed --algo TNhaplotyper2 --tumor_sample HCC1395_tumor --normal_sample HCC1395_BL --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon_tnseq_42_curated_v4.vcf.gz HCC1395_tumor_vs_HCC1395_BL.tnseq.vcf.gz --algo OrientationBias --tumor_sample HCC1395_tumor HCC1395_tumor_vs_HCC1395_BL.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample HCC1395_tumor --normal_sample HCC1395_BL --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments HCC1395_tumor_vs_HCC1395_BL.tnseq.segments HCC1395_tumor_vs_HCC1395_BL.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr21:14226759, elapsed 0.5s, est remaining 8.9s, peak mem 224MB, user 2.0s, sys 0.1s, output queue size 57
progress 10% @chr21:14964616, elapsed 0.6s, est remaining 5.7s, peak mem 240MB, user 4.6s, sys 0.2s, output queue size 96
progress 15% @chr21:29027814, elapsed 0.8s, est remaining 4.4s, peak mem 248MB, user 6.3s, sys 0.2s, output queue size 10
progress 20% @chr21:30746851, elapsed 0.9s, est remaining 3.7s, peak mem 259MB, user 7.9s, sys 0.2s, output queue size 10
progress 25% @chr21:32346856, elapsed 1.1s, est remaining 3.4s, peak mem 263MB, user 10.0s, sys 0.2s, output queue size 9
progress 30% @chr21:33355216, elapsed 1.3s, est remaining 3.1s, peak mem 267MB, user 11.9s, sys 0.3s, output queue size 26
progress 35% @chr21:33903426, elapsed 1.6s, est remaining 2.9s, peak mem 282MB, user 14.0s, sys 0.3s, output queue size 74
progress 40% @chr21:36269913, elapsed 2.3s, est remaining 3.4s, peak mem 453MB, user 17.4s, sys 0.3s, output queue size 68
progress 45% @chr21:37150720, elapsed 2.5s, est remaining 3.0s, peak mem 457MB, user 20.1s, sys 0.4s, output queue size 161
progress 50% @chr21:39202225, elapsed 2.6s, est remaining 2.6s, peak mem 465MB, user 22.9s, sys 0.5s, output queue size 43
progress 55% @chr21:38379928, elapsed 2.8s, est remaining 2.3s, peak mem 489MB, user 24.8s, sys 0.5s, output queue size 138
progress 60% @chr21:41740738, elapsed 5.0s, est remaining 3.4s, peak mem 844MB, user 40.8s, sys 0.8s, output queue size 15
progress 65% @chr21:42287789, elapsed 5.3s, est remaining 2.9s, peak mem 860MB, user 44.1s, sys 0.9s, output queue size 111
progress 70% @chr21:43419759, elapsed 5.4s, est remaining 2.3s, peak mem 877MB, user 45.5s, sys 0.9s, output queue size 227
progress 75% @chr21:44120248, elapsed 5.6s, est remaining 1.9s, peak mem 877MB, user 47.8s, sys 0.9s, output queue size 325
progress 80% @chr21:44413791, elapsed 5.8s, est remaining 1.5s, peak mem 899MB, user 50.2s, sys 0.9s, output queue size 431
progress 85% @chr21:45220736, elapsed 6.2s, est remaining 1.1s, peak mem 907MB, user 53.5s, sys 0.9s, output queue size 504
progress 90% @chr21:46116551, elapsed 6.6s, est remaining 0.7s, peak mem 907MB, user 56.7s, sys 1.0s, output queue size 613
progress 95% @chr21:46283968, elapsed 6.9s, est remaining 0.4s, peak mem 907MB, user 61.8s, sys 1.0s, output queue size 15
progress 100% @chr21:46661700, elapsed 7.2s, est remaining 0.0s, peak mem 907MB, user 64.9s, sys 1.0s, output queue size 2
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000606a6
  features: 1f8bfbff fffa320b
  extended: f1bf07ab 00407f5a
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 12 max 64
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 163002590 333302564
output file size: 71258
reads: 7311657
contig: 1979 intervals 801713 bases
"assemble": 288 calls 3.049 user 0.029 sys 3.176 real
"assemble_addRead": 288 calls 0.190 user 0.010 sys 0.092 real
"assemble_buildGraph": 670 calls 1.605 user 0.002 sys 1.560 real
"assemble_computecigar": 418 calls 0.150 user 0.000 sys 0.193 real
"assemble_kg_build_calcsize": 670 calls 0.946 user 0.000 sys 0.930 real
"assemble_kg_build_clear": 902 calls 0.119 user 0.000 sys 0.127 real
"assemble_kg_build_prepare": 1340 calls 0.740 user 0.027 sys 0.874 real
"assemble_kg_build_threading": 438 calls 0.609 user 0.002 sys 0.573 real
"assemble_kg_op1": 438 calls 0.326 user 0.001 sys 0.377 real
"assemble_kg_op2": 438 calls 0.000 user 0.000 sys 0.008 real
"assemble_kg_op3": 438 calls 0.020 user 0.000 sys 0.008 real
"assemble_sg_clean": 418 calls 0.020 user 0.000 sys 0.051 real
"assemble_sg_create": 418 calls 0.060 user 0.000 sys 0.068 real
"checkGraph": 288 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 288 calls 0.180 user 0.000 sys 0.203 real
advance: 2074 calls 22.125 user 0.693 sys 23.098 real
assemble_region: 288 calls 3.419 user 0.039 sys 3.476 real
build_pileup: 1963 calls 0.255 user 0.000 sys 0.217 real
build_stats: 1987 calls 3.932 user 0.070 sys 3.836 real
build_variants: 215 calls 0.000 user 0.000 sys 0.002 real
calc: 3888 calls 2.900 user 0.001 sys 2.990 real
calc_region: 215 calls 21.378 user 0.019 sys 21.940 real
call_region: 215 calls 0.328 user 0.000 sys 0.395 real
clip_region: 503 calls 0.296 user 0.000 sys 0.299 real
done: 1 calls 0.742 user 0.000 sys 0.751 real
execute: 1 calls 0.006 user 0.001 sys 7.242 real
fetch: 8147 calls 5.580 user 0.012 sys 5.628 real
fetch_ref: 8489 calls 0.044 user 0.020 sys 0.045 real
fetch_region: 288 calls 0.070 user 0.000 sys 0.116 real
fetch_vcf: 2074 calls 0.771 user 0.001 sys 0.828 real
idle: 44 calls 0.083 user 0.000 sys 13.346 real
init: 1 calls 0.050 user 0.010 sys 0.060 real
pairhmm: 4281 calls 36.639 user 0.031 sys 36.719 real
realign: 215 calls 2.958 user 0.000 sys 3.266 real
region: 4053 calls 24.997 user 0.059 sys 25.669 real
tracker: 4053 calls 0.070 user 0.000 sys 0.020 real
trim_region: 288 calls 0.000 user 0.000 sys 0.004 real
overall: 951414784 mem 85.647 user 1.159 sys 8.491 real