cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta --interval_padding 100 -i HCC1395_BL.recalibrated.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% @chr21:14521050, elapsed 0.1s, est remaining 2.1s, peak mem 135MB, user 0.7s, sys 0.0s, output queue size 7
progress 10% @chr21:25606349, elapsed 0.2s, est remaining 1.5s, peak mem 144MB, user 1.3s, sys 0.1s, output queue size 106
progress 15% @chr21:29027814, elapsed 0.2s, est remaining 1.2s, peak mem 147MB, user 1.9s, sys 0.1s, output queue size 22
progress 20% @chr21:30755039, elapsed 0.3s, est remaining 1.0s, peak mem 153MB, user 2.4s, sys 0.1s, output queue size 16
progress 25% @chr21:32375298, elapsed 0.3s, est remaining 1.0s, peak mem 156MB, user 3.0s, sys 0.1s, output queue size 63
progress 30% @chr21:33426784, elapsed 0.4s, est remaining 0.9s, peak mem 162MB, user 3.7s, sys 0.1s, output queue size 75
progress 35% @chr21:33908982, elapsed 0.4s, est remaining 0.8s, peak mem 165MB, user 4.3s, sys 0.1s, output queue size 74
progress 40% @chr21:33549376, elapsed 0.5s, est remaining 0.8s, peak mem 207MB, user 5.2s, sys 0.2s, output queue size 158
progress 45% @chr21:37157061, elapsed 0.7s, est remaining 0.9s, peak mem 219MB, user 6.2s, sys 0.2s, output queue size 160
progress 50% @chr21:39277151, elapsed 0.8s, est remaining 0.8s, peak mem 231MB, user 6.8s, sys 0.2s, output queue size 264
progress 55% @chr21:41401870, elapsed 0.9s, est remaining 0.7s, peak mem 249MB, user 7.5s, sys 0.2s, output queue size 370
progress 60% @chr21:41484073, elapsed 1.3s, est remaining 0.9s, peak mem 348MB, user 11.2s, sys 0.3s, output queue size 27
progress 65% @chr21:42395224, elapsed 1.6s, est remaining 0.8s, peak mem 357MB, user 12.7s, sys 0.4s, output queue size 113
progress 70% @chr21:43071885, elapsed 1.6s, est remaining 0.7s, peak mem 363MB, user 13.9s, sys 0.4s, output queue size 216
progress 75% @chr21:44115591, elapsed 1.7s, est remaining 0.6s, peak mem 366MB, user 14.5s, sys 0.5s, output queue size 327
progress 80% @chr21:44413791, elapsed 1.8s, est remaining 0.4s, peak mem 366MB, user 15.5s, sys 0.5s, output queue size 429
progress 85% @chr21:44966934, elapsed 1.9s, est remaining 0.3s, peak mem 366MB, user 16.3s, sys 0.5s, output queue size 502
progress 90% @chr21:46119688, elapsed 2.0s, est remaining 0.2s, peak mem 366MB, user 17.4s, sys 0.5s, output queue size 614
progress 95% @chr21:46322539, elapsed 2.0s, est remaining 0.1s, peak mem 366MB, user 18.9s, sys 0.5s, output queue size 74
progress 100% @chr21:46661700, elapsed 2.2s, est remaining 0.0s, peak mem 366MB, user 19.9s, sys 0.6s, output queue size 2
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  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: 163002590
output file size: 51811
reads: 1955548
contig: 1979 intervals 801713 bases
"assemble": 227 calls 0.979 user 0.010 sys 0.931 real
"assemble_addRead": 227 calls 0.000 user 0.000 sys 0.020 real
"assemble_buildGraph": 511 calls 0.419 user 0.000 sys 0.442 real
"assemble_computecigar": 321 calls 0.133 user 0.003 sys 0.164 real
"assemble_kg_build_calcsize": 511 calls 0.235 user 0.000 sys 0.265 real
"assemble_kg_build_clear": 699 calls 0.046 user 0.000 sys 0.021 real
"assemble_kg_build_prepare": 1022 calls 0.277 user 0.010 sys 0.211 real
"assemble_kg_build_threading": 323 calls 0.168 user 0.000 sys 0.166 real
"assemble_kg_op1": 323 calls 0.082 user 0.000 sys 0.113 real
"assemble_kg_op2": 323 calls 0.010 user 0.000 sys 0.006 real
"assemble_kg_op3": 323 calls 0.000 user 0.000 sys 0.006 real
"assemble_sg_clean": 321 calls 0.080 user 0.000 sys 0.036 real
"assemble_sg_create": 321 calls 0.040 user 0.000 sys 0.051 real
"checkGraph": 227 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 227 calls 0.140 user 0.003 sys 0.171 real
advance: 2074 calls 7.048 user 0.187 sys 7.740 real
assemble_region: 227 calls 1.128 user 0.013 sys 1.125 real
build_pileup: 1957 calls 0.043 user 0.000 sys 0.056 real
build_stats: 1979 calls 1.651 user 0.063 sys 1.767 real
build_variants: 179 calls 0.000 user 0.000 sys 0.001 real
calc: 3869 calls 0.791 user 0.000 sys 0.943 real
calc_region: 179 calls 4.224 user 0.028 sys 4.346 real
call_region: 179 calls 0.061 user 0.000 sys 0.086 real
clip_region: 406 calls 0.105 user 0.000 sys 0.070 real
done: 1 calls 0.377 user 0.000 sys 0.379 real
execute: 1 calls 0.002 user 0.000 sys 2.162 real
fetch: 8147 calls 1.457 user 0.060 sys 1.304 real
fetch_ref: 8428 calls 0.051 user 0.003 sys 0.047 real
fetch_region: 227 calls 0.030 user 0.000 sys 0.020 real
fetch_vcf: 2074 calls 0.875 user 0.010 sys 0.913 real
idle: 40 calls 0.047 user 0.000 sys 13.163 real
init: 1 calls 0.060 user 0.020 sys 0.076 real
pairhmm: 1058 calls 7.643 user 0.064 sys 7.690 real
realign: 179 calls 0.759 user 0.000 sys 0.801 real
region: 4053 calls 5.423 user 0.041 sys 5.528 real
tracker: 4053 calls 0.030 user 0.000 sys 0.015 real
trim_region: 227 calls 0.010 user 0.000 sys 0.004 real
overall: 384634880 mem 25.630 user 0.699 sys 3.486 real