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% @chr21:14373517, elapsed 0.1s, est remaining 1.6s, peak mem 151MB, user 0.4s, sys 0.0s, output queue size 56
progress 10% @chr21:25698577, elapsed 0.1s, est remaining 1.1s, peak mem 160MB, user 0.9s, sys 0.1s, output queue size 106
progress 15% @chr21:29036171, elapsed 0.2s, est remaining 0.9s, peak mem 165MB, user 1.4s, sys 0.1s, output queue size 22
progress 20% @chr21:30755039, elapsed 0.2s, est remaining 0.8s, peak mem 169MB, user 1.8s, sys 0.1s, output queue size 16
progress 25% @chr21:32375298, elapsed 0.3s, est remaining 0.8s, peak mem 172MB, user 2.3s, sys 0.1s, output queue size 63
progress 30% @chr21:33426784, elapsed 0.3s, est remaining 0.7s, peak mem 177MB, user 2.8s, sys 0.1s, output queue size 75
progress 35% @chr21:34379405, elapsed 0.3s, est remaining 0.6s, peak mem 182MB, user 3.3s, sys 0.1s, output queue size 74
progress 40% @chr21:33549376, elapsed 0.4s, est remaining 0.6s, peak mem 235MB, user 3.9s, sys 0.1s, output queue size 160
progress 45% @chr21:37188395, elapsed 0.6s, est remaining 0.7s, peak mem 238MB, user 4.5s, sys 0.1s, output queue size 166
progress 50% @chr21:39264791, elapsed 0.6s, est remaining 0.6s, peak mem 255MB, user 5.3s, sys 0.2s, output queue size 264
progress 55% @chr21:41398797, elapsed 0.7s, est remaining 0.6s, peak mem 265MB, user 5.8s, sys 0.2s, output queue size 370
progress 60% @chr21:41802612, elapsed 1.2s, est remaining 0.8s, peak mem 369MB, user 9.1s, sys 0.3s, output queue size 16
progress 65% @chr21:42403846, elapsed 1.3s, est remaining 0.7s, peak mem 369MB, user 10.1s, sys 0.3s, output queue size 112
progress 70% @chr21:43071885, elapsed 1.3s, est remaining 0.6s, peak mem 369MB, user 11.0s, sys 0.3s, output queue size 216
progress 75% @chr21:44126800, elapsed 1.4s, est remaining 0.5s, peak mem 369MB, user 11.6s, sys 0.3s, output queue size 327
progress 80% @chr21:44369077, elapsed 1.5s, est remaining 0.4s, peak mem 369MB, user 12.3s, sys 0.3s, output queue size 429
progress 85% @chr21:44666346, elapsed 1.5s, est remaining 0.3s, peak mem 369MB, user 13.0s, sys 0.3s, output queue size 503
progress 90% @chr21:46003020, elapsed 1.6s, est remaining 0.2s, peak mem 369MB, user 13.7s, sys 0.4s, output queue size 612
progress 95% @chr21:46314616, elapsed 1.7s, est remaining 0.1s, peak mem 369MB, user 14.9s, sys 0.4s, output queue size 74
progress 100% @chr21:46661700, elapsed 1.8s, est remaining 0.0s, peak mem 369MB, user 15.6s, sys 0.4s, 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
output file size: 51811
reads: 1955548
contig: 1979 intervals 801713 bases
"assemble": 227 calls 0.650 user 0.027 sys 0.732 real
"assemble_addRead": 227 calls 0.040 user 0.010 sys 0.016 real
"assemble_buildGraph": 511 calls 0.345 user 0.027 sys 0.329 real
"assemble_computecigar": 321 calls 0.132 user 0.000 sys 0.114 real
"assemble_kg_build_calcsize": 511 calls 0.161 user 0.010 sys 0.188 real
"assemble_kg_build_clear": 699 calls 0.013 user 0.000 sys 0.017 real
"assemble_kg_build_prepare": 1022 calls 0.141 user 0.000 sys 0.177 real
"assemble_kg_build_threading": 323 calls 0.184 user 0.017 sys 0.131 real
"assemble_kg_op1": 323 calls 0.090 user 0.000 sys 0.099 real
"assemble_kg_op2": 323 calls 0.000 user 0.000 sys 0.005 real
"assemble_kg_op3": 323 calls 0.012 user 0.000 sys 0.005 real
"assemble_sg_clean": 321 calls 0.010 user 0.000 sys 0.027 real
"assemble_sg_create": 321 calls 0.004 user 0.000 sys 0.039 real
"checkGraph": 227 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 227 calls 0.132 user 0.000 sys 0.119 real
advance: 2074 calls 5.215 user 0.144 sys 5.716 real
assemble_region: 227 calls 0.822 user 0.037 sys 0.870 real
build_pileup: 1957 calls 0.030 user 0.000 sys 0.042 real
build_stats: 1979 calls 1.393 user 0.013 sys 1.390 real
build_variants: 179 calls 0.000 user 0.000 sys 0.001 real
calc: 3869 calls 0.742 user 0.002 sys 0.721 real
calc_region: 179 calls 3.978 user 0.044 sys 4.122 real
call_region: 179 calls 0.073 user 0.000 sys 0.073 real
clip_region: 406 calls 0.020 user 0.000 sys 0.059 real
done: 1 calls 0.487 user 0.000 sys 0.487 real
execute: 1 calls 0.008 user 0.001 sys 1.755 real
fetch: 8147 calls 0.925 user 0.001 sys 1.029 real
fetch_ref: 8428 calls 0.045 user 0.001 sys 0.039 real
fetch_region: 227 calls 0.000 user 0.000 sys 0.018 real
fetch_vcf: 2074 calls 0.587 user 0.030 sys 0.668 real
idle: 42 calls 0.071 user 0.001 sys 12.911 real
init: 1 calls 0.050 user 0.000 sys 0.057 real
pairhmm: 1058 calls 7.215 user 0.061 sys 7.212 real
realign: 179 calls 0.639 user 0.000 sys 0.758 real
region: 4053 calls 4.820 user 0.082 sys 5.039 real
tracker: 4053 calls 0.020 user 0.000 sys 0.012 real
trim_region: 227 calls 0.000 user 0.000 sys 0.002 real
overall: 387571712 mem 20.936 user 0.479 sys 2.994 real