cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta -i reference-NA12878-downsampled-500k.bam -i HCC1395_tumor.recalibrated.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity_padded100bp.bed --algo TNhaplotyper2 --tumor_sample HCC1395_tumor --normal_sample reference-NA12878 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon_tnseq_42_curated_v4.vcf.gz positive_somatic_control_1.tnseq.vcf.gz --algo OrientationBias --tumor_sample HCC1395_tumor positive_somatic_control_1.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample HCC1395_tumor --normal_sample reference-NA12878 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments positive_somatic_control_1.tnseq.segments positive_somatic_control_1.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113697605, elapsed 1.2s, est remaining 22.3s, peak mem 144MB, user 12.3s, sys 0.6s, output queue size 4
progress 10% @chr2:3643344, elapsed 2.3s, est remaining 20.6s, peak mem 145MB, user 23.8s, sys 1.4s, output queue size 1
progress 15% @chr2:178606921, elapsed 3.4s, est remaining 19.5s, peak mem 147MB, user 35.5s, sys 2.1s, output queue size 12
progress 20% @chr3:57489409, elapsed 4.5s, est remaining 17.9s, peak mem 147MB, user 46.2s, sys 2.7s, output queue size 0
progress 25% @chr4:70530939, elapsed 5.6s, est remaining 16.8s, peak mem 147MB, user 56.9s, sys 3.5s, output queue size 8
progress 30% @chr5:135571753, elapsed 6.8s, est remaining 15.9s, peak mem 149MB, user 67.8s, sys 4.1s, output queue size 4
progress 35% @chr6:104957999, elapsed 7.9s, est remaining 14.6s, peak mem 150MB, user 77.6s, sys 4.9s, output queue size 3
progress 40% @chr7:106248199, elapsed 9.1s, est remaining 13.6s, peak mem 151MB, user 88.9s, sys 5.5s, output queue size 18
progress 45% @chr8:143812166, elapsed 10.3s, est remaining 12.6s, peak mem 152MB, user 100.0s, sys 6.3s, output queue size 2
progress 50% @chr10:21514996, elapsed 11.4s, est remaining 11.4s, peak mem 154MB, user 111.4s, sys 7.0s, output queue size 14
progress 55% @chr11:34135075, elapsed 12.6s, est remaining 10.3s, peak mem 154MB, user 122.7s, sys 8.0s, output queue size 4
progress 60% @chr12:12718707, elapsed 13.7s, est remaining 9.1s, peak mem 155MB, user 133.8s, sys 8.6s, output queue size 16
progress 65% @chr13:32155391, elapsed 14.8s, est remaining 8.0s, peak mem 155MB, user 145.5s, sys 9.3s, output queue size 10
progress 70% @chr15:35521993, elapsed 16.0s, est remaining 6.9s, peak mem 157MB, user 157.3s, sys 10.0s, output queue size 4
progress 75% @chr16:28488491, elapsed 17.1s, est remaining 5.7s, peak mem 157MB, user 168.4s, sys 10.5s, output queue size 2
progress 80% @chr17:40034816, elapsed 18.4s, est remaining 4.6s, peak mem 157MB, user 181.0s, sys 11.2s, output queue size 1
progress 85% @chr19:1808122, elapsed 19.6s, est remaining 3.5s, peak mem 157MB, user 193.1s, sys 11.7s, output queue size 3
progress 90% @chr19:54630974, elapsed 20.7s, est remaining 2.3s, peak mem 158MB, user 204.5s, sys 12.3s, output queue size 6
progress 95% @chr22:32068396, elapsed 22.8s, est remaining 1.2s, peak mem 332MB, user 223.6s, sys 13.2s, output queue size 5
progress 100% @chr6_GL000251v2_alt:3938900, elapsed 23.6s, est remaining 0.0s, peak mem 332MB, user 230.1s, sys 13.6s, output queue size 10
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 00050654
  features: 1f8bfbff fffa320b
  extended: d19f47ab 00000018
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8175M CPU @ 2.50GHz
threads: 12 max 48
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 71721858 81484549
output file size: 50711
reads: 1502003
contig: 178193 intervals 76355618 bases
"assemble": 207 calls 0.559 user 0.012 sys 0.551 real
"assemble_addRead": 207 calls 0.010 user 0.000 sys 0.010 real
"assemble_buildGraph": 465 calls 0.247 user 0.002 sys 0.243 real
"assemble_computecigar": 304 calls 0.121 user 0.009 sys 0.117 real
"assemble_kg_build_calcsize": 465 calls 0.112 user 0.000 sys 0.112 real
"assemble_kg_build_clear": 618 calls 0.010 user 0.000 sys 0.009 real
"assemble_kg_build_prepare": 930 calls 0.168 user 0.010 sys 0.109 real
"assemble_kg_build_threading": 312 calls 0.111 user 0.000 sys 0.125 real
"assemble_kg_op1": 312 calls 0.040 user 0.000 sys 0.068 real
"assemble_kg_op2": 312 calls 0.000 user 0.000 sys 0.005 real
"assemble_kg_op3": 312 calls 0.010 user 0.000 sys 0.007 real
"assemble_sg_clean": 304 calls 0.030 user 0.000 sys 0.030 real
"assemble_sg_create": 304 calls 0.030 user 0.000 sys 0.047 real
"checkGraph": 207 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 207 calls 0.121 user 0.009 sys 0.122 real
advance: 189104 calls 22.464 user 0.509 sys 29.081 real
assemble_region: 207 calls 0.689 user 0.021 sys 0.685 real
build_pileup: 70976 calls 0.723 user 0.026 sys 1.030 real
build_stats: 71686 calls 4.150 user 0.158 sys 4.882 real
build_variants: 162 calls 0.000 user 0.000 sys 0.001 real
calc: 128670 calls 5.684 user 0.102 sys 7.196 real
calc_region: 162 calls 2.366 user 0.021 sys 2.405 real
call_region: 162 calls 0.010 user 0.000 sys 0.044 real
clip_region: 369 calls 0.060 user 0.000 sys 0.035 real
done: 1 calls 0.649 user 0.000 sys 0.655 real
execute: 1 calls 0.012 user 0.000 sys 23.605 real
fetch: 743546 calls 1.339 user 0.217 sys 1.521 real
fetch_ref: 745712 calls 3.147 user 0.695 sys 5.392 real
fetch_region: 207 calls 0.020 user 0.000 sys 0.009 real
fetch_vcf: 189104 calls 75.564 user 1.624 sys 96.525 real
idle: 35 calls 0.022 user 0.009 sys 13.589 real
init: 1 calls 0.106 user 0.000 sys 0.104 real
pairhmm: 466 calls 4.083 user 0.048 sys 4.112 real
realign: 162 calls 0.390 user 0.000 sys 0.351 real
region: 367297 calls 3.152 user 0.124 sys 3.364 real
tracker: 367297 calls 0.803 user 0.158 sys 1.363 real
trim_region: 207 calls 0.000 user 0.000 sys 0.002 real
overall: 348884992 mem 268.576 user 18.992 sys 25.167 real