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% @chr1:113698162, elapsed 0.7s, est remaining 12.8s, peak mem 145MB, user 6.8s, sys 0.4s, output queue size 4
progress 10% @chr2:3643344, elapsed 1.3s, est remaining 11.8s, peak mem 145MB, user 13.1s, sys 0.9s, output queue size 6
progress 15% @chr2:178609108, elapsed 2.0s, est remaining 11.2s, peak mem 146MB, user 20.0s, sys 1.2s, output queue size 12
progress 20% @chr3:57483276, elapsed 2.6s, est remaining 10.3s, peak mem 146MB, user 26.0s, sys 1.7s, output queue size 0
progress 25% @chr4:70598256, elapsed 3.3s, est remaining 9.8s, peak mem 146MB, user 32.8s, sys 2.2s, output queue size 4
progress 30% @chr5:135571753, elapsed 4.0s, est remaining 9.3s, peak mem 148MB, user 39.7s, sys 2.6s, output queue size 4
progress 35% @chr6:104957999, elapsed 4.6s, est remaining 8.5s, peak mem 149MB, user 45.8s, sys 2.9s, output queue size 2
progress 40% @chr7:106872437, elapsed 5.3s, est remaining 7.9s, peak mem 151MB, user 52.6s, sys 3.3s, output queue size 5
progress 45% @chr8:143810379, elapsed 5.9s, est remaining 7.3s, peak mem 152MB, user 59.2s, sys 3.7s, output queue size 3
progress 50% @chr10:21726144, elapsed 6.6s, est remaining 6.6s, peak mem 154MB, user 65.8s, sys 4.2s, output queue size 1
progress 55% @chr11:34132926, elapsed 7.3s, est remaining 5.9s, peak mem 154MB, user 71.9s, sys 4.8s, output queue size 0
progress 60% @chr12:12718707, elapsed 7.9s, est remaining 5.2s, peak mem 154MB, user 78.1s, sys 5.3s, output queue size 8
progress 65% @chr13:32149648, elapsed 8.5s, est remaining 4.6s, peak mem 154MB, user 84.7s, sys 5.6s, output queue size 10
progress 70% @chr15:35381722, elapsed 9.2s, est remaining 3.9s, peak mem 154MB, user 91.1s, sys 6.1s, output queue size 2
progress 75% @chr16:28494582, elapsed 9.8s, est remaining 3.3s, peak mem 154MB, user 97.5s, sys 6.6s, output queue size 0
progress 80% @chr17:40032956, elapsed 10.6s, est remaining 2.6s, peak mem 154MB, user 104.5s, sys 7.1s, output queue size 2
progress 85% @chr19:1796611, elapsed 11.2s, est remaining 2.0s, peak mem 155MB, user 111.1s, sys 7.7s, output queue size 3
progress 90% @chr19:54630974, elapsed 11.9s, est remaining 1.3s, peak mem 155MB, user 117.7s, sys 8.2s, output queue size 3
progress 95% @chr22:31897382, elapsed 13.4s, est remaining 0.7s, peak mem 330MB, user 132.5s, sys 9.1s, output queue size 10
progress 100% @chrY:21525110, elapsed 14.0s, est remaining 0.0s, peak mem 330MB, user 138.5s, sys 9.5s, output queue size 431
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
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: 71721858 81484557
output file size: 50711
reads: 1502003
contig: 178193 intervals 76355618 bases
"assemble": 207 calls 0.459 user 0.010 sys 0.432 real
"assemble_addRead": 207 calls 0.025 user 0.000 sys 0.007 real
"assemble_buildGraph": 465 calls 0.209 user 0.010 sys 0.185 real
"assemble_computecigar": 304 calls 0.055 user 0.019 sys 0.087 real
"assemble_kg_build_calcsize": 465 calls 0.065 user 0.000 sys 0.086 real
"assemble_kg_build_clear": 618 calls 0.012 user 0.000 sys 0.007 real
"assemble_kg_build_prepare": 930 calls 0.082 user 0.000 sys 0.083 real
"assemble_kg_build_threading": 312 calls 0.144 user 0.010 sys 0.095 real
"assemble_kg_op1": 312 calls 0.090 user 0.000 sys 0.060 real
"assemble_kg_op2": 312 calls 0.000 user 0.000 sys 0.004 real
"assemble_kg_op3": 312 calls 0.000 user 0.000 sys 0.005 real
"assemble_sg_clean": 304 calls 0.020 user 0.000 sys 0.023 real
"assemble_sg_create": 304 calls 0.023 user 0.001 sys 0.037 real
"checkGraph": 207 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 207 calls 0.065 user 0.019 sys 0.091 real
advance: 189104 calls 14.156 user 0.503 sys 19.286 real
assemble_region: 207 calls 0.549 user 0.029 sys 0.532 real
build_pileup: 70976 calls 0.346 user 0.028 sys 0.473 real
build_stats: 71686 calls 2.161 user 0.138 sys 2.650 real
build_variants: 162 calls 0.000 user 0.000 sys 0.001 real
calc: 128670 calls 2.553 user 0.070 sys 3.108 real
calc_region: 162 calls 1.747 user 0.009 sys 1.797 real
call_region: 162 calls 0.020 user 0.000 sys 0.041 real
clip_region: 369 calls 0.027 user 0.000 sys 0.031 real
done: 1 calls 0.442 user 0.000 sys 0.446 real
execute: 1 calls 0.005 user 0.001 sys 14.056 real
fetch: 743546 calls 0.924 user 0.075 sys 0.980 real
fetch_ref: 745712 calls 1.564 user 0.419 sys 2.790 real
fetch_region: 207 calls 0.001 user 0.000 sys 0.009 real
fetch_vcf: 189104 calls 41.433 user 1.203 sys 56.451 real
idle: 35 calls 0.006 user 0.000 sys 12.893 real
init: 1 calls 0.050 user 0.010 sys 0.059 real
pairhmm: 466 calls 2.983 user 0.016 sys 3.019 real
realign: 162 calls 0.405 user 0.001 sys 0.344 real
region: 367297 calls 2.332 user 0.102 sys 2.441 real
tracker: 367297 calls 0.357 user 0.041 sys 0.587 real
trim_region: 207 calls 0.000 user 0.000 sys 0.002 real
overall: 346812416 mem 157.934 user 12.565 sys 15.359 real