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% @chr1:113710154, elapsed 0.7s, est remaining 12.7s, peak mem 145MB, user 6.8s, sys 0.5s, output queue size 4
progress 10% @chr2:3643344, elapsed 1.3s, est remaining 11.9s, peak mem 145MB, user 13.1s, sys 1.0s, output queue size 6
progress 15% @chr2:178606921, elapsed 2.0s, est remaining 11.3s, peak mem 146MB, user 19.8s, sys 1.6s, output queue size 12
progress 20% @chr3:57483276, elapsed 2.6s, est remaining 10.4s, peak mem 147MB, user 26.1s, sys 2.0s, output queue size 1
progress 25% @chr4:70530939, elapsed 3.3s, est remaining 9.8s, peak mem 147MB, user 33.0s, sys 2.5s, output queue size 8
progress 30% @chr5:135850325, elapsed 3.9s, est remaining 9.2s, peak mem 150MB, user 39.9s, sys 2.9s, output queue size 4
progress 35% @chr6:104957999, elapsed 4.5s, est remaining 8.4s, peak mem 151MB, user 45.9s, sys 3.2s, output queue size 3
progress 40% @chr7:106248199, elapsed 5.2s, est remaining 7.9s, peak mem 151MB, user 52.7s, sys 3.6s, output queue size 14
progress 45% @chr8:143835562, elapsed 5.9s, est remaining 7.2s, peak mem 152MB, user 59.5s, sys 4.1s, output queue size 0
progress 50% @chr10:21726144, elapsed 6.5s, est remaining 6.5s, peak mem 154MB, user 66.1s, sys 4.4s, output queue size 1
progress 55% @chr11:34132025, elapsed 7.2s, est remaining 5.9s, peak mem 154MB, user 72.5s, sys 4.8s, output queue size 1
progress 60% @chr12:12718707, elapsed 7.8s, est remaining 5.2s, peak mem 154MB, user 78.6s, sys 5.1s, output queue size 9
progress 65% @chr13:32134804, elapsed 8.4s, est remaining 4.5s, peak mem 154MB, user 85.3s, sys 5.5s, output queue size 4
progress 70% @chr15:35372050, elapsed 9.0s, est remaining 3.9s, peak mem 155MB, user 91.8s, sys 5.9s, output queue size 4
progress 75% @chr16:28488491, elapsed 9.7s, est remaining 3.2s, peak mem 155MB, user 98.3s, sys 6.3s, output queue size 2
progress 80% @chr17:40032956, elapsed 10.4s, est remaining 2.6s, peak mem 156MB, user 105.6s, sys 6.6s, output queue size 2
progress 85% @chr19:1796611, elapsed 11.0s, est remaining 1.9s, peak mem 156MB, user 112.5s, sys 6.9s, output queue size 3
progress 90% @chr19:54632916, elapsed 11.6s, est remaining 1.3s, peak mem 157MB, user 119.2s, sys 7.3s, output queue size 1
progress 95% @chr22:31897382, elapsed 13.1s, est remaining 0.7s, peak mem 330MB, user 134.0s, sys 7.8s, output queue size 10
progress 100% @chrY:18773006, elapsed 13.8s, est remaining 0.0s, peak mem 331MB, user 140.0s, sys 8.2s, output queue size 433
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 81484550
output file size: 50711
reads: 1502003
contig: 178193 intervals 76355618 bases
"assemble": 207 calls 0.377 user 0.000 sys 0.406 real
"assemble_addRead": 207 calls 0.010 user 0.000 sys 0.007 real
"assemble_buildGraph": 465 calls 0.107 user 0.000 sys 0.173 real
"assemble_computecigar": 304 calls 0.070 user 0.000 sys 0.087 real
"assemble_kg_build_calcsize": 465 calls 0.044 user 0.000 sys 0.084 real
"assemble_kg_build_clear": 618 calls 0.020 user 0.000 sys 0.007 real
"assemble_kg_build_prepare": 930 calls 0.110 user 0.000 sys 0.077 real
"assemble_kg_build_threading": 312 calls 0.063 user 0.000 sys 0.085 real
"assemble_kg_op1": 312 calls 0.030 user 0.000 sys 0.058 real
"assemble_kg_op2": 312 calls 0.010 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 0.025 user 0.000 sys 0.022 real
"assemble_sg_create": 304 calls 0.050 user 0.000 sys 0.036 real
"checkGraph": 207 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 207 calls 0.080 user 0.000 sys 0.091 real
advance: 189104 calls 15.091 user 0.381 sys 18.923 real
assemble_region: 207 calls 0.477 user 0.000 sys 0.505 real
build_pileup: 70976 calls 0.283 user 0.013 sys 0.465 real
build_stats: 71686 calls 1.961 user 0.057 sys 2.211 real
build_variants: 162 calls 0.000 user 0.000 sys 0.001 real
calc: 128670 calls 2.167 user 0.058 sys 2.917 real
calc_region: 162 calls 1.676 user 0.011 sys 1.774 real
call_region: 162 calls 0.034 user 0.000 sys 0.038 real
clip_region: 369 calls 0.000 user 0.000 sys 0.028 real
done: 1 calls 0.439 user 0.000 sys 0.445 real
execute: 1 calls 0.004 user 0.000 sys 13.781 real
fetch: 743546 calls 0.716 user 0.107 sys 0.833 real
fetch_ref: 745712 calls 1.843 user 0.441 sys 2.726 real
fetch_region: 207 calls 0.002 user 0.000 sys 0.007 real
fetch_vcf: 189104 calls 43.386 user 0.919 sys 55.878 real
idle: 35 calls 0.011 user 0.009 sys 12.867 real
init: 1 calls 0.060 user 0.000 sys 0.059 real
pairhmm: 466 calls 2.992 user 0.010 sys 2.992 real
realign: 162 calls 0.279 user 0.000 sys 0.338 real
region: 367297 calls 2.197 user 0.042 sys 2.385 real
tracker: 367297 calls 0.298 user 0.090 sys 0.552 real
trim_region: 207 calls 0.000 user 0.000 sys 0.002 real
overall: 347435008 mem 155.686 user 11.075 sys 15.078 real