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 12.6s, peak mem 143MB, user 6.9s, sys 0.3s, output queue size 4
progress 10% @chr2:3603546, elapsed 1.3s, est remaining 11.5s, peak mem 144MB, user 13.2s, sys 0.8s, output queue size 6
progress 15% @chr2:178606921, elapsed 1.9s, est remaining 11.0s, peak mem 145MB, user 20.0s, sys 1.3s, output queue size 12
progress 20% @chr3:57483276, elapsed 2.5s, est remaining 10.1s, peak mem 145MB, user 26.2s, sys 1.6s, output queue size 0
progress 25% @chr4:70532355, elapsed 3.2s, est remaining 9.6s, peak mem 145MB, user 33.0s, sys 1.9s, output queue size 7
progress 30% @chr5:135873921, elapsed 3.8s, est remaining 9.0s, peak mem 147MB, user 39.9s, sys 2.4s, output queue size 4
progress 35% @chr6:104957999, elapsed 4.4s, est remaining 8.2s, peak mem 149MB, user 46.0s, sys 2.8s, output queue size 3
progress 40% @chr7:106867451, elapsed 5.1s, est remaining 7.6s, peak mem 151MB, user 52.7s, sys 3.1s, output queue size 5
progress 45% @chr8:143821497, elapsed 5.7s, est remaining 7.0s, peak mem 152MB, user 59.6s, sys 3.4s, output queue size 1
progress 50% @chr10:21726144, elapsed 6.4s, est remaining 6.4s, peak mem 154MB, user 66.2s, sys 3.8s, output queue size 2
progress 55% @chr11:34132025, elapsed 7.0s, est remaining 5.7s, peak mem 154MB, user 72.6s, sys 4.3s, output queue size 2
progress 60% @chr12:12718707, elapsed 7.6s, est remaining 5.1s, peak mem 154MB, user 78.7s, sys 4.7s, output queue size 9
progress 65% @chr13:32149648, elapsed 8.2s, est remaining 4.4s, peak mem 154MB, user 85.3s, sys 5.1s, output queue size 0
progress 70% @chr15:35381722, elapsed 8.9s, est remaining 3.8s, peak mem 154MB, user 91.7s, sys 5.5s, output queue size 2
progress 75% @chr16:28494582, elapsed 9.5s, est remaining 3.2s, peak mem 154MB, user 98.0s, sys 5.9s, output queue size 0
progress 80% @chr17:40035622, elapsed 10.2s, est remaining 2.5s, peak mem 154MB, user 105.0s, sys 6.5s, output queue size 2
progress 85% @chr19:1805788, elapsed 10.8s, est remaining 1.9s, peak mem 154MB, user 111.8s, sys 6.9s, output queue size 2
progress 90% @chr19:54632916, elapsed 11.4s, est remaining 1.3s, peak mem 154MB, user 118.3s, sys 7.4s, output queue size 0
progress 95% @chr22:31897382, elapsed 12.9s, est remaining 0.7s, peak mem 332MB, user 133.1s, sys 7.9s, output queue size 10
progress 100% @chrY:20759768, elapsed 13.5s, est remaining 0.0s, peak mem 332MB, user 139.0s, sys 8.3s, output queue size 206
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 81484553
output file size: 50711
reads: 1502003
contig: 178193 intervals 76355618 bases
"assemble": 207 calls 0.372 user 0.010 sys 0.405 real
"assemble_addRead": 207 calls 0.010 user 0.000 sys 0.007 real
"assemble_buildGraph": 465 calls 0.158 user 0.000 sys 0.172 real
"assemble_computecigar": 304 calls 0.081 user 0.009 sys 0.087 real
"assemble_kg_build_calcsize": 465 calls 0.060 user 0.000 sys 0.084 real
"assemble_kg_build_clear": 618 calls 0.000 user 0.000 sys 0.007 real
"assemble_kg_build_prepare": 930 calls 0.076 user 0.010 sys 0.077 real
"assemble_kg_build_threading": 312 calls 0.098 user 0.000 sys 0.085 real
"assemble_kg_op1": 312 calls 0.023 user 0.000 sys 0.059 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 0.013 user 0.000 sys 0.022 real
"assemble_sg_create": 304 calls 0.076 user 0.000 sys 0.035 real
"checkGraph": 207 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 207 calls 0.081 user 0.009 sys 0.090 real
advance: 189104 calls 15.096 user 0.306 sys 18.733 real
assemble_region: 207 calls 0.472 user 0.020 sys 0.503 real
build_pileup: 70976 calls 0.360 user 0.013 sys 0.446 real
build_stats: 71686 calls 1.827 user 0.077 sys 2.144 real
build_variants: 162 calls 0.000 user 0.000 sys 0.001 real
calc: 128670 calls 2.309 user 0.029 sys 2.845 real
calc_region: 162 calls 1.694 user 0.001 sys 1.761 real
call_region: 162 calls 0.053 user 0.000 sys 0.037 real
clip_region: 369 calls 0.032 user 0.000 sys 0.028 real
done: 1 calls 0.432 user 0.000 sys 0.440 real
execute: 1 calls 0.008 user 0.001 sys 13.523 real
fetch: 743546 calls 0.633 user 0.080 sys 0.813 real
fetch_ref: 745712 calls 1.860 user 0.497 sys 2.721 real
fetch_region: 207 calls 0.000 user 0.000 sys 0.007 real
fetch_vcf: 189104 calls 43.741 user 0.891 sys 55.408 real
idle: 35 calls 0.005 user 0.004 sys 12.863 real
init: 1 calls 0.040 user 0.010 sys 0.058 real
pairhmm: 466 calls 2.974 user 0.000 sys 2.970 real
realign: 162 calls 0.266 user 0.000 sys 0.336 real
region: 367297 calls 2.199 user 0.060 sys 2.366 real
tracker: 367297 calls 0.478 user 0.063 sys 0.537 real
trim_region: 207 calls 0.000 user 0.000 sys 0.002 real
overall: 348508160 mem 153.530 user 11.189 sys 14.813 real