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% @chr1:113711646, elapsed 1.0s, est remaining 19.4s, peak mem 120MB, user 8.0s, sys 0.8s, output queue size 5
progress 10% @chr2:3643344, elapsed 1.8s, est remaining 16.5s, peak mem 120MB, user 15.2s, sys 1.7s, output queue size 6
progress 15% @chr2:178588438, elapsed 2.7s, est remaining 15.1s, peak mem 120MB, user 22.4s, sys 2.5s, output queue size 10
progress 20% @chr3:57483276, elapsed 3.5s, est remaining 14.0s, peak mem 120MB, user 29.7s, sys 3.2s, output queue size 2
progress 25% @chr4:70602524, elapsed 4.4s, est remaining 13.1s, peak mem 120MB, user 37.1s, sys 4.0s, output queue size 4
progress 30% @chr5:135534877, elapsed 5.2s, est remaining 12.2s, peak mem 120MB, user 44.8s, sys 4.7s, output queue size 3
progress 35% @chr6:104843123, elapsed 6.0s, est remaining 11.1s, peak mem 120MB, user 51.4s, sys 5.5s, output queue size 2
progress 40% @chr7:106248199, elapsed 6.8s, est remaining 10.2s, peak mem 120MB, user 58.7s, sys 6.2s, output queue size 15
progress 45% @chr8:143815114, elapsed 7.6s, est remaining 9.3s, peak mem 120MB, user 65.9s, sys 7.0s, output queue size 1
progress 50% @chr10:21726144, elapsed 8.5s, est remaining 8.5s, peak mem 123MB, user 73.0s, sys 7.8s, output queue size 1
progress 55% @chr11:34132025, elapsed 9.3s, est remaining 7.6s, peak mem 123MB, user 80.1s, sys 8.6s, output queue size 2
progress 60% @chr12:12718707, elapsed 10.0s, est remaining 6.7s, peak mem 123MB, user 86.8s, sys 9.2s, output queue size 12
progress 65% @chr13:32078734, elapsed 10.8s, est remaining 5.8s, peak mem 123MB, user 93.9s, sys 9.7s, output queue size 10
progress 70% @chr15:35372050, elapsed 11.6s, est remaining 5.0s, peak mem 123MB, user 101.0s, sys 10.3s, output queue size 4
progress 75% @chr16:28487356, elapsed 12.3s, est remaining 4.1s, peak mem 123MB, user 108.3s, sys 10.9s, output queue size 3
progress 80% @chr17:40032956, elapsed 13.2s, est remaining 3.3s, peak mem 123MB, user 116.3s, sys 11.5s, output queue size 1
progress 85% @chr19:1810522, elapsed 14.0s, est remaining 2.5s, peak mem 123MB, user 124.3s, sys 12.1s, output queue size 3
progress 90% @chr19:54632916, elapsed 14.9s, est remaining 1.7s, peak mem 123MB, user 132.2s, sys 12.7s, output queue size 0
progress 95% @chr22:32081766, elapsed 16.7s, est remaining 0.9s, peak mem 273MB, user 149.6s, sys 13.6s, output queue size 10
progress 100% @chr6_GL000251v2_alt:3938900, elapsed 17.5s, est remaining 0.0s, peak mem 273MB, user 156.8s, sys 14.2s, output queue size 419
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 12 max 384
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 71721858 81484543
output file size: 50711
reads: 1502003
contig: 178193 intervals 76355618 bases
"assemble": 207 calls 0.495 user 0.004 sys 0.459 real
"assemble_addRead": 207 calls 0.000 user 0.000 sys 0.007 real
"assemble_buildGraph": 465 calls 0.203 user 0.000 sys 0.200 real
"assemble_computecigar": 304 calls 0.066 user 0.007 sys 0.107 real
"assemble_kg_build_calcsize": 465 calls 0.088 user 0.000 sys 0.100 real
"assemble_kg_build_clear": 618 calls 0.000 user 0.000 sys 0.007 real
"assemble_kg_build_prepare": 930 calls 0.108 user 0.001 sys 0.088 real
"assemble_kg_build_threading": 312 calls 0.095 user 0.000 sys 0.096 real
"assemble_kg_op1": 312 calls 0.063 user 0.000 sys 0.060 real
"assemble_kg_op2": 312 calls 0.010 user 0.001 sys 0.005 real
"assemble_kg_op3": 312 calls 0.010 user 0.000 sys 0.006 real
"assemble_sg_clean": 304 calls 0.038 user 0.000 sys 0.026 real
"assemble_sg_create": 304 calls 0.045 user 0.001 sys 0.040 real
"checkGraph": 207 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 207 calls 0.066 user 0.007 sys 0.112 real
advance: 189104 calls 15.958 user 0.619 sys 22.956 real
assemble_region: 207 calls 0.561 user 0.011 sys 0.581 real
build_pileup: 70976 calls 0.477 user 0.013 sys 0.655 real
build_stats: 71686 calls 2.675 user 0.084 sys 2.750 real
build_variants: 162 calls 0.000 user 0.000 sys 0.001 real
calc: 128670 calls 2.331 user 0.045 sys 3.485 real
calc_region: 162 calls 1.762 user 0.017 sys 1.843 real
call_region: 162 calls 0.049 user 0.000 sys 0.042 real
clip_region: 369 calls 0.029 user 0.004 sys 0.033 real
done: 1 calls 0.323 user 0.000 sys 0.330 real
execute: 1 calls 0.005 user 0.003 sys 17.524 real
fetch: 743546 calls 1.099 user 0.070 sys 1.068 real
fetch_ref: 745712 calls 2.709 user 0.857 sys 3.678 real
fetch_region: 207 calls 0.000 user 0.000 sys 0.008 real
fetch_vcf: 189104 calls 42.442 user 1.731 sys 67.032 real
idle: 35 calls 0.003 user 0.003 sys 12.903 real
init: 1 calls 0.038 user 0.019 sys 0.060 real
pairhmm: 466 calls 2.882 user 0.029 sys 2.894 real
realign: 162 calls 0.251 user 0.002 sys 0.350 real
region: 367297 calls 2.375 user 0.058 sys 2.544 real
tracker: 367297 calls 0.337 user 0.049 sys 0.701 real
trim_region: 207 calls 0.000 user 0.000 sys 0.002 real
overall: 286371840 mem 185.893 user 20.921 sys 18.942 real