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 0.8s, est remaining 15.8s, peak mem 145MB, user 7.6s, sys 0.4s, output queue size 4
progress 10% @chr2:3604215, elapsed 1.6s, est remaining 14.4s, peak mem 146MB, user 14.9s, sys 0.9s, output queue size 6
progress 15% @chr2:178604608, elapsed 2.4s, est remaining 13.6s, peak mem 147MB, user 22.6s, sys 1.3s, output queue size 12
progress 20% @chr3:57508282, elapsed 3.1s, est remaining 12.4s, peak mem 147MB, user 29.3s, sys 1.7s, output queue size 1
progress 25% @chr4:70632551, elapsed 3.8s, est remaining 11.5s, peak mem 148MB, user 36.4s, sys 2.1s, output queue size 4
progress 30% @chr5:135571753, elapsed 4.6s, est remaining 10.7s, peak mem 150MB, user 43.5s, sys 2.7s, output queue size 4
progress 35% @chr6:104791404, elapsed 5.3s, est remaining 9.8s, peak mem 151MB, user 50.2s, sys 3.2s, output queue size 7
progress 40% @chr7:106867451, elapsed 6.1s, est remaining 9.1s, peak mem 152MB, user 57.7s, sys 3.7s, output queue size 1
progress 45% @chr8:143835562, elapsed 6.9s, est remaining 8.4s, peak mem 152MB, user 65.2s, sys 4.2s, output queue size 0
progress 50% @chr10:21727756, elapsed 7.6s, est remaining 7.6s, peak mem 156MB, user 72.5s, sys 4.8s, output queue size 0
progress 55% @chr11:34127363, elapsed 8.4s, est remaining 6.9s, peak mem 156MB, user 79.7s, sys 5.3s, output queue size 4
progress 60% @chr12:12718707, elapsed 9.1s, est remaining 6.1s, peak mem 157MB, user 86.6s, sys 5.7s, output queue size 16
progress 65% @chr13:32078734, elapsed 9.9s, est remaining 5.3s, peak mem 157MB, user 93.8s, sys 6.2s, output queue size 10
progress 70% @chr15:35542313, elapsed 10.7s, est remaining 4.6s, peak mem 158MB, user 101.0s, sys 6.7s, output queue size 2
progress 75% @chr16:28487356, elapsed 11.4s, est remaining 3.8s, peak mem 159MB, user 108.2s, sys 7.0s, output queue size 3
progress 80% @chr17:40034816, elapsed 12.2s, est remaining 3.0s, peak mem 159MB, user 116.2s, sys 7.4s, output queue size 2
progress 85% @chr19:1785059, elapsed 12.9s, est remaining 2.3s, peak mem 159MB, user 123.6s, sys 7.9s, output queue size 17
progress 90% @chr19:54662811, elapsed 13.7s, est remaining 1.5s, peak mem 160MB, user 130.8s, sys 8.2s, output queue size 6
progress 95% @chr22:32049843, elapsed 15.5s, est remaining 0.8s, peak mem 324MB, user 148.3s, sys 8.9s, output queue size 10
progress 100% @chr6_GL000251v2_alt:3933919, elapsed 16.2s, est remaining 0.0s, peak mem 325MB, user 155.0s, sys 9.3s, output queue size 336
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000606a6
  features: 1f8bfbff fffa3203
  extended: f1bf07ab 00407f5a
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 12 max 48
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 71721858 81484554
output file size: 50711
reads: 1502003
contig: 178193 intervals 76355618 bases
"assemble": 207 calls 0.635 user 0.005 sys 0.503 real
"assemble_addRead": 207 calls 0.000 user 0.000 sys 0.009 real
"assemble_buildGraph": 465 calls 0.196 user 0.000 sys 0.216 real
"assemble_computecigar": 304 calls 0.081 user 0.009 sys 0.107 real
"assemble_kg_build_calcsize": 465 calls 0.126 user 0.000 sys 0.101 real
"assemble_kg_build_clear": 618 calls 0.010 user 0.000 sys 0.008 real
"assemble_kg_build_prepare": 930 calls 0.146 user 0.000 sys 0.092 real
"assemble_kg_build_threading": 312 calls 0.070 user 0.000 sys 0.110 real
"assemble_kg_op1": 312 calls 0.126 user 0.005 sys 0.070 real
"assemble_kg_op2": 312 calls 0.004 user 0.000 sys 0.005 real
"assemble_kg_op3": 312 calls 0.000 user 0.000 sys 0.006 real
"assemble_sg_clean": 304 calls 0.040 user 0.000 sys 0.029 real
"assemble_sg_create": 304 calls 0.040 user 0.000 sys 0.045 real
"checkGraph": 207 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 207 calls 0.081 user 0.009 sys 0.111 real
advance: 189104 calls 15.916 user 0.416 sys 21.832 real
assemble_region: 207 calls 0.716 user 0.015 sys 0.624 real
build_pileup: 70976 calls 0.402 user 0.031 sys 0.580 real
build_stats: 71686 calls 2.654 user 0.112 sys 3.099 real
build_variants: 162 calls 0.000 user 0.000 sys 0.001 real
calc: 128670 calls 3.102 user 0.078 sys 4.281 real
calc_region: 162 calls 2.071 user 0.002 sys 2.189 real
call_region: 162 calls 0.035 user 0.000 sys 0.046 real
clip_region: 369 calls 0.020 user 0.000 sys 0.033 real
done: 1 calls 0.430 user 0.000 sys 0.439 real
execute: 1 calls 0.005 user 0.001 sys 16.168 real
fetch: 743546 calls 0.838 user 0.146 sys 1.072 real
fetch_ref: 745712 calls 1.638 user 0.515 sys 2.897 real
fetch_region: 207 calls 0.000 user 0.000 sys 0.009 real
fetch_vcf: 189104 calls 45.373 user 1.039 sys 65.389 real
idle: 35 calls 0.002 user 0.005 sys 12.841 real
init: 1 calls 0.052 user 0.000 sys 0.058 real
pairhmm: 466 calls 3.525 user 0.009 sys 3.598 real
realign: 162 calls 0.364 user 0.000 sys 0.383 real
region: 367297 calls 2.831 user 0.048 sys 2.945 real
tracker: 367297 calls 0.535 user 0.087 sys 0.745 real
trim_region: 207 calls 0.010 user 0.000 sys 0.002 real
overall: 341131264 mem 183.708 user 13.592 sys 17.463 real