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_BL.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_BL --normal_sample reference-NA12878 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon_tnseq_42_curated_v4.vcf.gz negative_somatic_control_1.tnseq.vcf.gz --algo OrientationBias --tumor_sample HCC1395_BL negative_somatic_control_1.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample HCC1395_BL --normal_sample reference-NA12878 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments negative_somatic_control_1.tnseq.segments negative_somatic_control_1.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113705733, elapsed 0.9s, est remaining 16.4s, peak mem 144MB, user 8.4s, sys 0.5s, output queue size 5
progress 10% @chr2:3606092, elapsed 1.6s, est remaining 14.6s, peak mem 144MB, user 15.8s, sys 1.0s, output queue size 5
progress 15% @chr2:178588438, elapsed 2.4s, est remaining 13.5s, peak mem 145MB, user 23.4s, sys 1.5s, output queue size 9
progress 20% @chr3:57508282, elapsed 3.1s, est remaining 12.4s, peak mem 145MB, user 30.3s, sys 2.0s, output queue size 0
progress 25% @chr4:70631570, elapsed 3.8s, est remaining 11.5s, peak mem 146MB, user 37.9s, sys 2.5s, output queue size 3
progress 30% @chr5:135571753, elapsed 4.6s, est remaining 10.8s, peak mem 148MB, user 45.0s, sys 3.1s, output queue size 4
progress 35% @chr6:104832942, elapsed 5.3s, est remaining 9.9s, peak mem 149MB, user 52.0s, sys 3.4s, output queue size 3
progress 40% @chr7:106872437, elapsed 6.1s, est remaining 9.1s, peak mem 149MB, user 59.8s, sys 3.9s, output queue size 5
progress 45% @chr8:143813211, elapsed 6.8s, est remaining 8.4s, peak mem 150MB, user 67.3s, sys 4.4s, output queue size 0
progress 50% @chr10:21514996, elapsed 7.5s, est remaining 7.5s, peak mem 152MB, user 74.4s, sys 4.8s, output queue size 17
progress 55% @chr11:34135075, elapsed 8.2s, est remaining 6.7s, peak mem 152MB, user 81.7s, sys 5.2s, output queue size 6
progress 60% @chr12:12718707, elapsed 8.9s, est remaining 5.9s, peak mem 154MB, user 88.6s, sys 5.7s, output queue size 9
progress 65% @chr13:32149648, elapsed 9.6s, est remaining 5.2s, peak mem 154MB, user 95.8s, sys 6.2s, output queue size 0
progress 70% @chr15:35372050, elapsed 10.3s, est remaining 4.4s, peak mem 154MB, user 102.6s, sys 6.7s, output queue size 4
progress 75% @chr16:28488491, elapsed 11.0s, est remaining 3.7s, peak mem 154MB, user 109.7s, sys 7.2s, output queue size 2
progress 80% @chr17:40032956, elapsed 11.8s, est remaining 2.9s, peak mem 154MB, user 117.3s, sys 7.7s, output queue size 2
progress 85% @chr19:1799847, elapsed 12.5s, est remaining 2.2s, peak mem 154MB, user 124.5s, sys 8.3s, output queue size 14
progress 90% @chr19:54663432, elapsed 13.2s, est remaining 1.5s, peak mem 154MB, user 132.0s, sys 8.7s, output queue size 15
progress 95% @chr22:31944634, elapsed 14.9s, est remaining 0.8s, peak mem 332MB, user 149.1s, sys 9.4s, output queue size 10
progress 100% @chr6_GL000251v2_alt:3938900, elapsed 15.5s, est remaining 0.0s, peak mem 332MB, user 155.8s, sys 9.8s, output queue size 479
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 71692770
output file size: 46614
reads: 1501772
contig: 178193 intervals 76355618 bases
"assemble": 183 calls 0.492 user 0.010 sys 0.478 real
"assemble_addRead": 183 calls 0.010 user 0.000 sys 0.008 real
"assemble_buildGraph": 422 calls 0.198 user 0.000 sys 0.204 real
"assemble_computecigar": 264 calls 0.069 user 0.030 sys 0.085 real
"assemble_kg_build_calcsize": 422 calls 0.077 user 0.000 sys 0.099 real
"assemble_kg_build_clear": 573 calls 0.020 user 0.000 sys 0.009 real
"assemble_kg_build_prepare": 844 calls 0.090 user 0.000 sys 0.099 real
"assemble_kg_build_threading": 271 calls 0.120 user 0.000 sys 0.100 real
"assemble_kg_op1": 271 calls 0.067 user 0.000 sys 0.065 real
"assemble_kg_op2": 271 calls 0.000 user 0.000 sys 0.005 real
"assemble_kg_op3": 271 calls 0.010 user 0.000 sys 0.005 real
"assemble_sg_clean": 264 calls 0.002 user 0.000 sys 0.024 real
"assemble_sg_create": 264 calls 0.075 user 0.000 sys 0.038 real
"checkGraph": 183 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 183 calls 0.069 user 0.030 sys 0.089 real
advance: 189104 calls 17.199 user 0.465 sys 20.748 real
assemble_region: 183 calls 0.571 user 0.040 sys 0.577 real
build_pileup: 70974 calls 0.339 user 0.022 sys 0.560 real
build_stats: 71688 calls 2.642 user 0.090 sys 2.963 real
build_variants: 142 calls 0.000 user 0.000 sys 0.001 real
calc: 128670 calls 3.056 user 0.087 sys 3.926 real
calc_region: 142 calls 2.602 user 0.002 sys 2.649 real
call_region: 142 calls 0.085 user 0.000 sys 0.045 real
clip_region: 325 calls 0.028 user 0.000 sys 0.032 real
done: 1 calls 0.501 user 0.009 sys 0.515 real
execute: 1 calls 0.000 user 0.011 sys 15.554 real
fetch: 743546 calls 0.776 user 0.080 sys 1.080 real
fetch_ref: 745688 calls 1.714 user 0.669 sys 2.984 real
fetch_region: 183 calls 0.000 user 0.000 sys 0.008 real
fetch_vcf: 189104 calls 46.195 user 1.105 sys 62.546 real
idle: 34 calls 0.008 user 0.011 sys 12.863 real
init: 1 calls 0.060 user 0.000 sys 0.058 real
pairhmm: 472 calls 3.792 user 0.000 sys 3.780 real
realign: 142 calls 0.249 user 0.000 sys 0.368 real
region: 367297 calls 3.214 user 0.100 sys 3.350 real
tracker: 367297 calls 0.421 user 0.067 sys 0.702 real
trim_region: 183 calls 0.000 user 0.000 sys 0.002 real
overall: 348520448 mem 176.848 user 13.365 sys 16.850 real