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% @chr1:113710154, elapsed 0.7s, est remaining 12.9s, peak mem 144MB, user 6.8s, sys 0.5s, output queue size 4
progress 10% @chr2:3643344, elapsed 1.3s, est remaining 11.8s, peak mem 144MB, user 13.2s, sys 0.9s, output queue size 6
progress 15% @chr2:178606921, elapsed 2.0s, est remaining 11.1s, peak mem 145MB, user 20.1s, sys 1.2s, output queue size 12
progress 20% @chr3:57483276, elapsed 2.6s, est remaining 10.3s, peak mem 145MB, user 26.4s, sys 1.6s, output queue size 0
progress 25% @chr4:70530939, elapsed 3.2s, est remaining 9.7s, peak mem 145MB, user 33.2s, sys 2.0s, output queue size 9
progress 30% @chr5:135571753, elapsed 3.9s, est remaining 9.1s, peak mem 146MB, user 40.2s, sys 2.4s, output queue size 4
progress 35% @chr6:104791404, elapsed 4.5s, est remaining 8.3s, peak mem 148MB, user 46.5s, sys 2.7s, output queue size 6
progress 40% @chr7:106872437, elapsed 5.1s, est remaining 7.7s, peak mem 148MB, user 53.3s, sys 3.0s, output queue size 14
progress 45% @chr8:143821497, elapsed 5.8s, est remaining 7.1s, peak mem 149MB, user 60.1s, sys 3.4s, output queue size 1
progress 50% @chr10:21713672, elapsed 6.4s, est remaining 6.4s, peak mem 153MB, user 66.6s, sys 3.8s, output queue size 12
progress 55% @chr11:34132025, elapsed 7.0s, est remaining 5.8s, peak mem 153MB, user 73.0s, sys 4.2s, output queue size 2
progress 60% @chr12:12718707, elapsed 7.6s, est remaining 5.1s, peak mem 153MB, user 79.3s, sys 4.5s, output queue size 10
progress 65% @chr13:32149648, elapsed 8.3s, est remaining 4.5s, peak mem 153MB, user 85.9s, sys 4.9s, output queue size 4
progress 70% @chr15:35538174, elapsed 8.9s, est remaining 3.8s, peak mem 154MB, user 92.3s, sys 5.4s, output queue size 3
progress 75% @chr16:28494582, elapsed 9.5s, est remaining 3.2s, peak mem 154MB, user 98.9s, sys 5.8s, output queue size 2
progress 80% @chr17:40034816, elapsed 10.2s, est remaining 2.6s, peak mem 155MB, user 106.1s, sys 6.1s, output queue size 2
progress 85% @chr19:1805788, elapsed 10.9s, est remaining 1.9s, peak mem 156MB, user 113.0s, sys 6.4s, output queue size 2
progress 90% @chr19:54632916, elapsed 11.5s, est remaining 1.3s, peak mem 156MB, user 119.5s, sys 6.7s, output queue size 0
progress 95% @chr22:31897382, elapsed 13.0s, est remaining 0.7s, peak mem 325MB, user 134.9s, sys 7.3s, output queue size 10
progress 100% @chr6_GL000251v2_alt:3938900, elapsed 13.6s, est remaining 0.0s, peak mem 325MB, user 140.9s, sys 7.7s, output queue size 421
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 71692773
output file size: 46614
reads: 1501772
contig: 178193 intervals 76355618 bases
"assemble": 183 calls 0.431 user 0.010 sys 0.398 real
"assemble_addRead": 183 calls 0.000 user 0.000 sys 0.006 real
"assemble_buildGraph": 422 calls 0.177 user 0.000 sys 0.168 real
"assemble_computecigar": 264 calls 0.041 user 0.009 sys 0.071 real
"assemble_kg_build_calcsize": 422 calls 0.070 user 0.000 sys 0.086 real
"assemble_kg_build_clear": 573 calls 0.000 user 0.000 sys 0.006 real
"assemble_kg_build_prepare": 844 calls 0.118 user 0.000 sys 0.084 real
"assemble_kg_build_threading": 271 calls 0.097 user 0.000 sys 0.079 real
"assemble_kg_op1": 271 calls 0.074 user 0.000 sys 0.055 real
"assemble_kg_op2": 271 calls 0.002 user 0.000 sys 0.004 real
"assemble_kg_op3": 271 calls 0.000 user 0.000 sys 0.005 real
"assemble_sg_clean": 264 calls 0.030 user 0.000 sys 0.020 real
"assemble_sg_create": 264 calls 0.030 user 0.000 sys 0.031 real
"checkGraph": 183 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 183 calls 0.041 user 0.009 sys 0.074 real
advance: 189104 calls 15.484 user 0.263 sys 18.524 real
assemble_region: 183 calls 0.472 user 0.020 sys 0.480 real
build_pileup: 70974 calls 0.424 user 0.020 sys 0.448 real
build_stats: 71688 calls 1.965 user 0.092 sys 2.186 real
build_variants: 142 calls 0.000 user 0.000 sys 0.001 real
calc: 128670 calls 2.204 user 0.049 sys 2.886 real
calc_region: 142 calls 2.684 user 0.001 sys 2.666 real
call_region: 142 calls 0.000 user 0.000 sys 0.037 real
clip_region: 325 calls 0.040 user 0.000 sys 0.027 real
done: 1 calls 0.433 user 0.000 sys 0.443 real
execute: 1 calls 0.003 user 0.000 sys 13.577 real
fetch: 743546 calls 0.635 user 0.079 sys 0.833 real
fetch_ref: 745688 calls 1.626 user 0.425 sys 2.683 real
fetch_region: 183 calls 0.000 user 0.000 sys 0.006 real
fetch_vcf: 189104 calls 43.051 user 0.733 sys 55.613 real
idle: 35 calls 0.049 user 0.000 sys 12.871 real
init: 1 calls 0.060 user 0.000 sys 0.058 real
pairhmm: 472 calls 3.415 user 0.010 sys 3.367 real
realign: 142 calls 0.377 user 0.001 sys 0.340 real
region: 367297 calls 3.187 user 0.088 sys 3.248 real
tracker: 367297 calls 0.316 user 0.058 sys 0.540 real
trim_region: 183 calls 0.000 user 0.000 sys 0.002 real
overall: 341712896 mem 155.167 user 10.313 sys 14.863 real