cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta --interval_padding 100 -i Sig_18_Blood.recalibrated.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed --algo TNhaplotyper2 --tumor_sample Sig_18_Blood --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon.hotspot_protected.raw.vcf.gz Sig_18_Blood.tnseq_tumor_only.vcf.gz --algo OrientationBias --tumor_sample Sig_18_Blood Sig_18_Blood.tnseq_tumor_only.orientation_data.tsv --algo ContaminationModel --tumor_sample Sig_18_Blood --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments Sig_18_Blood.tnseq_tumor_only.segments Sig_18_Blood.tnseq_tumor_only.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr21:14512344, elapsed 0.2s, est remaining 4.6s, peak mem 149MB, user 0.9s, sys 0.0s, output queue size 55
progress 10% @chr21:25588735, elapsed 0.4s, est remaining 3.3s, peak mem 156MB, user 2.0s, sys 0.1s, output queue size 28
progress 15% @chr21:29030495, elapsed 0.5s, est remaining 2.8s, peak mem 163MB, user 3.0s, sys 0.1s, output queue size 23
progress 20% @chr21:30829335, elapsed 0.6s, est remaining 2.5s, peak mem 166MB, user 3.9s, sys 0.1s, output queue size 65
progress 25% @chr21:32346856, elapsed 0.8s, est remaining 2.3s, peak mem 173MB, user 4.9s, sys 0.2s, output queue size 65
progress 30% @chr21:32793662, elapsed 0.9s, est remaining 2.2s, peak mem 179MB, user 5.9s, sys 0.2s, output queue size 75
progress 35% @chr21:34379405, elapsed 1.1s, est remaining 2.1s, peak mem 186MB, user 7.0s, sys 0.2s, output queue size 74
progress 40% @chr21:36244948, elapsed 1.4s, est remaining 2.0s, peak mem 240MB, user 8.2s, sys 0.2s, output queue size 173
progress 45% @chr21:33549376, elapsed 2.1s, est remaining 2.5s, peak mem 265MB, user 9.7s, sys 0.3s, output queue size 268
progress 50% @chr21:39198663, elapsed 2.4s, est remaining 2.4s, peak mem 285MB, user 12.2s, sys 0.4s, output queue size 263
progress 55% @chr21:41338278, elapsed 2.7s, est remaining 2.2s, peak mem 290MB, user 14.2s, sys 0.4s, output queue size 148
progress 60% @chr21:41810653, elapsed 4.2s, est remaining 2.8s, peak mem 455MB, user 18.1s, sys 0.5s, output queue size 22
progress 65% @chr21:42362379, elapsed 4.9s, est remaining 2.6s, peak mem 472MB, user 27.1s, sys 0.6s, output queue size 97
progress 70% @chr21:42903082, elapsed 5.0s, est remaining 2.1s, peak mem 474MB, user 28.1s, sys 0.7s, output queue size 219
progress 75% @chr21:44130497, elapsed 5.1s, est remaining 1.7s, peak mem 474MB, user 29.2s, sys 0.7s, output queue size 327
progress 80% @chr21:44233457, elapsed 5.3s, est remaining 1.3s, peak mem 474MB, user 30.8s, sys 0.7s, output queue size 433
progress 85% @chr21:45282249, elapsed 5.4s, est remaining 1.0s, peak mem 474MB, user 31.9s, sys 0.7s, output queue size 514
progress 90% @chr21:46128803, elapsed 5.7s, est remaining 0.6s, peak mem 474MB, user 33.6s, sys 0.7s, output queue size 629
progress 95% @chr21:46366484, elapsed 5.9s, est remaining 0.3s, peak mem 474MB, user 35.1s, sys 0.7s, output queue size 721
progress 100% @chr21:46334297, elapsed 6.1s, est remaining 0.0s, peak mem 474MB, user 38.7s, sys 0.8s, output queue size 91
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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 128
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 208827488
output file size: 57860
reads: 2481283
contig: 1979 intervals 801713 bases
"assemble": 236 calls 1.844 user 0.031 sys 2.608 real
"assemble_addRead": 236 calls 0.069 user 0.000 sys 0.066 real
"assemble_buildGraph": 545 calls 0.877 user 0.001 sys 1.175 real
"assemble_computecigar": 331 calls 0.182 user 0.034 sys 0.294 real
"assemble_kg_build_calcsize": 545 calls 0.522 user 0.000 sys 0.679 real
"assemble_kg_build_clear": 752 calls 0.084 user 0.000 sys 0.089 real
"assemble_kg_build_prepare": 1090 calls 0.438 user 0.030 sys 0.661 real
"assemble_kg_build_threading": 338 calls 0.311 user 0.000 sys 0.439 real
"assemble_kg_op1": 338 calls 0.278 user 0.000 sys 0.376 real
"assemble_kg_op2": 338 calls 0.007 user 0.000 sys 0.020 real
"assemble_kg_op3": 338 calls 0.010 user 0.000 sys 0.008 real
"assemble_sg_clean": 331 calls 0.035 user 0.000 sys 0.062 real
"assemble_sg_create": 331 calls 0.066 user 0.000 sys 0.126 real
"checkGraph": 236 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 236 calls 0.192 user 0.034 sys 0.304 real
advance: 2074 calls 10.158 user 0.216 sys 14.560 real
assemble_region: 236 calls 2.105 user 0.065 sys 2.983 real
build_pileup: 1969 calls 0.133 user 0.000 sys 0.200 real
build_stats: 1999 calls 3.312 user 0.141 sys 4.904 real
build_variants: 195 calls 0.000 user 0.000 sys 0.002 real
calc: 3915 calls 1.990 user 0.002 sys 2.674 real
calc_region: 195 calls 13.242 user 0.042 sys 18.160 real
call_region: 195 calls 0.236 user 0.010 sys 0.304 real
clip_region: 431 calls 0.180 user 0.000 sys 0.237 real
done: 1 calls 1.089 user 0.002 sys 1.095 real
execute: 1 calls 0.001 user 0.010 sys 6.260 real
fetch: 8147 calls 2.655 user 0.012 sys 3.721 real
fetch_ref: 8437 calls 0.055 user 0.010 sys 0.123 real
fetch_region: 236 calls 0.050 user 0.000 sys 0.068 real
fetch_vcf: 2074 calls 0.905 user 0.010 sys 1.313 real
idle: 50 calls 0.053 user 0.000 sys 25.655 real
init: 1 calls 0.084 user 0.019 sys 0.111 real
pairhmm: 2129 calls 23.509 user 0.040 sys 31.832 real
realign: 195 calls 1.880 user 0.001 sys 2.567 real
region: 4053 calls 15.458 user 0.115 sys 21.335 real
tracker: 4053 calls 0.065 user 0.001 sys 0.063 real
trim_region: 236 calls 0.000 user 0.000 sys 0.005 real
overall: 497643520 mem 53.730 user 0.988 sys 8.626 real