cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta --interval_padding 100 -i 1136_814-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed --algo TNhaplotyper2 --tumor_sample 1136_814-N1-BDNA-1_A237CFYLT3_1 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon.hotspot_protected.raw.vcf.gz 1136_814-N1-BDNA-1_A237CFYLT3_1.tnseq_tumor_only.vcf.gz --algo OrientationBias --tumor_sample 1136_814-N1-BDNA-1_A237CFYLT3_1 1136_814-N1-BDNA-1_A237CFYLT3_1.tnseq_tumor_only.orientation_data.tsv --algo ContaminationModel --tumor_sample 1136_814-N1-BDNA-1_A237CFYLT3_1 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments 1136_814-N1-BDNA-1_A237CFYLT3_1.tnseq_tumor_only.segments 1136_814-N1-BDNA-1_A237CFYLT3_1.tnseq_tumor_only.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113705733, elapsed 20.9s, est remaining 396.5s, peak mem 940MB, user 196.6s, sys 2.8s, output queue size 32
progress 10% @chr2:3681534, elapsed 47.0s, est remaining 423.1s, peak mem 1174MB, user 414.3s, sys 6.0s, output queue size 39
progress 15% @chr2:178609108, elapsed 75.8s, est remaining 429.4s, peak mem 1177MB, user 659.0s, sys 8.2s, output queue size 12
progress 20% @chr3:57457621, elapsed 106.1s, est remaining 424.4s, peak mem 1196MB, user 923.3s, sys 10.0s, output queue size 22
progress 25% @chr4:70782991, elapsed 134.2s, est remaining 402.7s, peak mem 1239MB, user 1165.1s, sys 12.1s, output queue size 300
progress 30% @chr5:135009271, elapsed 152.6s, est remaining 356.0s, peak mem 1239MB, user 1331.6s, sys 13.9s, output queue size 275
progress 35% @chr6:105373269, elapsed 210.9s, est remaining 391.7s, peak mem 1242MB, user 1813.6s, sys 16.5s, output queue size 559
progress 40% @chr7:106867451, elapsed 252.3s, est remaining 378.5s, peak mem 1308MB, user 2147.0s, sys 19.3s, output queue size 565
progress 45% @chr8:143838580, elapsed 291.9s, est remaining 356.8s, peak mem 1335MB, user 2509.6s, sys 21.9s, output queue size 742
progress 50% @chr10:21732799, elapsed 334.4s, est remaining 334.4s, peak mem 1367MB, user 2868.6s, sys 24.8s, output queue size 30
progress 55% @chr11:34154601, elapsed 376.6s, est remaining 308.1s, peak mem 1398MB, user 3205.2s, sys 27.6s, output queue size 187
progress 60% @chr12:14643474, elapsed 418.9s, est remaining 279.3s, peak mem 1410MB, user 3564.4s, sys 30.1s, output queue size 179
progress 65% @chr13:32228356, elapsed 454.3s, est remaining 244.6s, peak mem 1422MB, user 3874.3s, sys 32.2s, output queue size 196
progress 70% @chr15:35084093, elapsed 484.9s, est remaining 207.8s, peak mem 1428MB, user 4132.5s, sys 36.3s, output queue size 307
progress 75% @chr16:28501876, elapsed 524.6s, est remaining 174.9s, peak mem 1484MB, user 4504.6s, sys 39.1s, output queue size 139
progress 80% @chr17:40126104, elapsed 552.7s, est remaining 138.2s, peak mem 1499MB, user 4780.5s, sys 41.7s, output queue size 154
progress 85% @chr19:1815966, elapsed 586.0s, est remaining 103.4s, peak mem 1501MB, user 5081.4s, sys 44.0s, output queue size 37
progress 90% @chr19:54630974, elapsed 625.7s, est remaining 69.5s, peak mem 1518MB, user 5429.0s, sys 46.1s, output queue size 19
progress 95% @chr22:32151967, elapsed 657.6s, est remaining 34.6s, peak mem 1572MB, user 5717.7s, sys 48.3s, output queue size 67
progress 100% @chrX:156009716, elapsed 694.6s, est remaining 0.0s, peak mem 1572MB, user 6038.9s, sys 50.7s, output queue size 497
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 00050654
  features: 1f8bfbff fffa320b
  extended: d19f47ab 00000018
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8175M CPU @ 2.50GHz
threads: 12 max 96
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 31902249847
output file size: 3908633
reads: 458522109
contig: 178193 intervals 76355618 bases
"assemble": 26637 calls 312.160 user 0.761 sys 315.452 real
"assemble_addRead": 26637 calls 9.577 user 0.051 sys 9.784 real
"assemble_buildGraph": 57932 calls 160.262 user 0.224 sys 163.166 real
"assemble_computecigar": 39721 calls 16.224 user 0.037 sys 16.132 real
"assemble_kg_build_calcsize": 57932 calls 78.002 user 0.050 sys 79.524 real
"assemble_kg_build_clear": 75073 calls 14.765 user 0.043 sys 14.736 real
"assemble_kg_build_prepare": 115864 calls 79.214 user 0.252 sys 79.364 real
"assemble_kg_build_threading": 40791 calls 76.596 user 0.079 sys 77.711 real
"assemble_kg_op1": 40791 calls 32.938 user 0.047 sys 32.981 real
"assemble_kg_op2": 40791 calls 0.903 user 0.000 sys 0.929 real
"assemble_kg_op3": 40791 calls 1.197 user 0.030 sys 1.190 real
"assemble_sg_clean": 39721 calls 5.303 user 0.000 sys 5.328 real
"assemble_sg_create": 39721 calls 7.791 user 0.036 sys 7.921 real
"checkGraph": 26637 calls 0.087 user 0.000 sys 0.120 real
"findHaplotype": 26637 calls 17.681 user 0.057 sys 17.656 real
advance: 189104 calls 1750.012 user 24.447 sys 1777.246 real
assemble_region: 26637 calls 339.830 user 0.888 sys 343.560 real
build_pileup: 186700 calls 19.027 user 0.050 sys 19.477 real
build_stats: 187481 calls 542.510 user 2.293 sys 555.607 real
build_variants: 21465 calls 0.172 user 0.000 sys 0.228 real
calc: 364262 calls 256.168 user 0.304 sys 266.816 real
calc_region: 21465 calls 1897.603 user 1.968 sys 1951.425 real
call_region: 21465 calls 40.408 user 0.112 sys 42.026 real
clip_region: 48102 calls 36.680 user 0.045 sys 37.198 real
done: 1 calls 53.073 user 0.546 sys 53.630 real
execute: 1 calls 0.008 user 0.002 sys 694.634 real
fetch: 743546 calls 565.047 user 1.132 sys 583.788 real
fetch_ref: 772142 calls 29.077 user 1.759 sys 8.327 real
fetch_region: 26637 calls 13.635 user 0.000 sys 13.657 real
fetch_vcf: 189104 calls 75.783 user 2.159 sys 80.281 real
idle: 681 calls 0.092 user 0.002 sys 650.191 real
init: 1 calls 0.063 user 0.031 sys 0.096 real
pairhmm: 353924 calls 3653.887 user 1.820 sys 3664.075 real
realign: 21465 calls 288.123 user 0.162 sys 319.235 real
region: 367297 calls 2268.607 user 2.957 sys 2326.694 real
tracker: 367297 calls 2.254 user 0.051 sys 2.219 real
trim_region: 26637 calls 0.494 user 0.010 sys 0.489 real
overall: 1956380672 mem 8289.283 user 56.868 sys 749.625 real