cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta --interval_padding 100 -i 1136_5WB-N1-BDNA-1_B23KFG5LT4_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_5WB-N1-BDNA-1_B23KFG5LT4_1 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon.hotspot_protected.raw.vcf.gz 1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq_tumor_only.vcf.gz --algo OrientationBias --tumor_sample 1136_5WB-N1-BDNA-1_B23KFG5LT4_1 1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq_tumor_only.orientation_data.tsv --algo ContaminationModel --tumor_sample 1136_5WB-N1-BDNA-1_B23KFG5LT4_1 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments 1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq_tumor_only.segments 1136_5WB-N1-BDNA-1_B23KFG5LT4_1.tnseq_tumor_only.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113705733, elapsed 10.3s, est remaining 196.0s, peak mem 727MB, user 105.2s, sys 3.0s, output queue size 46
progress 10% @chr2:3752663, elapsed 22.6s, est remaining 203.1s, peak mem 803MB, user 221.2s, sys 4.8s, output queue size 450
progress 15% @chr2:178600754, elapsed 38.4s, est remaining 217.4s, peak mem 923MB, user 362.2s, sys 7.0s, output queue size 351
progress 20% @chr3:57445931, elapsed 52.4s, est remaining 209.6s, peak mem 944MB, user 499.9s, sys 9.7s, output queue size 54
progress 25% @chr4:70704837, elapsed 66.0s, est remaining 198.0s, peak mem 950MB, user 618.4s, sys 11.9s, output queue size 297
progress 30% @chr5:134612591, elapsed 75.5s, est remaining 176.2s, peak mem 962MB, user 709.8s, sys 14.0s, output queue size 277
progress 35% @chr6:93409555, elapsed 97.6s, est remaining 181.3s, peak mem 1044MB, user 913.3s, sys 16.1s, output queue size 573
progress 40% @chr7:107935315, elapsed 117.7s, est remaining 176.6s, peak mem 1048MB, user 1080.8s, sys 18.2s, output queue size 649
progress 45% @chr8:143816420, elapsed 138.5s, est remaining 169.2s, peak mem 1078MB, user 1284.9s, sys 20.5s, output queue size 741
progress 50% @chr10:21766161, elapsed 154.2s, est remaining 154.2s, peak mem 1078MB, user 1427.8s, sys 22.4s, output queue size 21
progress 55% @chr11:34145984, elapsed 168.7s, est remaining 138.0s, peak mem 1078MB, user 1551.8s, sys 24.1s, output queue size 186
progress 60% @chr12:14840325, elapsed 186.3s, est remaining 124.2s, peak mem 1078MB, user 1695.5s, sys 26.0s, output queue size 224
progress 65% @chr13:32225689, elapsed 199.6s, est remaining 107.5s, peak mem 1078MB, user 1832.6s, sys 27.9s, output queue size 384
progress 70% @chr15:38313116, elapsed 231.9s, est remaining 99.4s, peak mem 1125MB, user 2159.1s, sys 29.9s, output queue size 309
progress 75% @chr16:28494999, elapsed 249.3s, est remaining 83.1s, peak mem 1125MB, user 2329.5s, sys 31.9s, output queue size 1614
progress 80% @chr17:40099964, elapsed 261.6s, est remaining 65.4s, peak mem 1130MB, user 2453.2s, sys 33.5s, output queue size 156
progress 85% @chr19:1817607, elapsed 274.8s, est remaining 48.5s, peak mem 1135MB, user 2583.6s, sys 35.3s, output queue size 34
progress 90% @chr19:54665715, elapsed 287.6s, est remaining 32.0s, peak mem 1139MB, user 2699.4s, sys 36.6s, output queue size 19
progress 95% @chr22:31815316, elapsed 302.5s, est remaining 15.9s, peak mem 1204MB, user 2838.8s, sys 38.2s, output queue size 67
progress 100% @chr6_GL000251v2_alt:3938900, elapsed 313.9s, est remaining 0.0s, peak mem 1204MB, user 2943.6s, sys 40.0s, output queue size 7
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: 22944236418
output file size: 2770121
reads: 259247536
contig: 178193 intervals 76355618 bases
"assemble": 19057 calls 131.285 user 0.720 sys 134.274 real
"assemble_addRead": 19057 calls 3.658 user 0.031 sys 3.699 real
"assemble_buildGraph": 42913 calls 60.506 user 0.277 sys 61.970 real
"assemble_computecigar": 28094 calls 9.812 user 0.030 sys 10.068 real
"assemble_kg_build_calcsize": 42913 calls 30.210 user 0.060 sys 32.017 real
"assemble_kg_build_clear": 57026 calls 6.235 user 0.040 sys 6.060 real
"assemble_kg_build_prepare": 85826 calls 35.007 user 0.220 sys 35.356 real
"assemble_kg_build_threading": 28800 calls 27.483 user 0.141 sys 27.129 real
"assemble_kg_op1": 28800 calls 14.619 user 0.049 sys 15.132 real
"assemble_kg_op2": 28800 calls 0.601 user 0.008 sys 0.508 real
"assemble_kg_op3": 28800 calls 0.543 user 0.007 sys 0.674 real
"assemble_sg_clean": 28094 calls 2.920 user 0.025 sys 3.015 real
"assemble_sg_create": 28094 calls 4.976 user 0.014 sys 5.259 real
"checkGraph": 19057 calls 0.060 user 0.010 sys 0.070 real
"findHaplotype": 19057 calls 10.473 user 0.030 sys 10.923 real
advance: 189104 calls 1009.536 user 17.918 sys 1029.643 real
assemble_region: 19057 calls 145.640 user 0.801 sys 149.177 real
build_pileup: 186874 calls 7.895 user 0.066 sys 8.332 real
build_stats: 187638 calls 213.163 user 1.479 sys 225.630 real
build_variants: 15382 calls 0.140 user 0.000 sys 0.132 real
calc: 364517 calls 120.268 user 0.559 sys 127.912 real
calc_region: 15382 calls 839.912 user 1.543 sys 859.433 real
call_region: 15382 calls 16.407 user 0.040 sys 16.437 real
clip_region: 34439 calls 13.953 user 0.038 sys 13.925 real
done: 1 calls 12.254 user 0.047 sys 12.303 real
execute: 1 calls 0.004 user 0.002 sys 313.935 real
fetch: 743546 calls 238.507 user 1.062 sys 250.408 real
fetch_ref: 764562 calls 26.898 user 1.423 sys 6.381 real
fetch_region: 19057 calls 5.968 user 0.000 sys 5.832 real
fetch_vcf: 189104 calls 59.322 user 1.525 sys 66.615 real
idle: 179 calls 0.022 user 0.003 sys 157.260 real
init: 1 calls 0.028 user 0.030 sys 0.061 real
pairhmm: 158849 calls 1402.752 user 2.170 sys 1410.580 real
realign: 15382 calls 128.715 user 0.281 sys 140.342 real
region: 367297 calls 997.950 user 2.463 sys 1021.574 real
tracker: 367297 calls 1.488 user 0.079 sys 1.613 real
trim_region: 19057 calls 0.286 user 0.000 sys 0.307 real
overall: 1296658432 mem 3726.440 user 44.670 sys 327.324 real