cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta -i 1029_11H-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam -i 1029_11H-T1-TDNA-1_B23KFCWLT4_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 1029_11H-T1-TDNA-1_B23KFCWLT4_1 --normal_sample 1029_11H-N1-BDNA-1_B23KGCJLT4_1 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon_tnseq_42_curated_v4.vcf.gz 1029_11H.tnseq.vcf.gz --algo OrientationBias --tumor_sample 1029_11H-T1-TDNA-1_B23KFCWLT4_1 1029_11H.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample 1029_11H-T1-TDNA-1_B23KFCWLT4_1 --normal_sample 1029_11H-N1-BDNA-1_B23KGCJLT4_1 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments 1029_11H.tnseq.segments 1029_11H.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:119928943, elapsed 42.9s, est remaining 814.8s, peak mem 3243MB, user 416.5s, sys 6.4s, output queue size 163
progress 10% @chr2:21001730, elapsed 130.6s, est remaining 1175.8s, peak mem 4362MB, user 1090.1s, sys 12.2s, output queue size 639
progress 15% @chr2:185799697, elapsed 206.9s, est remaining 1172.2s, peak mem 5181MB, user 1702.6s, sys 17.4s, output queue size 273
progress 20% @chr3:98264285, elapsed 294.4s, est remaining 1177.4s, peak mem 5235MB, user 2469.3s, sys 23.1s, output queue size 412
progress 25% @chr4:88494165, elapsed 364.1s, est remaining 1092.3s, peak mem 5446MB, user 3073.1s, sys 28.6s, output queue size 100
progress 30% @chr5:147375090, elapsed 419.3s, est remaining 978.3s, peak mem 5448MB, user 3501.3s, sys 32.6s, output queue size 198
progress 35% @chr6:131700469, elapsed 554.1s, est remaining 1029.0s, peak mem 5602MB, user 4495.6s, sys 37.7s, output queue size 614
progress 40% @chr7:128857118, elapsed 698.1s, est remaining 1047.1s, peak mem 6070MB, user 5528.9s, sys 43.4s, output queue size 1563
progress 45% @chr9:1055722, elapsed 808.7s, est remaining 988.4s, peak mem 6109MB, user 6506.1s, sys 47.9s, output queue size 16
progress 50% @chr10:32847833, elapsed 897.8s, est remaining 897.8s, peak mem 6523MB, user 7247.9s, sys 52.8s, output queue size 70
progress 55% @chr11:47980913, elapsed 1004.4s, est remaining 821.8s, peak mem 6523MB, user 8083.1s, sys 57.8s, output queue size 21
progress 60% @chr12:21882766, elapsed 1079.0s, est remaining 719.4s, peak mem 6523MB, user 8748.9s, sys 62.1s, output queue size 69
progress 65% @chr13:49376967, elapsed 1168.9s, est remaining 629.4s, peak mem 6609MB, user 9404.5s, sys 66.3s, output queue size 545
progress 70% @chr15:43148755, elapsed 1324.4s, est remaining 567.6s, peak mem 7737MB, user 10636.7s, sys 71.3s, output queue size 454
progress 75% @chr16:30953185, elapsed 1392.9s, est remaining 464.3s, peak mem 7737MB, user 11296.9s, sys 75.5s, output queue size 22
progress 80% @chr17:42586053, elapsed 1473.2s, est remaining 368.3s, peak mem 7737MB, user 12069.8s, sys 80.4s, output queue size 121
progress 85% @chr19:5708342, elapsed 1589.5s, est remaining 280.5s, peak mem 7737MB, user 12964.5s, sys 85.8s, output queue size 400
progress 90% @chr19:55621751, elapsed 1666.9s, est remaining 185.2s, peak mem 7737MB, user 13642.7s, sys 89.5s, output queue size 50
progress 95% @chr22:36504515, elapsed 1734.1s, est remaining 91.3s, peak mem 7737MB, user 14222.7s, sys 93.7s, output queue size 0
progress 100% @chr6_GL000254v2_alt:3881705, elapsed 1828.8s, est remaining 0.0s, peak mem 7737MB, user 15005.0s, sys 98.6s, output queue size 1
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: 34853343684 99946753954
output file size: 2168680
reads: 2014757509
contig: 201779 intervals 37922265 bases
"assemble": 18996 calls 688.565 user 0.931 sys 690.306 real
"assemble_addRead": 18996 calls 23.402 user 0.088 sys 24.513 real
"assemble_buildGraph": 42882 calls 343.321 user 0.210 sys 346.357 real
"assemble_computecigar": 28846 calls 8.946 user 0.000 sys 8.812 real
"assemble_kg_build_calcsize": 42882 calls 172.667 user 0.069 sys 174.116 real
"assemble_kg_build_clear": 53660 calls 42.317 user 0.042 sys 42.547 real
"assemble_kg_build_prepare": 85764 calls 200.811 user 0.472 sys 199.318 real
"assemble_kg_build_threading": 32104 calls 155.963 user 0.101 sys 157.529 real
"assemble_kg_op1": 32104 calls 77.555 user 0.066 sys 77.582 real
"assemble_kg_op2": 32104 calls 0.514 user 0.000 sys 0.691 real
"assemble_kg_op3": 32104 calls 0.744 user 0.011 sys 0.821 real
"assemble_sg_clean": 28846 calls 3.054 user 0.030 sys 3.132 real
"assemble_sg_create": 28846 calls 3.808 user 0.010 sys 3.889 real
"checkGraph": 18996 calls 0.080 user 0.000 sys 0.083 real
"findHaplotype": 18996 calls 11.090 user 0.010 sys 10.948 real
advance: 208647 calls 6189.593 user 75.779 sys 6253.972 real
assemble_region: 18996 calls 723.398 user 1.039 sys 726.229 real
build_pileup: 202458 calls 25.625 user 0.053 sys 25.478 real
build_stats: 207057 calls 429.397 user 0.577 sys 435.696 real
build_variants: 8360 calls 0.185 user 0.000 sys 0.155 real
calc: 407430 calls 467.091 user 0.329 sys 484.429 real
calc_region: 8360 calls 4949.760 user 2.362 sys 4970.603 real
call_region: 8360 calls 98.053 user 0.132 sys 99.010 real
clip_region: 27356 calls 83.900 user 0.070 sys 84.154 real
done: 1 calls 46.365 user 0.239 sys 46.614 real
execute: 1 calls 0.005 user 0.002 sys 1828.850 real
fetch: 821727 calls 1472.108 user 1.689 sys 1514.871 real
fetch_ref: 846716 calls 26.613 user 1.099 sys 5.212 real
fetch_region: 18996 calls 62.519 user 0.037 sys 62.437 real
fetch_vcf: 208647 calls 60.611 user 1.534 sys 63.799 real
idle: 587 calls 0.026 user 0.004 sys 565.865 real
init: 1 calls 0.029 user 0.029 sys 0.062 real
pairhmm: 1205859 calls 10894.913 user 2.046 sys 10905.450 real
realign: 8360 calls 654.200 user 0.241 sys 675.639 real
region: 410426 calls 5782.474 user 3.578 sys 5806.011 real
tracker: 410426 calls 1.470 user 0.059 sys 1.621 real
trim_region: 18996 calls 0.283 user 0.000 sys 0.265 real
overall: 8113291264 mem 21866.436 user 103.680 sys 1876.546 real