cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta --interval_padding 100 -i 1136_7OO-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_7OO-N1-BDNA-1_A237CFYLT3_1 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon.hotspot_protected.raw.vcf.gz 1136_7OO-N1-BDNA-1_A237CFYLT3_1.tnseq_tumor_only.vcf.gz --algo OrientationBias --tumor_sample 1136_7OO-N1-BDNA-1_A237CFYLT3_1 1136_7OO-N1-BDNA-1_A237CFYLT3_1.tnseq_tumor_only.orientation_data.tsv --algo ContaminationModel --tumor_sample 1136_7OO-N1-BDNA-1_A237CFYLT3_1 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments 1136_7OO-N1-BDNA-1_A237CFYLT3_1.tnseq_tumor_only.segments 1136_7OO-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 13.8s, est remaining 262.1s, peak mem 728MB, user 125.7s, sys 2.1s, output queue size 28
progress 10% @chr2:3695617, elapsed 32.1s, est remaining 288.9s, peak mem 974MB, user 273.6s, sys 3.6s, output queue size 86
progress 15% @chr2:178606921, elapsed 52.2s, est remaining 295.7s, peak mem 1005MB, user 428.9s, sys 5.0s, output queue size 12
progress 20% @chr3:57457621, elapsed 71.8s, est remaining 287.1s, peak mem 1005MB, user 591.5s, sys 6.3s, output queue size 53
progress 25% @chr4:70782991, elapsed 92.6s, est remaining 277.7s, peak mem 1007MB, user 749.0s, sys 7.7s, output queue size 300
progress 30% @chr5:135028679, elapsed 104.8s, est remaining 244.6s, peak mem 1007MB, user 857.2s, sys 9.1s, output queue size 276
progress 35% @chr6:105376025, elapsed 137.1s, est remaining 254.6s, peak mem 1014MB, user 1118.4s, sys 10.4s, output queue size 560
progress 40% @chr7:107613232, elapsed 163.7s, est remaining 245.5s, peak mem 1046MB, user 1312.6s, sys 12.1s, output queue size 581
progress 45% @chr8:143813211, elapsed 188.6s, est remaining 230.5s, peak mem 1076MB, user 1532.5s, sys 13.8s, output queue size 23
progress 50% @chr10:21739930, elapsed 209.8s, est remaining 209.8s, peak mem 1076MB, user 1708.5s, sys 15.4s, output queue size 20
progress 55% @chr11:34136542, elapsed 234.8s, est remaining 192.1s, peak mem 1112MB, user 1896.1s, sys 17.2s, output queue size 36
progress 60% @chr12:14639762, elapsed 259.5s, est remaining 173.0s, peak mem 1155MB, user 2086.5s, sys 18.7s, output queue size 178
progress 65% @chr13:32234474, elapsed 279.0s, est remaining 150.2s, peak mem 1155MB, user 2257.1s, sys 20.5s, output queue size 196
progress 70% @chr15:38296771, elapsed 296.9s, est remaining 127.2s, peak mem 1172MB, user 2410.0s, sys 22.2s, output queue size 306
progress 75% @chr16:28591928, elapsed 325.8s, est remaining 108.6s, peak mem 1216MB, user 2680.2s, sys 24.2s, output queue size 140
progress 80% @chr17:40126104, elapsed 346.1s, est remaining 86.5s, peak mem 1239MB, user 2860.9s, sys 26.2s, output queue size 152
progress 85% @chr19:1818382, elapsed 372.7s, est remaining 65.8s, peak mem 1241MB, user 3077.1s, sys 28.1s, output queue size 38
progress 90% @chr19:54636394, elapsed 396.7s, est remaining 44.1s, peak mem 1271MB, user 3271.4s, sys 29.5s, output queue size 20
progress 95% @chr22:32151387, elapsed 415.5s, est remaining 21.9s, peak mem 1307MB, user 3434.2s, sys 31.1s, output queue size 67
progress 100% @chr6_GL000251v2_alt:3938900, elapsed 428.1s, est remaining 0.0s, peak mem 1307MB, user 3544.5s, sys 32.6s, 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 128
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 24196057026
output file size: 3632995
reads: 327100396
contig: 178193 intervals 76355618 bases
"assemble": 25580 calls 178.825 user 0.407 sys 180.716 real
"assemble_addRead": 25580 calls 4.611 user 0.040 sys 4.983 real
"assemble_buildGraph": 55677 calls 83.008 user 0.146 sys 86.557 real
"assemble_computecigar": 38214 calls 12.732 user 0.040 sys 13.084 real
"assemble_kg_build_calcsize": 55677 calls 38.619 user 0.039 sys 41.460 real
"assemble_kg_build_clear": 71878 calls 6.437 user 0.035 sys 6.433 real
"assemble_kg_build_prepare": 111354 calls 45.851 user 0.080 sys 43.923 real
"assemble_kg_build_threading": 39476 calls 41.834 user 0.064 sys 42.612 real
"assemble_kg_op1": 39476 calls 24.949 user 0.075 sys 25.362 real
"assemble_kg_op2": 39476 calls 0.811 user 0.001 sys 0.914 real
"assemble_kg_op3": 39476 calls 0.919 user 0.010 sys 0.893 real
"assemble_sg_clean": 38214 calls 4.217 user 0.004 sys 4.013 real
"assemble_sg_create": 38214 calls 6.099 user 0.023 sys 5.704 real
"checkGraph": 25580 calls 0.132 user 0.000 sys 0.094 real
"findHaplotype": 25580 calls 13.989 user 0.041 sys 14.295 real
advance: 189104 calls 986.293 user 14.056 sys 995.902 real
assemble_region: 25580 calls 197.854 user 0.499 sys 200.401 real
build_pileup: 186635 calls 8.743 user 0.032 sys 8.961 real
build_stats: 187608 calls 284.405 user 1.234 sys 297.056 real
build_variants: 20855 calls 0.171 user 0.000 sys 0.204 real
calc: 364552 calls 135.892 user 0.293 sys 147.247 real
calc_region: 20855 calls 1238.180 user 0.966 sys 1269.177 real
call_region: 20855 calls 25.961 user 0.045 sys 26.779 real
clip_region: 46435 calls 19.376 user 0.025 sys 20.436 real
done: 1 calls 30.575 user 0.328 sys 30.912 real
execute: 1 calls 0.005 user 0.002 sys 428.093 real
fetch: 743546 calls 287.369 user 0.659 sys 290.381 real
fetch_ref: 771085 calls 25.072 user 1.366 sys 6.481 real
fetch_region: 25580 calls 6.271 user 0.003 sys 6.830 real
fetch_vcf: 189104 calls 53.446 user 1.333 sys 60.593 real
idle: 400 calls 0.096 user 0.000 sys 373.695 real
init: 1 calls 0.034 user 0.039 sys 0.073 real
pairhmm: 379457 calls 2466.278 user 0.834 sys 2481.288 real
realign: 20855 calls 189.575 user 0.059 sys 213.119 real
region: 367297 calls 1451.540 user 1.605 sys 1486.433 real
tracker: 367297 calls 1.443 user 0.042 sys 1.495 real
trim_region: 25580 calls 0.458 user 0.000 sys 0.460 real
overall: 1609355264 mem 5109.497 user 37.923 sys 459.794 real