cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta -i 1029_0W2-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam -i 1029_0W2-T1-TDNA-1_A23KCGYLT4_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_0W2-T1-TDNA-1_A23KCGYLT4_1 --normal_sample 1029_0W2-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_0W2.tnseq.vcf.gz --algo OrientationBias --tumor_sample 1029_0W2-T1-TDNA-1_A23KCGYLT4_1 1029_0W2.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample 1029_0W2-T1-TDNA-1_A23KCGYLT4_1 --normal_sample 1029_0W2-N1-BDNA-1_B23KGCJLT4_1 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments 1029_0W2.tnseq.segments 1029_0W2.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:119922603, elapsed 48.6s, est remaining 923.0s, peak mem 1933MB, user 447.8s, sys 5.5s, output queue size 162
progress 10% @chr2:20670464, elapsed 121.7s, est remaining 1095.3s, peak mem 2522MB, user 1090.1s, sys 9.9s, output queue size 640
progress 15% @chr2:189676491, elapsed 238.9s, est remaining 1353.8s, peak mem 3657MB, user 1986.7s, sys 15.7s, output queue size 403
progress 20% @chr3:98732864, elapsed 370.7s, est remaining 1482.6s, peak mem 3657MB, user 3082.8s, sys 21.1s, output queue size 422
progress 25% @chr4:88487069, elapsed 459.2s, est remaining 1377.5s, peak mem 3657MB, user 3813.0s, sys 26.0s, output queue size 97
progress 30% @chr5:147631413, elapsed 519.8s, est remaining 1212.8s, peak mem 3657MB, user 4299.0s, sys 29.8s, output queue size 199
progress 35% @chr6:131733588, elapsed 637.0s, est remaining 1183.0s, peak mem 3744MB, user 5294.0s, sys 35.2s, output queue size 607
progress 40% @chr7:128851455, elapsed 885.1s, est remaining 1327.6s, peak mem 4134MB, user 7113.1s, sys 40.3s, output queue size 1567
progress 45% @chr9:116800, elapsed 1071.4s, est remaining 1309.5s, peak mem 4551MB, user 8832.9s, sys 47.3s, output queue size 82
progress 50% @chr10:32854400, elapsed 1176.9s, est remaining 1176.9s, peak mem 4551MB, user 9744.5s, sys 52.4s, output queue size 68
progress 55% @chr11:48163458, elapsed 1281.3s, est remaining 1048.3s, peak mem 4551MB, user 10623.0s, sys 57.2s, output queue size 7
progress 60% @chr12:22519115, elapsed 1401.0s, est remaining 934.0s, peak mem 4551MB, user 11648.7s, sys 62.9s, output queue size 645
progress 65% @chr13:49482737, elapsed 1487.7s, est remaining 801.0s, peak mem 4551MB, user 12357.1s, sys 67.3s, output queue size 558
progress 70% @chr15:43160681, elapsed 1585.2s, est remaining 679.4s, peak mem 4551MB, user 13223.9s, sys 71.8s, output queue size 457
progress 75% @chr16:30953185, elapsed 1718.7s, est remaining 572.9s, peak mem 4551MB, user 14469.3s, sys 76.9s, output queue size 22
progress 80% @chr17:42585125, elapsed 1820.2s, est remaining 455.1s, peak mem 4551MB, user 15392.0s, sys 82.7s, output queue size 121
progress 85% @chr19:5696670, elapsed 1925.3s, est remaining 339.8s, peak mem 4551MB, user 16264.1s, sys 87.9s, output queue size 401
progress 90% @chr19:55731999, elapsed 2016.4s, est remaining 224.0s, peak mem 4551MB, user 17046.4s, sys 92.6s, output queue size 61
progress 95% @chr22:36504098, elapsed 2121.5s, est remaining 111.7s, peak mem 4708MB, user 17971.8s, sys 98.1s, output queue size 3
progress 100% @chrY:25622443, elapsed 2181.5s, est remaining 0.0s, peak mem 4708MB, user 18501.4s, sys 102.4s, output queue size 31
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 00050657
  features: bfebfbff 7ffefbff
  extended: d39ff7eb 00000818
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8259CL CPU @ 2.50GHz
threads: 12 max 96
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 26404493781 76694971856
output file size: 3820928
reads: 1263973677
contig: 201779 intervals 37922265 bases
"assemble": 30670 calls 1192.517 user 1.155 sys 1195.074 real
"assemble_addRead": 30670 calls 35.022 user 0.152 sys 36.266 real
"assemble_buildGraph": 66441 calls 611.610 user 0.293 sys 611.141 real
"assemble_computecigar": 49074 calls 19.200 user 0.100 sys 18.945 real
"assemble_kg_build_calcsize": 66441 calls 284.766 user 0.025 sys 286.256 real
"assemble_kg_build_clear": 79729 calls 74.650 user 0.061 sys 73.651 real
"assemble_kg_build_prepare": 132882 calls 296.862 user 0.611 sys 299.048 real
"assemble_kg_build_threading": 53153 calls 304.778 user 0.107 sys 303.696 real
"assemble_kg_op1": 53153 calls 159.538 user 0.043 sys 160.053 real
"assemble_kg_op2": 53153 calls 1.161 user 0.028 sys 1.188 real
"assemble_kg_op3": 53153 calls 1.942 user 0.010 sys 1.800 real
"assemble_sg_clean": 49074 calls 7.203 user 0.000 sys 7.316 real
"assemble_sg_create": 49074 calls 9.697 user 0.012 sys 9.879 real
"checkGraph": 30670 calls 0.104 user 0.010 sys 0.164 real
"findHaplotype": 30670 calls 22.464 user 0.132 sys 22.367 real
advance: 208647 calls 6243.558 user 73.894 sys 6313.476 real
assemble_region: 30670 calls 1250.841 user 1.479 sys 1254.700 real
build_pileup: 202454 calls 32.514 user 0.060 sys 32.524 real
build_stats: 207279 calls 546.142 user 0.988 sys 552.696 real
build_variants: 16597 calls 0.190 user 0.010 sys 0.257 real
calc: 407887 calls 595.796 user 0.273 sys 609.662 real
calc_region: 16597 calls 7482.612 user 2.060 sys 7522.971 real
call_region: 16597 calls 141.368 user 0.190 sys 143.284 real
clip_region: 47267 calls 126.065 user 0.102 sys 125.728 real
done: 1 calls 76.477 user 1.031 sys 77.517 real
execute: 1 calls 0.009 user 0.002 sys 2181.471 real
fetch: 821727 calls 1444.722 user 1.714 sys 1475.645 real
fetch_ref: 858390 calls 28.079 user 1.613 sys 6.961 real
fetch_region: 30670 calls 68.910 user 0.053 sys 69.975 real
fetch_vcf: 208647 calls 85.545 user 1.741 sys 90.064 real
idle: 959 calls 0.053 user 0.000 sys 939.326 real
init: 1 calls 0.079 user 0.001 sys 0.080 real
pairhmm: 1027941 calls 14055.908 user 0.849 sys 14064.899 real
realign: 16597 calls 653.005 user 0.147 sys 683.840 real
region: 410426 calls 8868.170 user 3.795 sys 8914.481 real
tracker: 410426 calls 2.632 user 0.091 sys 2.686 real
trim_region: 30670 calls 0.424 user 0.000 sys 0.456 real
overall: 5492051968 mem 26107.061 user 109.464 sys 2260.457 real