cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta --interval_padding 100 -i HCC1395_BL.recalibrated.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed --algo TNhaplotyper2 --tumor_sample HCC1395_BL --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon.hotspot_protected.raw.vcf.gz HCC1395_BL.tnseq_tumor_only.vcf.gz --algo OrientationBias --tumor_sample HCC1395_BL HCC1395_BL.tnseq_tumor_only.orientation_data.tsv --algo ContaminationModel --tumor_sample HCC1395_BL --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments HCC1395_BL.tnseq_tumor_only.segments HCC1395_BL.tnseq_tumor_only.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr21:14516792, elapsed 0.1s, est remaining 2.6s, peak mem 141MB, user 0.6s, sys 0.2s, output queue size 55
progress 10% @chr21:25607303, elapsed 0.2s, est remaining 1.8s, peak mem 144MB, user 1.4s, sys 0.2s, output queue size 107
progress 15% @chr21:28992664, elapsed 0.3s, est remaining 1.5s, peak mem 147MB, user 2.1s, sys 0.2s, output queue size 74
progress 20% @chr21:30746851, elapsed 0.3s, est remaining 1.2s, peak mem 150MB, user 2.7s, sys 0.3s, output queue size 16
progress 25% @chr21:32357437, elapsed 0.4s, est remaining 1.2s, peak mem 156MB, user 3.4s, sys 0.3s, output queue size 63
progress 30% @chr21:33426784, elapsed 0.5s, est remaining 1.1s, peak mem 159MB, user 4.2s, sys 0.3s, output queue size 75
progress 35% @chr21:34379405, elapsed 0.5s, est remaining 1.0s, peak mem 168MB, user 4.9s, sys 0.3s, output queue size 74
progress 40% @chr21:33549376, elapsed 0.6s, est remaining 0.9s, peak mem 210MB, user 5.8s, sys 0.4s, output queue size 161
progress 45% @chr21:37157061, elapsed 0.8s, est remaining 1.0s, peak mem 216MB, user 7.0s, sys 0.4s, output queue size 160
progress 50% @chr21:39277151, elapsed 0.9s, est remaining 0.9s, peak mem 234MB, user 7.6s, sys 0.4s, output queue size 264
progress 55% @chr21:41403167, elapsed 1.0s, est remaining 0.8s, peak mem 243MB, user 8.4s, sys 0.4s, output queue size 369
progress 60% @chr21:41766760, elapsed 1.7s, est remaining 1.2s, peak mem 352MB, user 12.8s, sys 1.0s, output queue size 15
progress 65% @chr21:42388829, elapsed 1.8s, est remaining 1.0s, peak mem 354MB, user 14.2s, sys 1.0s, output queue size 112
progress 70% @chr21:43065103, elapsed 1.9s, est remaining 0.8s, peak mem 363MB, user 15.5s, sys 1.1s, output queue size 216
progress 75% @chr21:44126800, elapsed 2.0s, est remaining 0.7s, peak mem 363MB, user 16.2s, sys 1.1s, output queue size 327
progress 80% @chr21:44435031, elapsed 2.1s, est remaining 0.5s, peak mem 363MB, user 17.3s, sys 1.2s, output queue size 429
progress 85% @chr21:44666346, elapsed 2.2s, est remaining 0.4s, peak mem 363MB, user 18.3s, sys 1.2s, output queue size 503
progress 90% @chr21:41501593, elapsed 2.3s, est remaining 0.3s, peak mem 363MB, user 20.1s, sys 1.2s, output queue size 602
progress 95% @chr21:46322539, elapsed 2.4s, est remaining 0.1s, peak mem 363MB, user 21.1s, sys 1.3s, output queue size 101
progress 100% @chr21:46661700, elapsed 2.5s, est remaining 0.0s, peak mem 363MB, user 22.3s, sys 1.3s, output queue size 2
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 12 max 384
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 163002590
output file size: 51811
reads: 1955548
contig: 1979 intervals 801713 bases
"assemble": 227 calls 1.068 user 0.051 sys 1.130 real
"assemble_addRead": 227 calls 0.011 user 0.000 sys 0.023 real
"assemble_buildGraph": 511 calls 0.442 user 0.015 sys 0.521 real
"assemble_computecigar": 321 calls 0.097 user 0.038 sys 0.182 real
"assemble_kg_build_calcsize": 511 calls 0.233 user 0.000 sys 0.302 real
"assemble_kg_build_clear": 699 calls 0.042 user 0.000 sys 0.029 real
"assemble_kg_build_prepare": 1022 calls 0.251 user 0.025 sys 0.275 real
"assemble_kg_build_threading": 323 calls 0.208 user 0.015 sys 0.204 real
"assemble_kg_op1": 323 calls 0.124 user 0.001 sys 0.136 real
"assemble_kg_op2": 323 calls 0.016 user 0.000 sys 0.008 real
"assemble_kg_op3": 323 calls 0.000 user 0.000 sys 0.007 real
"assemble_sg_clean": 321 calls 0.066 user 0.000 sys 0.042 real
"assemble_sg_create": 321 calls 0.091 user 0.001 sys 0.059 real
"checkGraph": 227 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 227 calls 0.100 user 0.038 sys 0.190 real
advance: 2074 calls 7.889 user 0.556 sys 8.968 real
assemble_region: 227 calls 1.179 user 0.089 sys 1.348 real
build_pileup: 1957 calls 0.055 user 0.000 sys 0.074 real
build_stats: 1979 calls 1.811 user 0.201 sys 2.117 real
build_variants: 179 calls 0.000 user 0.000 sys 0.002 real
calc: 3869 calls 1.003 user 0.040 sys 1.095 real
calc_region: 179 calls 4.591 user 0.016 sys 4.679 real
call_region: 179 calls 0.158 user 0.000 sys 0.105 real
clip_region: 406 calls 0.092 user 0.000 sys 0.085 real
done: 1 calls 0.686 user 0.000 sys 0.695 real
execute: 1 calls 0.006 user 0.002 sys 2.528 real
fetch: 8147 calls 1.507 user 0.021 sys 1.599 real
fetch_ref: 8428 calls 0.076 user 0.018 sys 0.077 real
fetch_region: 227 calls 0.010 user 0.000 sys 0.027 real
fetch_vcf: 2074 calls 1.025 user 0.020 sys 1.026 real
idle: 41 calls 0.049 user 0.000 sys 13.390 real
init: 1 calls 0.064 user 0.019 sys 0.086 real
pairhmm: 1058 calls 8.714 user 0.063 sys 8.789 real
realign: 179 calls 0.671 user 0.001 sys 0.855 real
region: 4053 calls 5.819 user 0.105 sys 6.100 real
tracker: 4053 calls 0.068 user 0.000 sys 0.019 real
trim_region: 227 calls 0.010 user 0.000 sys 0.004 real
overall: 381509632 mem 29.354 user 1.599 sys 3.900 real