cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr19_47340800-47341813.bed.gz -i HCC1395_BL.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_1.haplotyper.chr19_47340800-47341813.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr19:49134034, elapsed 0.0s, est remaining 0.2s, peak mem 69MB, user 0.0s, sys 0.0s, output queue size 391
progress 10% @chr19:50629784, elapsed 0.0s, est remaining 0.2s, peak mem 69MB, user 0.0s, sys 0.1s, output queue size 987
progress 15% @chr19:52553107, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 1357
progress 20% @chr19:54813125, elapsed 0.0s, est remaining 0.1s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 1738
progress 25% @chr19:56221575, elapsed 0.0s, est remaining 0.1s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 2177
progress 30% @chr19:58243965, elapsed 0.0s, est remaining 0.1s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 2419
progress 35% @chr21:28966370, elapsed 0.1s, est remaining 0.2s, peak mem 90MB, user 0.6s, sys 0.2s, output queue size 84
progress 40% @chr21:36460976, elapsed 0.3s, est remaining 0.4s, peak mem 147MB, user 1.5s, sys 0.2s, output queue size 105
progress 45% @chr21:42383033, elapsed 0.9s, est remaining 1.1s, peak mem 273MB, user 7.3s, sys 0.3s, output queue size 112
progress 50% @chr21:45512188, elapsed 1.1s, est remaining 1.1s, peak mem 273MB, user 9.1s, sys 0.4s, output queue size 115
progress 55% @chr22:19405786, elapsed 1.1s, est remaining 0.9s, peak mem 276MB, user 9.7s, sys 0.4s, output queue size 317
progress 60% @chr22:22195903, elapsed 1.1s, est remaining 0.8s, peak mem 276MB, user 9.7s, sys 0.5s, output queue size 797
progress 65% @chr22:23882459, elapsed 1.1s, est remaining 0.6s, peak mem 276MB, user 9.7s, sys 0.5s, output queue size 1014
progress 70% @chr22:29286684, elapsed 1.2s, est remaining 0.5s, peak mem 276MB, user 9.7s, sys 0.5s, output queue size 1527
progress 75% @chr22:31838685, elapsed 1.2s, est remaining 0.4s, peak mem 276MB, user 9.8s, sys 0.5s, output queue size 2064
progress 80% @chr22:37947281, elapsed 1.2s, est remaining 0.3s, peak mem 276MB, user 9.8s, sys 0.6s, output queue size 2628
progress 85% @chr22:41257948, elapsed 1.2s, est remaining 0.2s, peak mem 276MB, user 9.8s, sys 0.6s, output queue size 669
progress 90% @chr22:46256561, elapsed 1.2s, est remaining 0.1s, peak mem 276MB, user 9.8s, sys 0.7s, output queue size 1282
progress 95% @chr22:50720184, elapsed 1.2s, est remaining 0.1s, peak mem 276MB, user 9.8s, sys 0.7s, output queue size 1856
progress 100% @chrY:21537475, elapsed 1.2s, est remaining 0.0s, peak mem 276MB, user 9.8s, sys 0.7s, output queue size 2431
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: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71692776
output file size: 77725
reads: 1001089
contig: 9624 intervals 1921786 bases
"assemble": 315 calls 0.651 user 0.012 sys 0.688 real
"assemble_addRead": 315 calls 0.000 user 0.000 sys 0.033 real
"assemble_buildGraph": 650 calls 0.239 user 0.009 sys 0.338 real
"assemble_computecigar": 513 calls 0.306 user 0.042 sys 0.375 real
"assemble_kg_build_calcsize": 650 calls 0.103 user 0.000 sys 0.184 real
"assemble_kg_build_clear": 775 calls 0.012 user 0.000 sys 0.015 real
"assemble_kg_build_prepare": 1300 calls 0.181 user 0.002 sys 0.153 real
"assemble_kg_build_threading": 525 calls 0.126 user 0.009 sys 0.150 real
"assemble_kg_op1": 525 calls 0.035 user 0.000 sys 0.033 real
"assemble_kg_op2": 525 calls 0.010 user 0.000 sys 0.008 real
"assemble_kg_op3": 525 calls 0.009 user 0.000 sys 0.011 real
"assemble_sg_clean": 513 calls 0.044 user 0.000 sys 0.040 real
"assemble_sg_create": 513 calls 0.087 user 0.000 sys 0.053 real
"checkGraph": 315 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 315 calls 0.327 user 0.042 sys 0.394 real
active: 19646 calls 0.001 user 0.013 sys 0.014 real
advance: 10022 calls 2.138 user 0.121 sys 3.023 real
annotate: 358 calls 0.040 user 0.000 sys 0.026 real
assemble_region: 315 calls 0.978 user 0.053 sys 1.118 real
build_variants: 312 calls 0.000 user 0.000 sys 0.001 real
calc: 19646 calls 0.162 user 0.000 sys 0.293 real
calc_region: 312 calls 3.705 user 0.005 sys 3.953 real
call_region: 312 calls 0.040 user 0.000 sys 0.050 real
clip_region: 627 calls 0.047 user 0.000 sys 0.062 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.005 user 0.000 sys 1.300 real
fetch: 19646 calls 0.150 user 0.001 sys 0.133 real
fetch_db: 312 calls 0.011 user 0.000 sys 0.081 real
fetch_ref: 19961 calls 0.019 user 0.019 sys 0.081 real
fetch_region: 315 calls 0.024 user 0.007 sys 0.017 real
idle: 39 calls 0.006 user 0.006 sys 13.430 real
init: 1 calls 0.045 user 0.001 sys 0.044 real
pairhmm: 1803 calls 6.196 user 0.012 sys 7.041 real
realign: 598 calls 0.536 user 0.002 sys 0.524 real
region: 19646 calls 6.750 user 0.095 sys 6.706 real
tracker: 19646 calls 0.023 user 0.000 sys 0.023 real
trim_region: 315 calls 0.000 user 0.000 sys 0.004 real
overall: 289546240 mem 12.640 user 1.253 sys 2.414 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory