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% @chr19:49139668, elapsed 0.0s, est remaining 0.2s, peak mem 70MB, user 0.0s, sys 0.1s, output queue size 404
progress 10% @chr19:50629784, elapsed 0.0s, est remaining 0.2s, peak mem 70MB, user 0.0s, sys 0.1s, output queue size 1001
progress 15% @chr19:52553107, elapsed 0.0s, est remaining 0.1s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 1371
progress 20% @chr19:54805951, elapsed 0.0s, est remaining 0.1s, peak mem 75MB, user 0.0s, sys 0.1s, output queue size 1748
progress 25% @chr19:56208449, elapsed 0.0s, est remaining 0.1s, peak mem 75MB, user 0.0s, sys 0.2s, output queue size 2192
progress 30% @chr19:58212161, elapsed 0.0s, est remaining 0.1s, peak mem 75MB, user 0.0s, sys 0.2s, output queue size 2433
progress 35% @chr21:29342399, elapsed 0.1s, est remaining 0.2s, peak mem 100MB, user 0.5s, sys 0.3s, output queue size 83
progress 40% @chr21:36460976, elapsed 0.3s, est remaining 0.4s, peak mem 142MB, user 1.4s, sys 0.4s, output queue size 107
progress 45% @chr21:42381982, elapsed 0.9s, est remaining 1.1s, peak mem 240MB, user 6.8s, sys 0.6s, output queue size 112
progress 50% @chr21:45525817, elapsed 1.1s, est remaining 1.1s, peak mem 242MB, user 8.5s, sys 0.6s, output queue size 115
progress 55% @chr22:19435638, elapsed 1.1s, est remaining 0.9s, peak mem 245MB, user 9.2s, sys 0.6s, output queue size 319
progress 60% @chr22:22195903, elapsed 1.2s, est remaining 0.8s, peak mem 245MB, user 9.2s, sys 0.6s, output queue size 798
progress 65% @chr22:23868481, elapsed 1.2s, est remaining 0.6s, peak mem 245MB, user 9.2s, sys 0.6s, output queue size 177
progress 70% @chr22:29288004, elapsed 1.2s, est remaining 0.5s, peak mem 245MB, user 9.2s, sys 0.7s, output queue size 685
progress 75% @chr22:31843645, elapsed 1.2s, est remaining 0.4s, peak mem 245MB, user 9.2s, sys 0.7s, output queue size 1230
progress 80% @chr22:37945042, elapsed 1.2s, est remaining 0.3s, peak mem 245MB, user 9.2s, sys 0.7s, output queue size 1788
progress 85% @chr22:41256021, elapsed 1.2s, est remaining 0.2s, peak mem 245MB, user 9.3s, sys 0.7s, output queue size 2310
progress 90% @chr22:46256561, elapsed 1.2s, est remaining 0.1s, peak mem 245MB, user 9.3s, sys 0.8s, output queue size 2922
progress 95% @chr22:50720184, elapsed 1.2s, est remaining 0.1s, peak mem 245MB, user 9.3s, sys 0.8s, output queue size 3500
progress 100% @chrY:19715352, elapsed 1.2s, est remaining 0.0s, peak mem 245MB, user 9.3s, sys 0.8s, output queue size 4071
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
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 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71692769
output file size: 77724
reads: 1001089
contig: 9624 intervals 1921786 bases
"assemble": 315 calls 0.515 user 0.030 sys 0.706 real
"assemble_addRead": 315 calls 0.008 user 0.000 sys 0.036 real
"assemble_buildGraph": 650 calls 0.258 user 0.017 sys 0.347 real
"assemble_computecigar": 513 calls 0.326 user 0.018 sys 0.378 real
"assemble_kg_build_calcsize": 650 calls 0.127 user 0.001 sys 0.188 real
"assemble_kg_build_clear": 775 calls 0.000 user 0.000 sys 0.016 real
"assemble_kg_build_prepare": 1300 calls 0.125 user 0.010 sys 0.156 real
"assemble_kg_build_threading": 525 calls 0.130 user 0.016 sys 0.155 real
"assemble_kg_op1": 525 calls 0.011 user 0.000 sys 0.033 real
"assemble_kg_op2": 525 calls 0.000 user 0.000 sys 0.009 real
"assemble_kg_op3": 525 calls 0.010 user 0.000 sys 0.012 real
"assemble_sg_clean": 513 calls 0.033 user 0.000 sys 0.042 real
"assemble_sg_create": 513 calls 0.064 user 0.002 sys 0.054 real
"checkGraph": 315 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 315 calls 0.353 user 0.018 sys 0.398 real
active: 19646 calls 0.000 user 0.003 sys 0.015 real
advance: 10022 calls 2.143 user 0.183 sys 3.084 real
annotate: 358 calls 0.027 user 0.000 sys 0.028 real
assemble_region: 315 calls 0.876 user 0.048 sys 1.143 real
build_variants: 312 calls 0.000 user 0.000 sys 0.002 real
calc: 19646 calls 0.221 user 0.004 sys 0.302 real
calc_region: 312 calls 3.786 user 0.038 sys 4.150 real
call_region: 312 calls 0.029 user 0.000 sys 0.054 real
clip_region: 627 calls 0.070 user 0.000 sys 0.067 real
done: 1 calls 0.001 user 0.000 sys 0.002 real
execute: 1 calls 0.004 user 0.001 sys 1.294 real
fetch: 19646 calls 0.106 user 0.023 sys 0.146 real
fetch_db: 312 calls 0.017 user 0.000 sys 0.084 real
fetch_ref: 19961 calls 0.026 user 0.016 sys 0.078 real
fetch_region: 315 calls 0.007 user 0.000 sys 0.014 real
idle: 39 calls 0.005 user 0.007 sys 13.202 real
init: 1 calls 0.038 user 0.002 sys 0.041 real
pairhmm: 1803 calls 6.441 user 0.073 sys 7.129 real
realign: 598 calls 0.520 user 0.003 sys 0.529 real
region: 19646 calls 6.293 user 0.139 sys 6.350 real
tracker: 19646 calls 0.010 user 0.007 sys 0.025 real
trim_region: 315 calls 0.010 user 0.000 sys 0.004 real
overall: 257769472 mem 12.663 user 1.339 sys 2.408 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory