cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr19_47340800-47341813.bed.gz -i Sig_18_Blood.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_2.haplotyper.chr19_47340800-47341813.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr19:49139961, elapsed 0.0s, est remaining 0.4s, peak mem 72MB, user 0.0s, sys 0.0s, output queue size 506
progress 10% @chr19:50629294, elapsed 0.0s, est remaining 0.3s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 891
progress 15% @chr19:52553107, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 1254
progress 20% @chr19:54839428, elapsed 0.1s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 1658
progress 25% @chr19:56413959, elapsed 0.1s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 2107
progress 30% @chr19:58294098, elapsed 0.1s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 2332
progress 35% @chr21:30348409, elapsed 0.2s, est remaining 0.3s, peak mem 105MB, user 0.7s, sys 0.3s, output queue size 83
progress 40% @chr21:36460976, elapsed 0.4s, est remaining 0.5s, peak mem 144MB, user 1.7s, sys 0.4s, output queue size 107
progress 45% @chr21:42388403, elapsed 1.2s, est remaining 1.5s, peak mem 249MB, user 10.1s, sys 0.5s, output queue size 113
progress 50% @chr21:45531389, elapsed 1.5s, est remaining 1.5s, peak mem 255MB, user 12.5s, sys 0.6s, output queue size 117
progress 55% @chr22:19408483, elapsed 1.7s, est remaining 1.4s, peak mem 258MB, user 13.2s, sys 0.7s, output queue size 11
progress 60% @chr22:22201834, elapsed 1.7s, est remaining 1.1s, peak mem 258MB, user 13.2s, sys 0.8s, output queue size 491
progress 65% @chr22:23883772, elapsed 1.7s, est remaining 0.9s, peak mem 258MB, user 13.2s, sys 0.8s, output queue size 709
progress 70% @chr22:29288004, elapsed 1.7s, est remaining 0.7s, peak mem 258MB, user 13.2s, sys 0.8s, output queue size 1218
progress 75% @chr22:31843645, elapsed 1.7s, est remaining 0.6s, peak mem 258MB, user 13.2s, sys 0.9s, output queue size 1760
progress 80% @chr22:37970687, elapsed 1.7s, est remaining 0.4s, peak mem 258MB, user 13.3s, sys 0.9s, output queue size 2326
progress 85% @chr22:41261446, elapsed 1.7s, est remaining 0.3s, peak mem 258MB, user 13.3s, sys 0.9s, output queue size 2843
progress 90% @chr22:46256561, elapsed 1.8s, est remaining 0.2s, peak mem 258MB, user 13.3s, sys 1.0s, output queue size 3449
progress 95% @chr22:50730721, elapsed 1.8s, est remaining 0.1s, peak mem 258MB, user 13.3s, sys 1.0s, output queue size 4025
progress 100% @chrY:17878267, elapsed 1.8s, est remaining 0.0s, peak mem 258MB, user 13.4s, sys 1.1s, output queue size 4603
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 384
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 74586800
output file size: 79931
reads: 1001133
contig: 9624 intervals 1921786 bases
"assemble": 324 calls 0.719 user 0.027 sys 0.875 real
"assemble_addRead": 324 calls 0.020 user 0.000 sys 0.046 real
"assemble_buildGraph": 688 calls 0.331 user 0.014 sys 0.431 real
"assemble_computecigar": 523 calls 0.370 user 0.017 sys 0.426 real
"assemble_kg_build_calcsize": 688 calls 0.211 user 0.000 sys 0.239 real
"assemble_kg_build_clear": 826 calls 0.001 user 0.000 sys 0.023 real
"assemble_kg_build_prepare": 1376 calls 0.267 user 0.010 sys 0.217 real
"assemble_kg_build_threading": 550 calls 0.120 user 0.014 sys 0.186 real
"assemble_kg_op1": 550 calls 0.022 user 0.000 sys 0.038 real
"assemble_kg_op2": 550 calls 0.001 user 0.000 sys 0.010 real
"assemble_kg_op3": 550 calls 0.000 user 0.000 sys 0.012 real
"assemble_sg_clean": 523 calls 0.032 user 0.000 sys 0.043 real
"assemble_sg_create": 523 calls 0.036 user 0.003 sys 0.058 real
"checkGraph": 324 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 324 calls 0.392 user 0.017 sys 0.445 real
active: 19646 calls 0.010 user 0.009 sys 0.016 real
advance: 10022 calls 2.356 user 0.122 sys 3.234 real
annotate: 394 calls 0.011 user 0.008 sys 0.033 real
assemble_region: 324 calls 1.131 user 0.044 sys 1.370 real
build_variants: 322 calls 0.000 user 0.000 sys 0.002 real
calc: 19646 calls 0.232 user 0.001 sys 0.345 real
calc_region: 322 calls 5.410 user 0.074 sys 5.845 real
call_region: 322 calls 0.036 user 0.009 sys 0.065 real
clip_region: 646 calls 0.074 user 0.000 sys 0.084 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.007 user 0.003 sys 1.921 real
fetch: 19646 calls 0.124 user 0.009 sys 0.179 real
fetch_db: 322 calls 0.032 user 0.000 sys 0.091 real
fetch_ref: 19970 calls 0.020 user 0.015 sys 0.093 real
fetch_region: 324 calls 0.031 user 0.000 sys 0.019 real
idle: 39 calls 0.006 user 0.018 sys 13.995 real
init: 1 calls 0.030 user 0.010 sys 0.044 real
pairhmm: 2270 calls 10.013 user 0.034 sys 10.992 real
realign: 697 calls 0.752 user 0.011 sys 0.738 real
region: 19646 calls 9.895 user 0.167 sys 10.123 real
tracker: 19646 calls 0.010 user 0.000 sys 0.025 real
trim_region: 324 calls 0.000 user 0.000 sys 0.005 real
overall: 270700544 mem 17.348 user 1.644 sys 3.046 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory