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% @chr19:49139668, elapsed 0.0s, est remaining 0.3s, peak mem 72MB, user 0.0s, sys 0.0s, output queue size 440
progress 10% @chr19:50632286, elapsed 0.0s, est remaining 0.3s, peak mem 72MB, user 0.1s, sys 0.0s, output queue size 404
progress 15% @chr19:52553107, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.1s, sys 0.1s, output queue size 769
progress 20% @chr19:54819713, elapsed 0.1s, est remaining 0.2s, peak mem 72MB, user 0.1s, sys 0.1s, output queue size 1160
progress 25% @chr19:56222591, elapsed 0.1s, est remaining 0.2s, peak mem 72MB, user 0.1s, sys 0.1s, output queue size 1595
progress 30% @chr19:58294098, elapsed 0.1s, est remaining 0.2s, peak mem 72MB, user 0.1s, sys 0.1s, output queue size 1844
progress 35% @chr21:30319403, elapsed 0.2s, est remaining 0.3s, peak mem 99MB, user 0.8s, sys 0.3s, output queue size 82
progress 40% @chr21:36460976, elapsed 0.3s, est remaining 0.4s, peak mem 132MB, user 1.7s, sys 0.3s, output queue size 108
progress 45% @chr21:42383033, elapsed 1.2s, est remaining 1.4s, peak mem 255MB, user 9.8s, sys 0.4s, output queue size 113
progress 50% @chr21:45514976, elapsed 1.5s, est remaining 1.5s, peak mem 273MB, user 12.5s, sys 0.5s, output queue size 12
progress 55% @chr22:19721822, elapsed 1.5s, est remaining 1.3s, peak mem 276MB, user 13.1s, sys 0.5s, output queue size 277
progress 60% @chr22:22318898, elapsed 1.6s, est remaining 1.0s, peak mem 276MB, user 13.2s, sys 0.5s, output queue size 719
progress 65% @chr22:23884623, elapsed 1.6s, est remaining 0.8s, peak mem 276MB, user 13.2s, sys 0.5s, output queue size 931
progress 70% @chr22:29288004, elapsed 1.6s, est remaining 0.7s, peak mem 276MB, user 13.2s, sys 0.5s, output queue size 1436
progress 75% @chr22:31838685, elapsed 1.6s, est remaining 0.5s, peak mem 276MB, user 13.2s, sys 0.6s, output queue size 1978
progress 80% @chr22:37951460, elapsed 1.6s, est remaining 0.4s, peak mem 276MB, user 13.2s, sys 0.6s, output queue size 176
progress 85% @chr22:41257948, elapsed 1.6s, est remaining 0.3s, peak mem 276MB, user 13.2s, sys 0.6s, output queue size 694
progress 90% @chr22:46256561, elapsed 1.7s, est remaining 0.2s, peak mem 276MB, user 13.3s, sys 0.7s, output queue size 1303
progress 95% @chr22:50720184, elapsed 1.7s, est remaining 0.1s, peak mem 276MB, user 13.3s, sys 0.7s, output queue size 1877
progress 100% @chrY:23280013, elapsed 1.7s, est remaining 0.0s, peak mem 276MB, user 13.3s, sys 0.8s, output queue size 2455
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: 74586802
output file size: 79931
reads: 1001133
contig: 9624 intervals 1921786 bases
"assemble": 324 calls 0.617 user 0.039 sys 0.869 real
"assemble_addRead": 324 calls 0.013 user 0.000 sys 0.047 real
"assemble_buildGraph": 688 calls 0.323 user 0.013 sys 0.429 real
"assemble_computecigar": 523 calls 0.314 user 0.016 sys 0.405 real
"assemble_kg_build_calcsize": 688 calls 0.149 user 0.000 sys 0.237 real
"assemble_kg_build_clear": 826 calls 0.014 user 0.004 sys 0.021 real
"assemble_kg_build_prepare": 1376 calls 0.192 user 0.017 sys 0.217 real
"assemble_kg_build_threading": 550 calls 0.164 user 0.009 sys 0.186 real
"assemble_kg_op1": 550 calls 0.006 user 0.000 sys 0.038 real
"assemble_kg_op2": 550 calls 0.010 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 0.018 user 0.001 sys 0.042 real
"assemble_sg_create": 523 calls 0.026 user 0.003 sys 0.057 real
"checkGraph": 324 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 324 calls 0.332 user 0.016 sys 0.425 real
active: 19646 calls 0.020 user 0.000 sys 0.015 real
advance: 10022 calls 2.219 user 0.106 sys 3.142 real
annotate: 394 calls 0.009 user 0.000 sys 0.036 real
assemble_region: 324 calls 0.961 user 0.054 sys 1.345 real
build_variants: 322 calls 0.000 user 0.000 sys 0.002 real
calc: 19646 calls 0.244 user 0.000 sys 0.322 real
calc_region: 322 calls 6.543 user 0.042 sys 6.868 real
call_region: 322 calls 0.022 user 0.010 sys 0.067 real
clip_region: 646 calls 0.087 user 0.002 sys 0.087 real
done: 1 calls 0.000 user 0.000 sys 0.003 real
execute: 1 calls 0.001 user 0.009 sys 1.851 real
fetch: 19646 calls 0.145 user 0.006 sys 0.183 real
fetch_db: 322 calls 0.025 user 0.003 sys 0.088 real
fetch_ref: 19970 calls 0.020 user 0.008 sys 0.083 real
fetch_region: 324 calls 0.010 user 0.000 sys 0.018 real
idle: 39 calls 0.003 user 0.005 sys 14.439 real
init: 1 calls 0.028 user 0.012 sys 0.043 real
pairhmm: 2270 calls 9.971 user 0.037 sys 10.830 real
realign: 697 calls 0.699 user 0.001 sys 0.723 real
region: 19646 calls 9.705 user 0.130 sys 9.790 real
tracker: 19646 calls 0.010 user 0.000 sys 0.025 real
trim_region: 324 calls 0.010 user 0.000 sys 0.005 real
overall: 289542144 mem 17.086 user 1.221 sys 2.972 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory