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% @chr19:49142034, elapsed 0.0s, est remaining 0.2s, peak mem 69MB, user 0.0s, sys 0.0s, output queue size 323
progress 10% @chr19:50629784, elapsed 0.0s, est remaining 0.2s, peak mem 69MB, user 0.0s, sys 0.1s, output queue size 917
progress 15% @chr19:52553107, elapsed 0.0s, est remaining 0.2s, peak mem 69MB, user 0.0s, sys 0.1s, output queue size 1282
progress 20% @chr19:54804793, elapsed 0.0s, est remaining 0.1s, peak mem 69MB, user 0.0s, sys 0.1s, output queue size 1669
progress 25% @chr19:56224663, elapsed 0.0s, est remaining 0.1s, peak mem 69MB, user 0.0s, sys 0.1s, output queue size 2108
progress 30% @chr19:58260851, elapsed 0.0s, est remaining 0.1s, peak mem 69MB, user 0.0s, sys 0.1s, output queue size 2350
progress 35% @chr21:26844225, elapsed 0.1s, est remaining 0.3s, peak mem 105MB, user 0.6s, sys 0.2s, output queue size 118
progress 40% @chr21:36460976, elapsed 0.2s, est remaining 0.3s, peak mem 141MB, user 1.5s, sys 0.3s, output queue size 106
progress 45% @chr21:42385409, elapsed 1.2s, est remaining 1.4s, peak mem 276MB, user 8.8s, sys 0.4s, output queue size 121
progress 50% @chr21:45514976, elapsed 1.4s, est remaining 1.4s, peak mem 285MB, user 12.1s, sys 0.4s, output queue size 2
progress 55% @chr22:19435638, elapsed 1.5s, est remaining 1.2s, peak mem 288MB, user 12.7s, sys 0.5s, output queue size 230
progress 60% @chr22:22214908, elapsed 1.5s, est remaining 1.0s, peak mem 288MB, user 12.7s, sys 0.5s, output queue size 708
progress 65% @chr22:22704478, elapsed 1.5s, est remaining 0.8s, peak mem 288MB, user 12.7s, sys 0.5s, output queue size 958
progress 70% @chr22:29294124, elapsed 1.5s, est remaining 0.7s, peak mem 288MB, user 12.8s, sys 0.5s, output queue size 1436
progress 75% @chr22:31845018, elapsed 1.6s, est remaining 0.5s, peak mem 288MB, user 12.8s, sys 0.5s, output queue size 1976
progress 80% @chr22:37066826, elapsed 1.6s, est remaining 0.4s, peak mem 288MB, user 12.8s, sys 0.6s, output queue size 533
progress 85% @chr22:41357177, elapsed 1.6s, est remaining 0.3s, peak mem 288MB, user 12.8s, sys 0.6s, output queue size 1082
progress 90% @chr22:46256561, elapsed 1.6s, est remaining 0.2s, peak mem 288MB, user 12.8s, sys 0.7s, output queue size 1669
progress 95% @chr22:50730721, elapsed 1.6s, est remaining 0.1s, peak mem 288MB, user 12.8s, sys 0.7s, output queue size 2238
progress 100% @chrY:24626085, elapsed 1.6s, est remaining 0.0s, peak mem 288MB, user 12.8s, sys 0.8s, output queue size 2816
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: 74586810
output file size: 79931
reads: 1001133
contig: 9624 intervals 1921786 bases
"assemble": 324 calls 0.691 user 0.023 sys 0.850 real
"assemble_addRead": 324 calls 0.018 user 0.000 sys 0.045 real
"assemble_buildGraph": 688 calls 0.391 user 0.002 sys 0.418 real
"assemble_computecigar": 523 calls 0.262 user 0.008 sys 0.395 real
"assemble_kg_build_calcsize": 688 calls 0.264 user 0.000 sys 0.233 real
"assemble_kg_build_clear": 826 calls 0.011 user 0.000 sys 0.021 real
"assemble_kg_build_prepare": 1376 calls 0.134 user 0.010 sys 0.212 real
"assemble_kg_build_threading": 550 calls 0.127 user 0.002 sys 0.179 real
"assemble_kg_op1": 550 calls 0.040 user 0.008 sys 0.037 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 0.029 user 0.000 sys 0.042 real
"assemble_sg_create": 523 calls 0.053 user 0.002 sys 0.055 real
"checkGraph": 324 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 324 calls 0.285 user 0.009 sys 0.414 real
active: 19646 calls 0.017 user 0.000 sys 0.015 real
advance: 10022 calls 2.436 user 0.110 sys 3.122 real
annotate: 394 calls 0.026 user 0.003 sys 0.036 real
assemble_region: 324 calls 0.994 user 0.032 sys 1.313 real
build_variants: 322 calls 0.000 user 0.000 sys 0.002 real
calc: 19646 calls 0.222 user 0.000 sys 0.316 real
calc_region: 322 calls 5.626 user 0.046 sys 5.979 real
call_region: 322 calls 0.028 user 0.003 sys 0.068 real
clip_region: 646 calls 0.066 user 0.003 sys 0.088 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.003 user 0.001 sys 1.832 real
fetch: 19646 calls 0.192 user 0.035 sys 0.183 real
fetch_db: 322 calls 0.015 user 0.000 sys 0.086 real
fetch_ref: 19970 calls 0.007 user 0.013 sys 0.082 real
fetch_region: 324 calls 0.029 user 0.000 sys 0.021 real
idle: 39 calls 0.003 user 0.003 sys 14.765 real
init: 1 calls 0.033 user 0.017 sys 0.042 real
pairhmm: 2270 calls 10.007 user 0.042 sys 10.773 real
realign: 697 calls 0.585 user 0.009 sys 0.717 real
region: 19646 calls 9.303 user 0.111 sys 9.398 real
tracker: 19646 calls 0.006 user 0.001 sys 0.026 real
trim_region: 324 calls 0.017 user 0.003 sys 0.005 real
overall: 302170112 mem 16.912 user 1.381 sys 2.949 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory