cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr21_5117103-5117231.bed.gz -i HCC1395_BL.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant HCC1395_BL.haplotyper.chr21_5117103-5117231.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr21:14226859, elapsed 0.0s, est remaining 0.8s, peak mem 87MB, user 0.3s, sys 0.0s, output queue size 47
progress 10% @chr21:21410274, elapsed 0.1s, est remaining 0.6s, peak mem 93MB, user 0.5s, sys 0.0s, output queue size 85
progress 15% @chr21:26934466, elapsed 0.1s, est remaining 0.5s, peak mem 96MB, user 0.7s, sys 0.0s, output queue size 11
progress 20% @chr21:29591112, elapsed 0.1s, est remaining 0.4s, peak mem 102MB, user 0.9s, sys 0.0s, output queue size 64
progress 25% @chr21:31146895, elapsed 0.1s, est remaining 0.4s, peak mem 105MB, user 1.0s, sys 0.1s, output queue size 28
progress 30% @chr21:32325229, elapsed 0.2s, est remaining 0.4s, peak mem 105MB, user 1.4s, sys 0.1s, output queue size 20
progress 35% @chr21:32771326, elapsed 0.2s, est remaining 0.4s, peak mem 105MB, user 1.6s, sys 0.1s, output queue size 55
progress 40% @chr21:33559877, elapsed 0.2s, est remaining 0.3s, peak mem 105MB, user 1.8s, sys 0.1s, output queue size 7
progress 45% @chr21:33888152, elapsed 0.2s, est remaining 0.3s, peak mem 111MB, user 2.0s, sys 0.1s, output queue size 100
progress 50% @chr21:36230450, elapsed 0.3s, est remaining 0.3s, peak mem 150MB, user 2.3s, sys 0.1s, output queue size 48
progress 55% @chr21:36245048, elapsed 0.4s, est remaining 0.3s, peak mem 174MB, user 3.0s, sys 0.1s, output queue size 120
progress 60% @chr21:37420375, elapsed 0.4s, est remaining 0.3s, peak mem 177MB, user 3.3s, sys 0.2s, output queue size 15
progress 65% @chr21:39202325, elapsed 0.4s, est remaining 0.2s, peak mem 180MB, user 3.4s, sys 0.2s, output queue size 59
progress 70% @chr21:41245962, elapsed 0.5s, est remaining 0.2s, peak mem 192MB, user 3.7s, sys 0.2s, output queue size 150
progress 75% @chr21:41480933, elapsed 0.9s, est remaining 0.3s, peak mem 285MB, user 6.3s, sys 0.2s, output queue size 12
progress 80% @chr21:41889124, elapsed 1.4s, est remaining 0.4s, peak mem 363MB, user 11.2s, sys 0.3s, output queue size 43
progress 85% @chr21:41497133, elapsed 1.7s, est remaining 0.3s, peak mem 375MB, user 13.8s, sys 0.4s, output queue size 93
progress 90% @chr21:41501693, elapsed 1.8s, est remaining 0.2s, peak mem 375MB, user 15.3s, sys 0.5s, output queue size 131
progress 95% @chr21:43419021, elapsed 1.8s, est remaining 0.1s, peak mem 375MB, user 15.6s, sys 0.5s, output queue size 7
progress 100% @chr21:44120348, elapsed 1.8s, est remaining 0.0s, peak mem 375MB, user 15.9s, sys 0.5s, output queue size 0
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: 163002590
output file size: 61539
reads: 1955548
contig: 1576 intervals 300011 bases
"assemble": 223 calls 0.648 user 0.015 sys 0.899 real
"assemble_addRead": 223 calls 0.016 user 0.010 sys 0.071 real
"assemble_buildGraph": 457 calls 0.337 user 0.000 sys 0.454 real
"assemble_computecigar": 366 calls 0.368 user 0.009 sys 0.436 real
"assemble_kg_build_calcsize": 457 calls 0.160 user 0.000 sys 0.254 real
"assemble_kg_build_clear": 525 calls 0.022 user 0.000 sys 0.028 real
"assemble_kg_build_prepare": 914 calls 0.199 user 0.015 sys 0.237 real
"assemble_kg_build_threading": 389 calls 0.167 user 0.000 sys 0.192 real
"assemble_kg_op1": 389 calls 0.022 user 0.000 sys 0.035 real
"assemble_kg_op2": 389 calls 0.012 user 0.000 sys 0.012 real
"assemble_kg_op3": 389 calls 0.002 user 0.000 sys 0.010 real
"assemble_sg_clean": 366 calls 0.013 user 0.000 sys 0.042 real
"assemble_sg_create": 366 calls 0.023 user 0.000 sys 0.042 real
"checkGraph": 223 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 223 calls 0.389 user 0.009 sys 0.468 real
active: 3201 calls 0.000 user 0.000 sys 0.011 real
advance: 1625 calls 3.264 user 0.251 sys 3.907 real
annotate: 248 calls 0.087 user 0.000 sys 0.039 real
assemble_region: 223 calls 1.063 user 0.034 sys 1.441 real
build_variants: 219 calls 0.010 user 0.000 sys 0.003 real
calc: 3201 calls 0.363 user 0.002 sys 0.428 real
calc_region: 219 calls 8.176 user 0.123 sys 8.522 real
call_region: 219 calls 0.098 user 0.000 sys 0.098 real
clip_region: 442 calls 0.048 user 0.011 sys 0.097 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.001 user 0.000 sys 1.810 real
fetch: 3201 calls 0.306 user 0.022 sys 0.312 real
fetch_db: 219 calls 0.003 user 0.004 sys 0.056 real
fetch_ref: 3424 calls 0.018 user 0.000 sys 0.019 real
fetch_region: 223 calls 0.018 user 0.000 sys 0.028 real
idle: 39 calls 0.042 user 0.000 sys 12.508 real
init: 1 calls 0.020 user 0.017 sys 0.043 real
pairhmm: 3494 calls 13.237 user 0.140 sys 13.725 real
realign: 789 calls 0.684 user 0.001 sys 0.946 real
region: 3201 calls 11.808 user 0.178 sys 12.020 real
tracker: 3201 calls 0.007 user 0.000 sys 0.010 real
trim_region: 223 calls 0.003 user 0.000 sys 0.005 real
overall: 393334784 mem 20.859 user 0.631 sys 2.925 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory