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% @chr19:49138205, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.0s, output queue size 233
progress 10% @chr19:50629294, elapsed 0.0s, est remaining 0.2s, peak mem 72MB, user 0.0s, sys 0.0s, output queue size 830
progress 15% @chr19:52553107, elapsed 0.0s, est remaining 0.1s, peak mem 72MB, user 0.0s, sys 0.0s, output queue size 1196
progress 20% @chr19:54804793, elapsed 0.0s, est remaining 0.1s, peak mem 78MB, user 0.0s, sys 0.1s, output queue size 1583
progress 25% @chr19:56223631, elapsed 0.0s, est remaining 0.1s, peak mem 79MB, user 0.0s, sys 0.1s, output queue size 2021
progress 30% @chr19:58260851, elapsed 0.0s, est remaining 0.1s, peak mem 79MB, user 0.0s, sys 0.1s, output queue size 2265
progress 35% @chr21:28966370, elapsed 0.1s, est remaining 0.2s, peak mem 103MB, user 0.6s, sys 0.2s, output queue size 83
progress 40% @chr21:36245048, elapsed 0.3s, est remaining 0.4s, peak mem 147MB, user 1.5s, sys 0.2s, output queue size 107
progress 45% @chr21:41990895, elapsed 0.9s, est remaining 1.0s, peak mem 256MB, user 6.6s, sys 0.3s, output queue size 142
progress 50% @chr21:44539302, elapsed 1.1s, est remaining 1.1s, peak mem 261MB, user 8.5s, sys 0.3s, output queue size 117
progress 55% @chr22:19435638, elapsed 1.1s, est remaining 0.9s, peak mem 265MB, user 9.1s, sys 0.4s, output queue size 369
progress 60% @chr22:22195903, elapsed 1.1s, est remaining 0.8s, peak mem 265MB, user 9.1s, sys 0.4s, output queue size 851
progress 65% @chr22:23877042, elapsed 1.1s, est remaining 0.6s, peak mem 265MB, user 9.1s, sys 0.4s, output queue size 1065
progress 70% @chr22:29294124, elapsed 1.1s, est remaining 0.5s, peak mem 265MB, user 9.2s, sys 0.4s, output queue size 1574
progress 75% @chr22:31906205, elapsed 1.2s, est remaining 0.4s, peak mem 265MB, user 9.2s, sys 0.4s, output queue size 664
progress 80% @chr22:37972301, elapsed 1.2s, est remaining 0.3s, peak mem 265MB, user 9.2s, sys 0.4s, output queue size 1220
progress 85% @chr22:41355469, elapsed 1.2s, est remaining 0.2s, peak mem 265MB, user 9.2s, sys 0.5s, output queue size 1754
progress 90% @chr22:46256561, elapsed 1.2s, est remaining 0.1s, peak mem 265MB, user 9.2s, sys 0.5s, output queue size 2344
progress 95% @chr22:50744653, elapsed 1.2s, est remaining 0.1s, peak mem 265MB, user 9.2s, sys 0.6s, output queue size 2919
progress 100% @chr22:50679019, elapsed 1.2s, est remaining 0.0s, peak mem 265MB, user 9.2s, sys 0.6s, output queue size 3493
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 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71343278
output file size: 77735
reads: 1001089
contig: 9624 intervals 1921786 bases
"assemble": 315 calls 0.504 user 0.016 sys 0.700 real
"assemble_addRead": 315 calls 0.030 user 0.000 sys 0.034 real
"assemble_buildGraph": 650 calls 0.241 user 0.002 sys 0.347 real
"assemble_computecigar": 513 calls 0.347 user 0.018 sys 0.371 real
"assemble_kg_build_calcsize": 650 calls 0.136 user 0.000 sys 0.186 real
"assemble_kg_build_clear": 775 calls 0.014 user 0.000 sys 0.017 real
"assemble_kg_build_prepare": 1300 calls 0.127 user 0.012 sys 0.155 real
"assemble_kg_build_threading": 525 calls 0.095 user 0.002 sys 0.156 real
"assemble_kg_op1": 525 calls 0.021 user 0.000 sys 0.033 real
"assemble_kg_op2": 525 calls 0.010 user 0.000 sys 0.008 real
"assemble_kg_op3": 525 calls 0.000 user 0.000 sys 0.011 real
"assemble_sg_clean": 513 calls 0.033 user 0.000 sys 0.040 real
"assemble_sg_create": 513 calls 0.037 user 0.002 sys 0.053 real
"checkGraph": 315 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 315 calls 0.388 user 0.022 sys 0.390 real
active: 19646 calls 0.016 user 0.000 sys 0.014 real
advance: 10022 calls 2.163 user 0.060 sys 3.033 real
annotate: 358 calls 0.003 user 0.000 sys 0.026 real
assemble_region: 315 calls 0.921 user 0.038 sys 1.127 real
build_variants: 312 calls 0.000 user 0.000 sys 0.001 real
calc: 19646 calls 0.146 user 0.000 sys 0.299 real
calc_region: 312 calls 3.578 user 0.033 sys 3.915 real
call_region: 312 calls 0.024 user 0.000 sys 0.051 real
clip_region: 627 calls 0.021 user 0.000 sys 0.064 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.005 user 0.001 sys 1.273 real
fetch: 19646 calls 0.257 user 0.020 sys 0.150 real
fetch_db: 312 calls 0.046 user 0.000 sys 0.082 real
fetch_ref: 19961 calls 0.011 user 0.002 sys 0.076 real
fetch_region: 315 calls 0.000 user 0.000 sys 0.015 real
idle: 39 calls 0.007 user 0.012 sys 13.275 real
init: 1 calls 0.039 user 0.001 sys 0.042 real
pairhmm: 1803 calls 6.407 user 0.004 sys 7.056 real
realign: 598 calls 0.554 user 0.002 sys 0.523 real
region: 19646 calls 6.095 user 0.101 sys 6.139 real
tracker: 19646 calls 0.025 user 0.003 sys 0.024 real
trim_region: 315 calls 0.000 user 0.000 sys 0.004 real
overall: 278630400 mem 12.743 user 1.018 sys 2.394 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory