cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr4_30730753-30730788.bed.gz -i HCC1395_BL.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_1.haplotyper.chr4_30730753-30730788.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr4:86780402, elapsed 0.0s, est remaining 0.9s, peak mem 81MB, user 0.0s, sys 0.1s, output queue size 2056
progress 10% @chr4:152349994, elapsed 0.1s, est remaining 0.8s, peak mem 88MB, user 0.0s, sys 0.3s, output queue size 4457
progress 15% @chr5:36219596, elapsed 0.1s, est remaining 0.8s, peak mem 91MB, user 0.1s, sys 0.4s, output queue size 6937
progress 20% @chr5:91374114, elapsed 0.2s, est remaining 0.7s, peak mem 100MB, user 0.1s, sys 0.6s, output queue size 1378
progress 25% @chr5:141192553, elapsed 0.2s, est remaining 0.7s, peak mem 111MB, user 0.2s, sys 0.7s, output queue size 3784
progress 30% @chr5:177304625, elapsed 0.3s, est remaining 0.6s, peak mem 117MB, user 0.2s, sys 0.9s, output queue size 5901
progress 35% @chr6:30948547, elapsed 0.3s, est remaining 0.6s, peak mem 123MB, user 0.3s, sys 1.0s, output queue size 8089
progress 40% @chr6:43671762, elapsed 0.4s, est remaining 0.5s, peak mem 129MB, user 0.3s, sys 1.1s, output queue size 10641
progress 45% @chr6:106519131, elapsed 0.4s, est remaining 0.5s, peak mem 138MB, user 0.4s, sys 1.3s, output queue size 13102
progress 50% @chr6:149450683, elapsed 0.5s, est remaining 0.5s, peak mem 147MB, user 0.4s, sys 1.5s, output queue size 15194
progress 55% @chr7:13925863, elapsed 0.5s, est remaining 0.4s, peak mem 154MB, user 0.4s, sys 1.6s, output queue size 17457
progress 60% @chr7:64219314, elapsed 0.7s, est remaining 0.4s, peak mem 163MB, user 0.5s, sys 1.8s, output queue size 19524
progress 65% @chr7:100951841, elapsed 0.8s, est remaining 0.4s, peak mem 172MB, user 0.5s, sys 1.9s, output queue size 22041
progress 70% @chr7:139345501, elapsed 0.9s, est remaining 0.4s, peak mem 175MB, user 0.6s, sys 2.1s, output queue size 24405
progress 75% @chr8:13566992, elapsed 0.9s, est remaining 0.3s, peak mem 181MB, user 0.6s, sys 2.2s, output queue size 26471
progress 80% @chr8:38946124, elapsed 1.0s, est remaining 0.2s, peak mem 184MB, user 0.6s, sys 2.3s, output queue size 28101
progress 85% @chrX:14919672, elapsed 1.1s, est remaining 0.2s, peak mem 192MB, user 0.7s, sys 2.5s, output queue size 30599
progress 90% @chrX:55002962, elapsed 1.1s, est remaining 0.1s, peak mem 202MB, user 0.7s, sys 2.6s, output queue size 32963
progress 95% @chrX:111736714, elapsed 1.2s, est remaining 0.1s, peak mem 208MB, user 0.7s, sys 2.7s, output queue size 34906
progress 100% @chrX:156009816, elapsed 1.2s, est remaining 0.0s, peak mem 214MB, user 0.8s, sys 2.8s, output queue size 37115
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: 71692772
output file size: 22309
reads: 1001089
contig: 45710 intervals 9000068 bases
"assemble": 1 calls 0.000 user 0.000 sys 0.001 real
"assemble_addRead": 1 calls 0.000 user 0.000 sys 0.000 real
"assemble_buildGraph": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_computecigar": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_calcsize": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_clear": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_prepare": 4 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_threading": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_op1": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_op2": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_op3": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_sg_clean": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_sg_create": 2 calls 0.000 user 0.000 sys 0.000 real
"checkGraph": 1 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 1 calls 0.000 user 0.000 sys 0.000 real
active: 93348 calls 0.011 user 0.001 sys 0.018 real
advance: 47638 calls 0.009 user 0.005 sys 0.028 real
assemble_region: 1 calls 0.000 user 0.000 sys 0.001 real
calc: 93348 calls 0.003 user 0.004 sys 0.018 real
clip_region: 1 calls 0.000 user 0.000 sys 0.000 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.000 user 0.011 sys 2.160 real
fetch: 93348 calls 0.000 user 0.000 sys 0.019 real
fetch_ref: 93349 calls 0.054 user 0.028 sys 0.396 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 39 calls 0.003 user 0.017 sys 23.924 real
init: 1 calls 0.039 user 0.011 sys 0.047 real
region: 93348 calls 0.000 user 0.001 sys 0.021 real
tracker: 93348 calls 0.012 user 0.003 sys 0.093 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 228331520 mem 1.293 user 5.074 sys 3.289 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory