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% @chr4:86785231, elapsed 0.0s, est remaining 0.8s, peak mem 75MB, user 0.0s, sys 0.1s, output queue size 2311
progress 10% @chr4:152330694, elapsed 0.1s, est remaining 0.7s, peak mem 78MB, user 0.1s, sys 0.2s, output queue size 2381
progress 15% @chr5:36181818, elapsed 0.1s, est remaining 0.6s, peak mem 96MB, user 0.1s, sys 0.3s, output queue size 4857
progress 20% @chr5:91072447, elapsed 0.2s, est remaining 0.6s, peak mem 102MB, user 0.1s, sys 0.4s, output queue size 7433
progress 25% @chr5:141192553, elapsed 0.2s, est remaining 0.6s, peak mem 108MB, user 0.1s, sys 0.6s, output queue size 9835
progress 30% @chr5:177293824, elapsed 0.2s, est remaining 0.5s, peak mem 123MB, user 0.1s, sys 0.7s, output queue size 11954
progress 35% @chr6:30948547, elapsed 0.3s, est remaining 0.5s, peak mem 129MB, user 0.1s, sys 0.8s, output queue size 14152
progress 40% @chr6:43625363, elapsed 0.3s, est remaining 0.4s, peak mem 135MB, user 0.2s, sys 1.0s, output queue size 16689
progress 45% @chr6:106530176, elapsed 0.3s, est remaining 0.4s, peak mem 150MB, user 0.2s, sys 1.2s, output queue size 19155
progress 50% @chr6:149456666, elapsed 0.4s, est remaining 0.4s, peak mem 162MB, user 0.2s, sys 1.3s, output queue size 21252
progress 55% @chr7:13911239, elapsed 0.4s, est remaining 0.3s, peak mem 168MB, user 0.3s, sys 1.3s, output queue size 23517
progress 60% @chr7:64219314, elapsed 0.4s, est remaining 0.3s, peak mem 174MB, user 0.3s, sys 1.5s, output queue size 25581
progress 65% @chr7:100951841, elapsed 0.5s, est remaining 0.3s, peak mem 183MB, user 0.4s, sys 1.6s, output queue size 28100
progress 70% @chr7:139293232, elapsed 0.5s, est remaining 0.2s, peak mem 195MB, user 0.4s, sys 1.7s, output queue size 30462
progress 75% @chr8:13276262, elapsed 0.5s, est remaining 0.2s, peak mem 207MB, user 0.4s, sys 1.8s, output queue size 32526
progress 80% @chr8:38819522, elapsed 0.6s, est remaining 0.1s, peak mem 210MB, user 0.4s, sys 1.9s, output queue size 34148
progress 85% @chrX:15546803, elapsed 0.6s, est remaining 0.1s, peak mem 219MB, user 0.4s, sys 2.0s, output queue size 36659
progress 90% @chrX:54959827, elapsed 0.6s, est remaining 0.1s, peak mem 237MB, user 0.4s, sys 2.1s, output queue size 39015
progress 95% @chrX:111723798, elapsed 0.7s, est remaining 0.0s, peak mem 240MB, user 0.5s, sys 2.2s, output queue size 40951
progress 100% @chrX:156006083, elapsed 0.7s, est remaining 0.0s, peak mem 249MB, user 0.5s, sys 2.4s, output queue size 43171
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: 71692763
output file size: 22308
reads: 1001089
contig: 45710 intervals 9000068 bases
"assemble": 1 calls 0.000 user 0.000 sys 0.000 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 0.002 user 0.005 sys 0.017 real
advance: 47638 calls 0.002 user 0.009 sys 0.025 real
assemble_region: 1 calls 0.000 user 0.000 sys 0.000 real
calc: 93348 calls 0.007 user 0.007 sys 0.017 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 0.002 user 0.001 sys 1.484 real
fetch: 93348 calls 0.000 user 0.000 sys 0.018 real
fetch_ref: 93349 calls 0.062 user 0.098 sys 0.386 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 39 calls 0.002 user 0.002 sys 21.860 real
init: 1 calls 0.040 user 0.000 sys 0.043 real
region: 93348 calls 0.000 user 0.002 sys 0.021 real
tracker: 93348 calls 0.014 user 0.008 sys 0.084 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 264376320 mem 1.107 user 4.909 sys 2.603 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory