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 0.9s, peak mem 75MB, user 0.1s, sys 0.1s, output queue size 2297
progress 10% @chr4:152411161, elapsed 0.1s, est remaining 0.8s, peak mem 81MB, user 0.1s, sys 0.3s, output queue size 4703
progress 15% @chr5:36166519, elapsed 0.1s, est remaining 0.7s, peak mem 93MB, user 0.1s, sys 0.5s, output queue size 2178
progress 20% @chr5:91373684, elapsed 0.2s, est remaining 0.7s, peak mem 99MB, user 0.1s, sys 0.6s, output queue size 4760
progress 25% @chr5:141192553, elapsed 0.2s, est remaining 0.7s, peak mem 102MB, user 0.1s, sys 0.8s, output queue size 7161
progress 30% @chr5:177293824, elapsed 0.3s, est remaining 0.6s, peak mem 117MB, user 0.1s, sys 0.9s, output queue size 9285
progress 35% @chr6:31116025, elapsed 0.3s, est remaining 0.6s, peak mem 129MB, user 0.2s, sys 1.1s, output queue size 11478
progress 40% @chr6:43636381, elapsed 0.3s, est remaining 0.5s, peak mem 132MB, user 0.2s, sys 1.3s, output queue size 14019
progress 45% @chr6:106519131, elapsed 0.4s, est remaining 0.5s, peak mem 138MB, user 0.2s, sys 1.6s, output queue size 16481
progress 50% @chr6:149579834, elapsed 0.4s, est remaining 0.4s, peak mem 147MB, user 0.3s, sys 1.7s, output queue size 18599
progress 55% @chr7:13903840, elapsed 0.5s, est remaining 0.4s, peak mem 162MB, user 0.3s, sys 1.9s, output queue size 20836
progress 60% @chr7:64348090, elapsed 0.5s, est remaining 0.4s, peak mem 168MB, user 0.3s, sys 2.2s, output queue size 22913
progress 65% @chr7:100951841, elapsed 0.6s, est remaining 0.3s, peak mem 177MB, user 0.3s, sys 2.4s, output queue size 25422
progress 70% @chr7:139283024, elapsed 0.6s, est remaining 0.3s, peak mem 189MB, user 0.3s, sys 2.6s, output queue size 27791
progress 75% @chr8:13099347, elapsed 0.7s, est remaining 0.2s, peak mem 195MB, user 0.4s, sys 2.8s, output queue size 29855
progress 80% @chr8:38827168, elapsed 0.7s, est remaining 0.2s, peak mem 201MB, user 0.4s, sys 2.9s, output queue size 31472
progress 85% @chrX:15522346, elapsed 0.8s, est remaining 0.1s, peak mem 210MB, user 0.5s, sys 3.1s, output queue size 33980
progress 90% @chrX:55002251, elapsed 0.8s, est remaining 0.1s, peak mem 222MB, user 0.5s, sys 3.3s, output queue size 36347
progress 95% @chrX:111724934, elapsed 0.9s, est remaining 0.0s, peak mem 231MB, user 0.5s, sys 3.5s, output queue size 38283
progress 100% @chrX:154295860, elapsed 0.9s, est remaining 0.0s, peak mem 240MB, user 0.6s, sys 3.7s, output queue size 40498
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: 71692759
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 0.000 user 0.003 sys 0.018 real
advance: 47638 calls 0.021 user 0.006 sys 0.026 real
assemble_region: 1 calls 0.000 user 0.000 sys 0.000 real
calc: 93348 calls 0.000 user 0.001 sys 0.018 real
clip_region: 1 calls 0.000 user 0.000 sys 0.000 real
done: 1 calls 0.001 user 0.001 sys 0.224 real
execute: 1 calls 0.000 user 0.010 sys 1.928 real
fetch: 93348 calls 0.007 user 0.000 sys 0.019 real
fetch_ref: 93349 calls 0.105 user 0.089 sys 0.353 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 51 calls 0.003 user 0.008 sys 24.647 real
init: 1 calls 0.030 user 0.010 sys 0.042 real
region: 93348 calls 0.011 user 0.002 sys 0.025 real
tracker: 93348 calls 0.032 user 0.021 sys 0.087 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 254951424 mem 1.142 user 6.269 sys 3.046 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory