cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr4_30730753-30730788.bed.gz -i Sig_18_Blood.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_2.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 0.8s, peak mem 72MB, user 0.0s, sys 0.1s, output queue size 874
progress 10% @chr4:152352429, elapsed 0.1s, est remaining 0.8s, peak mem 75MB, user 0.1s, sys 0.2s, output queue size 3278
progress 15% @chr5:36166519, elapsed 0.1s, est remaining 0.7s, peak mem 84MB, user 0.1s, sys 0.4s, output queue size 5742
progress 20% @chr5:91153221, elapsed 0.2s, est remaining 0.7s, peak mem 90MB, user 0.1s, sys 0.5s, output queue size 8321
progress 25% @chr5:141192553, elapsed 0.2s, est remaining 0.6s, peak mem 99MB, user 0.2s, sys 0.6s, output queue size 10725
progress 30% @chr5:177303172, elapsed 0.2s, est remaining 0.6s, peak mem 108MB, user 0.2s, sys 0.8s, output queue size 12846
progress 35% @chr6:30948547, elapsed 0.3s, est remaining 0.5s, peak mem 117MB, user 0.2s, sys 0.9s, output queue size 15037
progress 40% @chr6:43640021, elapsed 0.3s, est remaining 0.5s, peak mem 129MB, user 0.2s, sys 1.1s, output queue size 17580
progress 45% @chr6:106519131, elapsed 0.4s, est remaining 0.5s, peak mem 138MB, user 0.3s, sys 1.2s, output queue size 20043
progress 50% @chr6:149450683, elapsed 0.4s, est remaining 0.4s, peak mem 147MB, user 0.3s, sys 1.3s, output queue size 22143
progress 55% @chr7:13914223, elapsed 0.5s, est remaining 0.4s, peak mem 150MB, user 0.4s, sys 1.4s, output queue size 24403
progress 60% @chr7:64348090, elapsed 0.5s, est remaining 0.3s, peak mem 165MB, user 0.4s, sys 1.5s, output queue size 26475
progress 65% @chr7:100951841, elapsed 0.6s, est remaining 0.3s, peak mem 177MB, user 0.4s, sys 1.7s, output queue size 28986
progress 70% @chr7:139523928, elapsed 0.6s, est remaining 0.3s, peak mem 183MB, user 0.5s, sys 1.8s, output queue size 2153
progress 75% @chr8:11309527, elapsed 0.7s, est remaining 0.2s, peak mem 195MB, user 0.5s, sys 1.9s, output queue size 4207
progress 80% @chr8:38842287, elapsed 0.7s, est remaining 0.2s, peak mem 195MB, user 0.5s, sys 2.0s, output queue size 5825
progress 85% @chrX:15534212, elapsed 0.7s, est remaining 0.1s, peak mem 207MB, user 0.5s, sys 2.1s, output queue size 8330
progress 90% @chrX:55000423, elapsed 0.8s, est remaining 0.1s, peak mem 207MB, user 0.6s, sys 2.3s, output queue size 10696
progress 95% @chrX:111718112, elapsed 0.8s, est remaining 0.0s, peak mem 213MB, user 0.6s, sys 2.4s, output queue size 12625
progress 100% @chrX:156009816, elapsed 0.9s, est remaining 0.0s, peak mem 228MB, user 0.6s, sys 2.6s, output queue size 14845
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: 74586810
output file size: 22310
reads: 1001133
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 0.000 user 0.020 sys 0.018 real
advance: 47638 calls 0.004 user 0.010 sys 0.026 real
assemble_region: 1 calls 0.000 user 0.000 sys 0.001 real
calc: 93348 calls 0.002 user 0.000 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 0.005 user 0.000 sys 1.622 real
fetch: 93348 calls 0.003 user 0.000 sys 0.019 real
fetch_ref: 93349 calls 0.065 user 0.029 sys 0.354 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 39 calls 0.012 user 0.023 sys 21.307 real
init: 1 calls 0.040 user 0.000 sys 0.043 real
region: 93348 calls 0.000 user 0.001 sys 0.022 real
tracker: 93348 calls 0.015 user 0.001 sys 0.087 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 239243264 mem 1.254 user 4.588 sys 2.742 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory