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 0.1s, est remaining 1.2s, peak mem 93MB, user 0.0s, sys 0.3s, output queue size 1387
progress 10% @chr4:152320545, elapsed 0.1s, est remaining 1.1s, peak mem 103MB, user 0.1s, sys 0.6s, output queue size 3783
progress 15% @chr5:36168313, elapsed 0.2s, est remaining 1.0s, peak mem 112MB, user 0.2s, sys 0.9s, output queue size 6252
progress 20% @chr5:91371400, elapsed 0.2s, est remaining 1.0s, peak mem 123MB, user 0.3s, sys 1.2s, output queue size 8832
progress 25% @chr5:141199775, elapsed 0.3s, est remaining 0.9s, peak mem 133MB, user 0.4s, sys 1.5s, output queue size 11235
progress 30% @chr5:177334284, elapsed 0.4s, est remaining 0.8s, peak mem 141MB, user 0.6s, sys 1.8s, output queue size 13370
progress 35% @chr6:30948547, elapsed 0.4s, est remaining 0.8s, peak mem 150MB, user 0.7s, sys 2.1s, output queue size 15546
progress 40% @chr6:43625363, elapsed 0.5s, est remaining 0.7s, peak mem 163MB, user 0.8s, sys 2.4s, output queue size 2321
progress 45% @chr6:106519131, elapsed 0.5s, est remaining 0.7s, peak mem 173MB, user 0.8s, sys 2.7s, output queue size 4788
progress 50% @chr6:149533458, elapsed 0.6s, est remaining 0.6s, peak mem 181MB, user 0.9s, sys 2.9s, output queue size 6894
progress 55% @chr7:13911239, elapsed 0.7s, est remaining 0.5s, peak mem 191MB, user 1.0s, sys 3.2s, output queue size 9143
progress 60% @chr7:64219314, elapsed 0.7s, est remaining 0.5s, peak mem 199MB, user 1.1s, sys 3.4s, output queue size 11215
progress 65% @chr7:100951841, elapsed 0.8s, est remaining 0.4s, peak mem 209MB, user 1.2s, sys 3.8s, output queue size 13732
progress 70% @chr7:139345501, elapsed 0.8s, est remaining 0.4s, peak mem 219MB, user 1.3s, sys 4.1s, output queue size 16095
progress 75% @chr8:13099347, elapsed 0.9s, est remaining 0.3s, peak mem 228MB, user 1.3s, sys 4.4s, output queue size 18154
progress 80% @chr8:38969421, elapsed 0.9s, est remaining 0.2s, peak mem 235MB, user 1.4s, sys 4.6s, output queue size 19798
progress 85% @chrX:15534212, elapsed 1.0s, est remaining 0.2s, peak mem 246MB, user 1.5s, sys 4.9s, output queue size 22287
progress 90% @chrX:54993911, elapsed 1.0s, est remaining 0.1s, peak mem 255MB, user 1.6s, sys 5.1s, output queue size 24649
progress 95% @chrX:111717846, elapsed 1.1s, est remaining 0.1s, peak mem 263MB, user 1.6s, sys 5.4s, output queue size 26584
progress 100% @chrX:152650428, elapsed 1.2s, est remaining 0.0s, peak mem 273MB, user 1.7s, sys 5.6s, output queue size 28803
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 00050654
  features: 1f8bfbff fffa320b
  extended: d19f47ab 00000018
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8124M CPU @ 3.00GHz
threads: 12 max 36
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71692767
output file size: 22308
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 0.028 user 0.016 sys 0.051 real
advance: 47638 calls 0.034 user 0.013 sys 0.050 real
assemble_region: 1 calls 0.000 user 0.000 sys 0.001 real
calc: 93348 calls 0.025 user 0.004 sys 0.050 real
clip_region: 1 calls 0.000 user 0.000 sys 0.000 real
done: 1 calls 0.001 user 0.000 sys 0.002 real
execute: 1 calls 0.004 user 0.002 sys 2.105 real
fetch: 93348 calls 0.004 user 0.013 sys 0.053 real
fetch_ref: 93349 calls 0.315 user 0.122 sys 0.608 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 39 calls 0.006 user 0.034 sys 24.192 real
init: 1 calls 0.048 user 0.012 sys 0.063 real
region: 93348 calls 0.029 user 0.020 sys 0.055 real
tracker: 93348 calls 0.077 user 0.016 sys 0.173 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 287154176 mem 2.317 user 7.400 sys 3.275 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory