cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr21_44120631-44120778.bed.gz -i HCC1395_BL.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant HCC1395_BL.haplotyper.chr21_44120631-44120778.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr21:44222913, elapsed 0.0s, est remaining 0.3s, peak mem 81MB, user 0.0s, sys 0.0s, output queue size 3
progress 10% @chr21:44286007, elapsed 0.0s, est remaining 0.4s, peak mem 102MB, user 0.1s, sys 0.0s, output queue size 39
progress 15% @chr21:44401681, elapsed 0.1s, est remaining 0.3s, peak mem 118MB, user 0.3s, sys 0.1s, output queue size 70
progress 20% @chr21:44533685, elapsed 0.1s, est remaining 0.2s, peak mem 124MB, user 0.3s, sys 0.1s, output queue size 99
progress 30% @chr21:44224713, elapsed 0.1s, est remaining 0.2s, peak mem 157MB, user 0.5s, sys 0.1s, output queue size 108
progress 35% @chr21:44657980, elapsed 0.1s, est remaining 0.3s, peak mem 168MB, user 0.8s, sys 0.1s, output queue size 7
progress 41% @chr21:44573759, elapsed 0.2s, est remaining 0.3s, peak mem 217MB, user 1.5s, sys 0.1s, output queue size 28
progress 45% @chr21:44901492, elapsed 0.2s, est remaining 0.3s, peak mem 217MB, user 2.0s, sys 0.1s, output queue size 42
progress 50% @chr21:44891809, elapsed 0.3s, est remaining 0.3s, peak mem 217MB, user 2.1s, sys 0.1s, output queue size 70
progress 55% @chr21:45488418, elapsed 0.3s, est remaining 0.2s, peak mem 217MB, user 2.2s, sys 0.1s, output queue size 106
progress 60% @chr21:45986944, elapsed 0.3s, est remaining 0.2s, peak mem 217MB, user 2.5s, sys 0.1s, output queue size 30
progress 65% @chr21:46121061, elapsed 0.3s, est remaining 0.2s, peak mem 217MB, user 2.8s, sys 0.1s, output queue size 12
progress 70% @chr21:46168308, elapsed 0.3s, est remaining 0.1s, peak mem 220MB, user 3.0s, sys 0.2s, output queue size 24
progress 75% @chr21:46254776, elapsed 0.4s, est remaining 0.1s, peak mem 220MB, user 3.1s, sys 0.2s, output queue size 53
progress 80% @chr21:46326377, elapsed 0.4s, est remaining 0.1s, peak mem 220MB, user 3.5s, sys 0.2s, output queue size 20
progress 85% @chr21:46363480, elapsed 0.4s, est remaining 0.1s, peak mem 220MB, user 3.6s, sys 0.2s, output queue size 31
progress 90% @chr21:46484757, elapsed 0.4s, est remaining 0.0s, peak mem 220MB, user 3.7s, sys 0.2s, output queue size 26
progress 95% @chr21:46366584, elapsed 0.4s, est remaining 0.0s, peak mem 220MB, user 3.8s, sys 0.2s, output queue size 55
progress 100% @chr21:46602278, elapsed 0.5s, est remaining 0.0s, peak mem 220MB, user 3.9s, sys 0.2s, output queue size 11
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 12 max 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 163002590
output file size: 38710
reads: 1955548
contig: 516 intervals 92221 bases
"assemble": 96 calls 0.147 user 0.000 sys 0.234 real
"assemble_addRead": 96 calls 0.000 user 0.000 sys 0.011 real
"assemble_buildGraph": 205 calls 0.078 user 0.000 sys 0.119 real
"assemble_computecigar": 140 calls 0.068 user 0.007 sys 0.148 real
"assemble_kg_build_calcsize": 205 calls 0.025 user 0.000 sys 0.070 real
"assemble_kg_build_clear": 265 calls 0.000 user 0.000 sys 0.005 real
"assemble_kg_build_prepare": 410 calls 0.025 user 0.000 sys 0.053 real
"assemble_kg_build_threading": 145 calls 0.052 user 0.000 sys 0.047 real
"assemble_kg_op1": 145 calls 0.000 user 0.000 sys 0.011 real
"assemble_kg_op2": 145 calls 0.012 user 0.000 sys 0.003 real
"assemble_kg_op3": 145 calls 0.000 user 0.000 sys 0.003 real
"assemble_sg_clean": 140 calls 0.000 user 0.000 sys 0.012 real
"assemble_sg_create": 140 calls 0.024 user 0.000 sys 0.016 real
"checkGraph": 96 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 96 calls 0.068 user 0.007 sys 0.152 real
active: 1044 calls 0.000 user 0.000 sys 0.003 real
advance: 528 calls 1.192 user 0.054 sys 1.516 real
annotate: 105 calls 0.006 user 0.000 sys 0.010 real
assemble_region: 96 calls 0.224 user 0.007 sys 0.398 real
build_variants: 95 calls 0.000 user 0.000 sys 0.001 real
calc: 1044 calls 0.134 user 0.000 sys 0.137 real
calc_region: 95 calls 1.540 user 0.035 sys 1.710 real
call_region: 95 calls 0.016 user 0.000 sys 0.016 real
clip_region: 191 calls 0.021 user 0.000 sys 0.019 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.008 user 0.001 sys 0.465 real
fetch: 1044 calls 0.065 user 0.000 sys 0.063 real
fetch_db: 95 calls 0.016 user 0.000 sys 0.030 real
fetch_ref: 1140 calls 0.006 user 0.010 sys 0.005 real
fetch_region: 96 calls 0.000 user 0.000 sys 0.004 real
idle: 49 calls 0.034 user 0.000 sys 12.473 real
init: 1 calls 0.030 user 0.010 sys 0.041 real
pairhmm: 430 calls 2.623 user 0.035 sys 2.871 real
realign: 197 calls 0.111 user 0.000 sys 0.177 real
region: 1044 calls 2.487 user 0.077 sys 2.592 real
tracker: 1044 calls 0.010 user 0.003 sys 0.003 real
trim_region: 96 calls 0.015 user 0.000 sys 0.002 real
overall: 231456768 mem 5.237 user 0.180 sys 1.569 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory