cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i HCC1395_tumor.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info HCC1395_tumor.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:156000001, elapsed 0.1s, est remaining 2.2s, peak mem 81MB, user 0.2s, sys 2.8s, output queue size 26
progress 10% @chr2:68000001, elapsed 0.2s, est remaining 2.0s, peak mem 81MB, user 0.4s, sys 5.8s, output queue size 13
progress 15% @chr2:228000001, elapsed 0.3s, est remaining 1.9s, peak mem 81MB, user 0.6s, sys 8.9s, output queue size 7
progress 20% @chr3:180000001, elapsed 0.4s, est remaining 1.7s, peak mem 81MB, user 0.8s, sys 12.0s, output queue size 11
progress 25% @chr4:115000001, elapsed 0.5s, est remaining 1.6s, peak mem 81MB, user 1.0s, sys 15.1s, output queue size 16
progress 30% @chr5:53000001, elapsed 0.6s, est remaining 1.5s, peak mem 81MB, user 1.2s, sys 18.3s, output queue size 33
progress 35% @chr6:59000001, elapsed 0.8s, est remaining 1.4s, peak mem 81MB, user 1.3s, sys 21.5s, output queue size 27
progress 40% @chr7:49000001, elapsed 0.9s, est remaining 1.3s, peak mem 81MB, user 1.5s, sys 24.6s, output queue size 21
progress 45% @chr8:29000001, elapsed 1.0s, est remaining 1.2s, peak mem 81MB, user 1.7s, sys 27.8s, output queue size 28
progress 50% @chr9:73000001, elapsed 1.1s, est remaining 1.1s, peak mem 81MB, user 2.0s, sys 30.9s, output queue size 26
progress 55% @chr10:120000001, elapsed 1.2s, est remaining 1.0s, peak mem 81MB, user 2.2s, sys 34.9s, output queue size 38
progress 60% @chr12:11000001, elapsed 1.4s, est remaining 0.9s, peak mem 81MB, user 2.5s, sys 39.4s, output queue size 51
progress 65% @chr12:130000001, elapsed 1.5s, est remaining 0.8s, peak mem 81MB, user 2.7s, sys 44.0s, output queue size 49
progress 70% @chr14:81000001, elapsed 1.7s, est remaining 0.7s, peak mem 81MB, user 2.8s, sys 48.9s, output queue size 30
progress 75% @chr16:30000001, elapsed 1.9s, est remaining 0.6s, peak mem 81MB, user 3.0s, sys 53.7s, output queue size 37
progress 80% @chr17:43000001, elapsed 2.0s, est remaining 0.5s, peak mem 81MB, user 3.2s, sys 58.5s, output queue size 46
progress 85% @chr20:42000001, elapsed 2.2s, est remaining 0.4s, peak mem 81MB, user 3.4s, sys 63.3s, output queue size 14
progress 90% @chrX:46000001, elapsed 2.4s, est remaining 0.3s, peak mem 93MB, user 3.9s, sys 67.7s, output queue size 114
progress 95% @chrY:19000001, elapsed 2.6s, est remaining 0.1s, peak mem 120MB, user 4.3s, sys 73.2s, output queue size 276
progress 100% @chr21:41000001, elapsed 3.0s, est remaining 0.0s, peak mem 168MB, user 5.2s, sys 81.1s, output queue size 3664
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: 31 max 384
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 49784679
reads: 1001320
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.032 user 0.016 sys 0.053 real
VcfLineRecordHelper::sort: 30 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.245 user 17.731 sys 18.762 real
calc: 3219322 calls 0.333 user 13.423 sys 12.367 real
done: 1 calls 0.032 user 0.016 sys 0.053 real
execute: 1 calls 0.001 user 0.002 sys 2.997 real
fetch: 3219322 calls 0.294 user 13.315 sys 12.343 real
idle: 82 calls 0.006 user 0.024 sys 36.822 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 221155328 mem 5.361 user 81.685 sys 4.058 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i HCC1395_tumor.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info HCC1395_tumor.md.score --metrics HCC1395_tumor.md.metrics HCC1395_tumor.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:173000001, elapsed 0.3s, est remaining 5.1s, peak mem 165MB, user 0.4s, sys 6.9s, output queue size 13
progress 10% @chr2:87000001, elapsed 0.5s, est remaining 4.4s, peak mem 180MB, user 0.7s, sys 13.2s, output queue size 6
progress 15% @chr2:230000001, elapsed 0.7s, est remaining 4.0s, peak mem 201MB, user 1.1s, sys 19.5s, output queue size 30
progress 20% @chr3:147000001, elapsed 0.9s, est remaining 3.7s, peak mem 210MB, user 1.5s, sys 25.7s, output queue size 18
progress 25% @chr4:128000001, elapsed 1.1s, est remaining 3.4s, peak mem 216MB, user 1.8s, sys 32.0s, output queue size 17
progress 30% @chr5:99000001, elapsed 1.3s, est remaining 3.1s, peak mem 231MB, user 2.0s, sys 38.3s, output queue size 6
progress 35% @chr6:61000001, elapsed 1.6s, est remaining 2.9s, peak mem 243MB, user 2.4s, sys 44.6s, output queue size 8
progress 40% @chr7:50000001, elapsed 1.8s, est remaining 2.7s, peak mem 249MB, user 2.7s, sys 50.9s, output queue size 14
progress 45% @chr8:48000001, elapsed 2.0s, est remaining 2.4s, peak mem 249MB, user 3.0s, sys 57.3s, output queue size 27
progress 50% @chr9:88000001, elapsed 2.2s, est remaining 2.2s, peak mem 255MB, user 3.3s, sys 63.9s, output queue size 10
progress 55% @chr10:101000001, elapsed 2.4s, est remaining 2.0s, peak mem 255MB, user 3.6s, sys 70.5s, output queue size 6
progress 60% @chr11:118000001, elapsed 2.7s, est remaining 1.8s, peak mem 255MB, user 3.8s, sys 77.6s, output queue size 10
progress 65% @chr13:32000001, elapsed 2.9s, est remaining 1.6s, peak mem 258MB, user 4.1s, sys 84.6s, output queue size 21
progress 70% @chr14:58000001, elapsed 3.1s, est remaining 1.3s, peak mem 261MB, user 4.4s, sys 91.8s, output queue size 7
progress 75% @chr16:24000001, elapsed 3.4s, est remaining 1.1s, peak mem 267MB, user 4.6s, sys 98.8s, output queue size 5
progress 80% @chr17:81000001, elapsed 3.6s, est remaining 0.9s, peak mem 267MB, user 4.9s, sys 106.1s, output queue size 9
progress 85% @chr20:21000001, elapsed 3.9s, est remaining 0.7s, peak mem 276MB, user 5.1s, sys 113.4s, output queue size 8
progress 90% @chrX:33000001, elapsed 4.3s, est remaining 0.5s, peak mem 480MB, user 7.9s, sys 119.0s, output queue size 114
progress 95% @chrY:26000001, elapsed 4.5s, est remaining 0.2s, peak mem 516MB, user 10.6s, sys 125.8s, output queue size 271
progress 100% @chr21:41000001, elapsed 5.6s, est remaining 0.0s, peak mem 528MB, user 14.7s, sys 132.7s, output queue size 3664
library HCC1395_tumor:
chimeric_paired 1295
duped 169120
duped_chimeric_paired 30
duped_paired 169118
duped_unpaired 2
optical_dup 5868
paired 999972
reads 1001320
secondary_supplementary 1340
unmapped 4
unpaired 4
optical dup clusters 5659, maxdup 4, total optical dup pairs 5868
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: 31 max 384
algo: Dedup
license: sentieon:Dedup=31
input file size: 49784679
reads: 1001320
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 23378 calls 0.028 user 0.045 sys 0.072 real
MateInfoByVcf::load: 23378 calls 3.741 user 1.759 sys 4.303 real
MateInfoByVcf::parse_events: 23378 calls 3.622 user 1.563 sys 3.968 real
advance: 3219322 calls 1.301 user 17.180 sys 18.709 real
calc: 3219322 calls 5.026 user 48.578 sys 54.873 real
done: 1 calls 0.000 user 0.000 sys 0.004 real
exec_no_coor: 1 calls 0.000 user 0.003 sys 0.001 real
execute: 1 calls 0.003 user 0.002 sys 5.679 real
fetch: 3219322 calls 0.535 user 16.646 sys 14.747 real
find_pairEnds: 23378 calls 0.291 user 0.056 sys 0.442 real
idle: 988 calls 0.068 user 0.097 sys 55.589 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 23378 calls 0.962 user 0.475 sys 1.925 real
vcfadvance: 23378 calls 0.023 user 0.193 sys 0.146 real
write: 3219322 calls 2.675 user 15.816 sys 18.938 real
overall: 553787392 mem 15.629 user 133.998 sys 6.705 real