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% @chr1:160000001, elapsed 0.1s, est remaining 1.3s, peak mem 81MB, user 0.1s, sys 1.5s, output queue size 6
progress 10% @chr2:69000001, elapsed 0.1s, est remaining 1.1s, peak mem 81MB, user 0.3s, sys 3.2s, output queue size 4
progress 15% @chr2:229000001, elapsed 0.2s, est remaining 1.1s, peak mem 81MB, user 0.5s, sys 4.8s, output queue size 6
progress 20% @chr3:151000001, elapsed 0.2s, est remaining 1.0s, peak mem 81MB, user 0.7s, sys 6.6s, output queue size 10
progress 25% @chr4:110000001, elapsed 0.3s, est remaining 0.9s, peak mem 81MB, user 0.8s, sys 8.2s, output queue size 5
progress 30% @chr5:84000001, elapsed 0.4s, est remaining 0.9s, peak mem 81MB, user 1.1s, sys 9.7s, output queue size 3
progress 35% @chr6:85000001, elapsed 0.4s, est remaining 0.8s, peak mem 81MB, user 1.4s, sys 11.2s, output queue size 19
progress 40% @chr7:47000001, elapsed 0.5s, est remaining 0.7s, peak mem 81MB, user 1.6s, sys 13.0s, output queue size 8
progress 45% @chr8:52000001, elapsed 0.5s, est remaining 0.7s, peak mem 81MB, user 1.9s, sys 14.5s, output queue size 6
progress 50% @chr9:68000001, elapsed 0.6s, est remaining 0.6s, peak mem 81MB, user 2.1s, sys 16.1s, output queue size 8
progress 55% @chr10:94000001, elapsed 0.7s, est remaining 0.5s, peak mem 81MB, user 2.2s, sys 17.8s, output queue size 13
progress 60% @chr11:116000001, elapsed 0.7s, est remaining 0.5s, peak mem 81MB, user 2.4s, sys 19.5s, output queue size 7
progress 65% @chr13:11000001, elapsed 0.8s, est remaining 0.4s, peak mem 81MB, user 2.6s, sys 21.2s, output queue size 5
progress 70% @chr14:78000001, elapsed 0.8s, est remaining 0.4s, peak mem 81MB, user 2.8s, sys 22.8s, output queue size 17
progress 75% @chr16:31000001, elapsed 0.9s, est remaining 0.3s, peak mem 81MB, user 3.0s, sys 24.5s, output queue size 6
progress 80% @chr17:79000001, elapsed 1.0s, est remaining 0.2s, peak mem 81MB, user 3.2s, sys 26.1s, output queue size 5
progress 85% @chr20:18000001, elapsed 1.0s, est remaining 0.2s, peak mem 81MB, user 3.5s, sys 27.7s, output queue size 25
progress 90% @chrX:39000001, elapsed 1.1s, est remaining 0.1s, peak mem 133MB, user 4.1s, sys 29.0s, output queue size 114
progress 95% @chrY:26000001, elapsed 1.2s, est remaining 0.1s, peak mem 165MB, user 4.6s, sys 31.0s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.5s, est remaining 0.0s, peak mem 188MB, user 5.4s, sys 33.4s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 31 max 192
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 49784676
reads: 1001320
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.027 user 0.017 sys 0.053 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.663 user 6.092 sys 8.264 real
calc: 3219322 calls 0.514 user 5.314 sys 6.082 real
done: 1 calls 0.027 user 0.017 sys 0.053 real
execute: 1 calls 0.001 user 0.001 sys 1.453 real
fetch: 3219322 calls 0.341 user 5.543 sys 6.040 real
idle: 81 calls 0.003 user 0.016 sys 36.387 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 234745856 mem 5.630 user 33.915 sys 2.524 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% @chr1:160000001, elapsed 0.1s, est remaining 1.9s, peak mem 201MB, user 0.3s, sys 2.3s, output queue size 1
progress 10% @chr2:72000001, elapsed 0.2s, est remaining 1.6s, peak mem 228MB, user 0.5s, sys 4.5s, output queue size 2
progress 15% @chr2:233000001, elapsed 0.3s, est remaining 1.4s, peak mem 246MB, user 0.7s, sys 6.7s, output queue size 3
progress 20% @chr3:151000001, elapsed 0.3s, est remaining 1.3s, peak mem 252MB, user 1.0s, sys 8.8s, output queue size 2
progress 25% @chr4:115000001, elapsed 0.4s, est remaining 1.2s, peak mem 259MB, user 1.3s, sys 10.9s, output queue size 2
progress 30% @chr5:85000001, elapsed 0.5s, est remaining 1.1s, peak mem 265MB, user 1.6s, sys 13.0s, output queue size 1
progress 35% @chr6:64000001, elapsed 0.6s, est remaining 1.0s, peak mem 273MB, user 1.9s, sys 15.1s, output queue size 1
progress 40% @chr7:54000001, elapsed 0.6s, est remaining 1.0s, peak mem 276MB, user 2.2s, sys 17.2s, output queue size 1
progress 45% @chr8:57000001, elapsed 0.7s, est remaining 0.9s, peak mem 279MB, user 2.4s, sys 19.4s, output queue size 3
progress 50% @chr9:73000001, elapsed 0.8s, est remaining 0.8s, peak mem 282MB, user 2.7s, sys 21.5s, output queue size 2
progress 55% @chr10:94000001, elapsed 0.9s, est remaining 0.7s, peak mem 282MB, user 2.9s, sys 23.7s, output queue size 1
progress 60% @chr11:120000001, elapsed 1.0s, est remaining 0.6s, peak mem 285MB, user 3.1s, sys 25.8s, output queue size 3
progress 65% @chr13:14000001, elapsed 1.0s, est remaining 0.6s, peak mem 295MB, user 3.4s, sys 27.9s, output queue size 1
progress 70% @chr14:58000001, elapsed 1.1s, est remaining 0.5s, peak mem 300MB, user 3.7s, sys 30.1s, output queue size 3
progress 75% @chr16:11000001, elapsed 1.2s, est remaining 0.4s, peak mem 303MB, user 4.0s, sys 32.7s, output queue size 3
progress 80% @chr17:81000001, elapsed 1.3s, est remaining 0.3s, peak mem 303MB, user 4.2s, sys 35.4s, output queue size 4
progress 85% @chr20:19000001, elapsed 1.4s, est remaining 0.2s, peak mem 309MB, user 4.6s, sys 37.8s, output queue size 3
progress 90% @chrX:42000001, elapsed 1.6s, est remaining 0.2s, peak mem 516MB, user 6.8s, sys 38.9s, output queue size 114
progress 95% @chrY:37000001, elapsed 1.7s, est remaining 0.1s, peak mem 556MB, user 8.4s, sys 40.1s, output queue size 276
progress 100% @chr21:41000001, elapsed 2.3s, est remaining 0.0s, peak mem 581MB, user 13.7s, sys 41.7s, 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: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 31 max 192
algo: Dedup
license: sentieon:Dedup=31
input file size: 49784676
reads: 1001320
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 23378 calls 0.006 user 0.011 sys 0.019 real
MateInfoByVcf::load: 23378 calls 4.468 user 0.662 sys 4.090 real
MateInfoByVcf::parse_events: 23378 calls 4.438 user 0.622 sys 3.993 real
advance: 3219322 calls 1.633 user 5.431 sys 6.997 real
calc: 3219322 calls 4.060 user 14.921 sys 19.820 real
done: 1 calls 0.000 user 0.000 sys 0.004 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.004 user 0.005 sys 2.378 real
fetch: 3219322 calls 0.505 user 5.231 sys 5.595 real
find_pairEnds: 23378 calls 0.280 user 0.018 sys 0.385 real
idle: 2581 calls 1.108 user 0.306 sys 44.428 real
init: 1 calls 0.000 user 0.000 sys 0.007 real
markDup: 23378 calls 1.005 user 0.040 sys 1.488 real
vcfadvance: 23378 calls 0.008 user 0.041 sys 0.025 real
write: 3219322 calls 1.797 user 5.022 sys 6.965 real
overall: 610160640 mem 16.283 user 42.485 sys 3.393 real