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% @chr1:159000001, elapsed 0.1s, est remaining 1.4s, peak mem 81MB, user 0.2s, sys 1.6s, output queue size 14
progress 10% @chr2:75000001, elapsed 0.1s, est remaining 1.3s, peak mem 81MB, user 0.3s, sys 3.5s, output queue size 7
progress 15% @chr2:212000001, elapsed 0.2s, est remaining 1.2s, peak mem 81MB, user 0.5s, sys 5.4s, output queue size 23
progress 20% @chr3:155000001, elapsed 0.3s, est remaining 1.1s, peak mem 81MB, user 0.6s, sys 7.4s, output queue size 18
progress 25% @chr4:116000001, elapsed 0.3s, est remaining 1.0s, peak mem 81MB, user 0.7s, sys 9.4s, output queue size 7
progress 30% @chr5:72000001, elapsed 0.4s, est remaining 1.0s, peak mem 81MB, user 0.8s, sys 11.4s, output queue size 14
progress 35% @chr6:67000001, elapsed 0.5s, est remaining 0.9s, peak mem 81MB, user 1.0s, sys 13.2s, output queue size 25
progress 40% @chr7:54000001, elapsed 0.5s, est remaining 0.8s, peak mem 81MB, user 1.2s, sys 15.1s, output queue size 1
progress 45% @chr8:61000001, elapsed 0.6s, est remaining 0.7s, peak mem 81MB, user 1.4s, sys 17.0s, output queue size 18
progress 50% @chr9:76000001, elapsed 0.7s, est remaining 0.7s, peak mem 81MB, user 1.5s, sys 18.9s, output queue size 16
progress 55% @chr10:95000001, elapsed 0.7s, est remaining 0.6s, peak mem 81MB, user 1.6s, sys 20.9s, output queue size 12
progress 60% @chr11:122000001, elapsed 0.8s, est remaining 0.5s, peak mem 81MB, user 1.8s, sys 22.8s, output queue size 20
progress 65% @chr13:17000001, elapsed 0.9s, est remaining 0.5s, peak mem 81MB, user 1.9s, sys 24.8s, output queue size 19
progress 70% @chr14:37000001, elapsed 0.9s, est remaining 0.4s, peak mem 81MB, user 2.0s, sys 26.7s, output queue size 24
progress 75% @chr16:15000001, elapsed 1.0s, est remaining 0.3s, peak mem 81MB, user 2.1s, sys 28.6s, output queue size 19
progress 80% @chr17:82000001, elapsed 1.1s, est remaining 0.3s, peak mem 81MB, user 2.2s, sys 30.6s, output queue size 2
progress 85% @chr20:22000001, elapsed 1.1s, est remaining 0.2s, peak mem 81MB, user 2.4s, sys 32.5s, output queue size 14
progress 90% @chrX:30000001, elapsed 1.2s, est remaining 0.1s, peak mem 126MB, user 3.0s, sys 34.1s, output queue size 114
progress 95% @chrY:30000001, elapsed 1.3s, est remaining 0.1s, peak mem 153MB, user 3.3s, sys 36.4s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.6s, est remaining 0.0s, peak mem 187MB, user 4.0s, sys 39.0s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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 192
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 49789689
reads: 1001320
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.033 user 0.007 sys 0.046 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.281 user 7.553 sys 9.138 real
calc: 3219322 calls 0.368 user 6.412 sys 6.775 real
done: 1 calls 0.033 user 0.007 sys 0.046 real
execute: 1 calls 0.003 user 0.002 sys 1.570 real
fetch: 3219322 calls 0.446 user 6.511 sys 6.704 real
idle: 74 calls 0.014 user 0.015 sys 35.685 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 231878656 mem 4.184 user 39.594 sys 2.630 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% @chr1:167000001, elapsed 0.1s, est remaining 2.1s, peak mem 196MB, user 0.2s, sys 2.7s, output queue size 15
progress 10% @chr2:55000001, elapsed 0.2s, est remaining 1.8s, peak mem 226MB, user 0.6s, sys 5.2s, output queue size 18
progress 15% @chr2:238000001, elapsed 0.3s, est remaining 1.7s, peak mem 244MB, user 0.9s, sys 7.6s, output queue size 17
progress 20% @chr3:157000001, elapsed 0.4s, est remaining 1.5s, peak mem 252MB, user 1.2s, sys 10.0s, output queue size 22
progress 25% @chr4:120000001, elapsed 0.5s, est remaining 1.4s, peak mem 262MB, user 1.5s, sys 12.4s, output queue size 15
progress 30% @chr5:64000001, elapsed 0.6s, est remaining 1.3s, peak mem 265MB, user 1.9s, sys 14.9s, output queue size 22
progress 35% @chr6:70000001, elapsed 0.7s, est remaining 1.2s, peak mem 271MB, user 2.2s, sys 17.3s, output queue size 17
progress 40% @chr7:59000001, elapsed 0.7s, est remaining 1.1s, peak mem 279MB, user 2.5s, sys 19.7s, output queue size 21
progress 45% @chr8:55000001, elapsed 0.8s, est remaining 1.0s, peak mem 280MB, user 2.8s, sys 22.2s, output queue size 19
progress 50% @chr9:76000001, elapsed 0.9s, est remaining 0.9s, peak mem 288MB, user 3.0s, sys 24.7s, output queue size 18
progress 55% @chr10:100000001, elapsed 1.0s, est remaining 0.8s, peak mem 288MB, user 3.3s, sys 27.1s, output queue size 9
progress 60% @chr11:127000001, elapsed 1.1s, est remaining 0.7s, peak mem 291MB, user 3.6s, sys 29.5s, output queue size 17
progress 65% @chr12:127000001, elapsed 1.2s, est remaining 0.6s, peak mem 291MB, user 3.9s, sys 32.0s, output queue size 22
progress 70% @chr14:69000001, elapsed 1.3s, est remaining 0.5s, peak mem 292MB, user 4.2s, sys 34.5s, output queue size 20
progress 75% @chr15:91000001, elapsed 1.4s, est remaining 0.5s, peak mem 294MB, user 4.5s, sys 36.9s, output queue size 24
progress 80% @chr17:73000001, elapsed 1.5s, est remaining 0.4s, peak mem 294MB, user 4.7s, sys 39.4s, output queue size 22
progress 85% @chr20:26000001, elapsed 1.5s, est remaining 0.3s, peak mem 301MB, user 5.0s, sys 41.8s, output queue size 19
progress 90% @chrX:40000001, elapsed 1.7s, est remaining 0.2s, peak mem 513MB, user 7.0s, sys 43.1s, output queue size 114
progress 95% @chrY:41000001, elapsed 1.8s, est remaining 0.1s, peak mem 550MB, user 8.1s, sys 44.4s, output queue size 276
progress 100% @chr21:41000001, elapsed 2.9s, est remaining 0.0s, peak mem 578MB, user 13.8s, sys 46.3s, 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 6.12.83
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 192
algo: Dedup
license: sentieon:Dedup=31
input file size: 49789689
reads: 1001320
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 23378 calls 0.000 user 0.000 sys 0.021 real
MateInfoByVcf::load: 23378 calls 4.067 user 0.749 sys 3.693 real
MateInfoByVcf::parse_events: 23378 calls 4.025 user 0.723 sys 3.591 real
advance: 3219322 calls 1.120 user 5.201 sys 7.625 real
calc: 3219322 calls 4.824 user 16.947 sys 22.014 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 0.003 user 0.000 sys 2.899 real
fetch: 3219322 calls 0.272 user 5.596 sys 6.335 real
find_pairEnds: 23378 calls 0.193 user 0.014 sys 0.348 real
idle: 2349 calls 0.220 user 0.221 sys 57.131 real
init: 1 calls 0.006 user 0.000 sys 0.006 real
markDup: 23378 calls 0.876 user 0.106 sys 1.374 real
vcfadvance: 23378 calls 0.012 user 0.082 sys 0.030 real
write: 3219322 calls 2.476 user 6.413 sys 7.908 real
overall: 606699520 mem 14.886 user 47.411 sys 3.923 real