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% @chr1:170000001, elapsed 0.1s, est remaining 2.5s, peak mem 78MB, user 0.1s, sys 3.3s, output queue size 21
progress 10% @chr2:70000001, elapsed 0.3s, est remaining 2.3s, peak mem 78MB, user 0.2s, sys 6.9s, output queue size 31
progress 15% @chr2:233000001, elapsed 0.4s, est remaining 2.1s, peak mem 78MB, user 0.4s, sys 10.5s, output queue size 2
progress 20% @chr3:152000001, elapsed 0.5s, est remaining 2.0s, peak mem 78MB, user 0.5s, sys 14.0s, output queue size 1
progress 25% @chr4:117000001, elapsed 0.6s, est remaining 1.8s, peak mem 78MB, user 0.6s, sys 17.6s, output queue size 1
progress 30% @chr5:86000001, elapsed 0.7s, est remaining 1.7s, peak mem 78MB, user 0.7s, sys 21.1s, output queue size 5
progress 35% @chr6:65000001, elapsed 0.8s, est remaining 1.6s, peak mem 78MB, user 0.7s, sys 24.7s, output queue size 4
progress 40% @chr7:53000001, elapsed 1.0s, est remaining 1.4s, peak mem 78MB, user 0.8s, sys 28.3s, output queue size 4
progress 45% @chr8:81000001, elapsed 1.1s, est remaining 1.4s, peak mem 78MB, user 1.0s, sys 33.5s, output queue size 9
progress 50% @chr9:63000001, elapsed 1.3s, est remaining 1.3s, peak mem 78MB, user 1.1s, sys 39.3s, output queue size 13
progress 55% @chr10:116000001, elapsed 1.5s, est remaining 1.3s, peak mem 78MB, user 1.3s, sys 45.6s, output queue size 12
progress 60% @chr11:110000001, elapsed 1.8s, est remaining 1.2s, peak mem 78MB, user 1.4s, sys 52.1s, output queue size 20
progress 65% @chr13:3000001, elapsed 2.0s, est remaining 1.1s, peak mem 78MB, user 1.6s, sys 58.5s, output queue size 12
progress 70% @chr14:53000001, elapsed 2.2s, est remaining 0.9s, peak mem 78MB, user 1.8s, sys 64.6s, output queue size 14
progress 75% @chr16:7000001, elapsed 2.4s, est remaining 0.8s, peak mem 78MB, user 1.9s, sys 70.7s, output queue size 10
progress 80% @chr17:73000001, elapsed 2.6s, est remaining 0.6s, peak mem 78MB, user 2.1s, sys 76.8s, output queue size 11
progress 85% @chr20:12000001, elapsed 2.8s, est remaining 0.5s, peak mem 78MB, user 2.3s, sys 82.7s, output queue size 10
progress 90% @chrX:27000001, elapsed 3.0s, est remaining 0.3s, peak mem 84MB, user 2.9s, sys 88.1s, output queue size 114
progress 95% @chrY:50000001, elapsed 3.3s, est remaining 0.2s, peak mem 123MB, user 3.3s, sys 95.2s, output queue size 276
progress 100% @chr21:41000001, elapsed 3.7s, est remaining 0.0s, peak mem 165MB, user 4.3s, sys 105.6s, 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: 49784680
reads: 1001320
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.035 user 0.012 sys 0.054 real
VcfLineRecordHelper::sort: 30 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.470 user 22.033 sys 24.435 real
calc: 3219322 calls 0.551 user 17.394 sys 17.237 real
done: 1 calls 0.035 user 0.012 sys 0.054 real
execute: 1 calls 0.003 user 0.002 sys 3.742 real
fetch: 3219322 calls 0.220 user 16.979 sys 17.255 real
idle: 74 calls 0.003 user 0.036 sys 36.278 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 218013696 mem 4.385 user 106.288 sys 4.802 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% @chr1:159000001, elapsed 0.1s, est remaining 2.0s, peak mem 177MB, user 0.3s, sys 2.4s, output queue size 2
progress 10% @chr2:75000001, elapsed 0.2s, est remaining 1.7s, peak mem 198MB, user 0.6s, sys 4.6s, output queue size 23
progress 15% @chr2:232000001, elapsed 0.3s, est remaining 1.5s, peak mem 210MB, user 0.8s, sys 6.8s, output queue size 13
progress 20% @chr3:156000001, elapsed 0.3s, est remaining 1.4s, peak mem 219MB, user 1.0s, sys 9.0s, output queue size 35
progress 25% @chr4:117000001, elapsed 0.4s, est remaining 1.3s, peak mem 237MB, user 1.2s, sys 11.2s, output queue size 24
progress 30% @chr5:88000001, elapsed 0.5s, est remaining 1.2s, peak mem 243MB, user 1.5s, sys 13.5s, output queue size 22
progress 35% @chr6:67000001, elapsed 0.6s, est remaining 1.1s, peak mem 249MB, user 1.7s, sys 15.7s, output queue size 23
progress 40% @chr7:58000001, elapsed 0.7s, est remaining 1.0s, peak mem 255MB, user 1.9s, sys 17.8s, output queue size 21
progress 45% @chr8:58000001, elapsed 0.7s, est remaining 0.9s, peak mem 258MB, user 2.1s, sys 20.1s, output queue size 20
progress 50% @chr9:73000001, elapsed 0.8s, est remaining 0.8s, peak mem 258MB, user 2.2s, sys 22.3s, output queue size 13
progress 55% @chr10:95000001, elapsed 0.9s, est remaining 0.7s, peak mem 261MB, user 2.5s, sys 24.5s, output queue size 25
progress 60% @chr11:121000001, elapsed 1.0s, est remaining 0.7s, peak mem 264MB, user 2.7s, sys 26.8s, output queue size 2
progress 65% @chr13:14000001, elapsed 1.1s, est remaining 0.6s, peak mem 270MB, user 2.9s, sys 29.1s, output queue size 1
progress 70% @chr14:60000001, elapsed 1.1s, est remaining 0.5s, peak mem 276MB, user 3.1s, sys 31.5s, output queue size 1
progress 75% @chr16:12000001, elapsed 1.2s, est remaining 0.4s, peak mem 279MB, user 3.2s, sys 34.0s, output queue size 1
progress 80% @chr17:59000001, elapsed 1.3s, est remaining 0.3s, peak mem 279MB, user 3.4s, sys 36.2s, output queue size 25
progress 85% @chr20:16000001, elapsed 1.5s, est remaining 0.3s, peak mem 282MB, user 3.7s, sys 41.4s, output queue size 29
progress 90% @chrX:26000001, elapsed 1.8s, est remaining 0.2s, peak mem 498MB, user 6.6s, sys 45.5s, output queue size 114
progress 95% @chrY:25000001, elapsed 2.0s, est remaining 0.1s, peak mem 510MB, user 9.3s, sys 50.4s, output queue size 271
progress 100% @chr21:41000001, elapsed 3.0s, est remaining 0.0s, peak mem 525MB, user 12.9s, sys 56.2s, 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: 49784680
reads: 1001320
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 23378 calls 0.013 user 0.035 sys 0.050 real
MateInfoByVcf::load: 23378 calls 3.695 user 0.969 sys 3.810 real
MateInfoByVcf::parse_events: 23378 calls 3.646 user 0.840 sys 3.580 real
advance: 3219322 calls 1.309 user 6.736 sys 8.558 real
calc: 3219322 calls 4.695 user 20.590 sys 25.421 real
done: 1 calls 0.000 user 0.000 sys 0.003 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.002 user 0.000 sys 3.035 real
fetch: 3219322 calls 0.394 user 6.433 sys 7.472 real
find_pairEnds: 23378 calls 0.294 user 0.058 sys 0.365 real
idle: 968 calls 0.068 user 0.104 sys 52.681 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 23378 calls 0.970 user 0.232 sys 1.483 real
vcfadvance: 23378 calls 0.010 user 0.063 sys 0.061 real
write: 3219322 calls 2.530 user 6.651 sys 9.224 real
overall: 550658048 mem 13.534 user 57.583 sys 4.056 real