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 1.3s, peak mem 81MB, user 0.1s, sys 1.5s, output queue size 3
progress 10% @chr2:72000001, elapsed 0.1s, est remaining 1.1s, peak mem 81MB, user 0.3s, sys 3.1s, output queue size 1
progress 15% @chr2:232000001, elapsed 0.2s, est remaining 1.0s, peak mem 81MB, user 0.4s, sys 4.9s, output queue size 25
progress 20% @chr3:152000001, elapsed 0.2s, est remaining 1.0s, peak mem 81MB, user 0.6s, sys 6.5s, output queue size 1
progress 25% @chr4:114000001, elapsed 0.3s, est remaining 0.9s, peak mem 81MB, user 0.7s, sys 8.3s, output queue size 18
progress 30% @chr5:87000001, elapsed 0.4s, est remaining 0.8s, peak mem 81MB, user 0.8s, sys 9.9s, output queue size 26
progress 35% @chr6:67000001, elapsed 0.4s, est remaining 0.8s, peak mem 81MB, user 0.9s, sys 11.7s, output queue size 22
progress 40% @chr7:56000001, elapsed 0.5s, est remaining 0.7s, peak mem 81MB, user 1.0s, sys 13.4s, output queue size 18
progress 45% @chr8:59000001, elapsed 0.5s, est remaining 0.7s, peak mem 81MB, user 1.1s, sys 15.1s, output queue size 27
progress 50% @chr9:74000001, elapsed 0.6s, est remaining 0.6s, peak mem 81MB, user 1.2s, sys 16.9s, output queue size 8
progress 55% @chr10:95000001, elapsed 0.7s, est remaining 0.5s, peak mem 81MB, user 1.3s, sys 18.6s, output queue size 19
progress 60% @chr11:122000001, elapsed 0.7s, est remaining 0.5s, peak mem 81MB, user 1.4s, sys 20.3s, output queue size 24
progress 65% @chr13:15000001, elapsed 0.8s, est remaining 0.4s, peak mem 81MB, user 1.5s, sys 22.0s, output queue size 15
progress 70% @chr14:61000001, elapsed 0.8s, est remaining 0.4s, peak mem 81MB, user 1.6s, sys 23.8s, output queue size 16
progress 75% @chr16:13000001, elapsed 0.9s, est remaining 0.3s, peak mem 81MB, user 1.7s, sys 25.5s, output queue size 16
progress 80% @chr18:1, elapsed 1.0s, est remaining 0.2s, peak mem 81MB, user 1.8s, sys 27.2s, output queue size 16
progress 85% @chr20:23000001, elapsed 1.0s, est remaining 0.2s, peak mem 81MB, user 1.9s, sys 28.9s, output queue size 27
progress 90% @chr21:45000001, elapsed 1.1s, est remaining 0.1s, peak mem 126MB, user 2.4s, sys 30.6s, output queue size 114
progress 95% @chrY:32000001, elapsed 1.2s, est remaining 0.1s, peak mem 157MB, user 2.7s, sys 32.9s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.4s, est remaining 0.0s, peak mem 187MB, user 3.4s, sys 35.7s, 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 192
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 49797077
reads: 1001320
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.022 user 0.010 sys 0.044 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.134 user 7.484 sys 8.690 real
calc: 3219322 calls 0.434 user 5.620 sys 6.150 real
done: 1 calls 0.022 user 0.010 sys 0.044 real
execute: 1 calls 0.005 user 0.005 sys 1.435 real
fetch: 3219322 calls 0.374 user 5.432 sys 6.019 real
idle: 74 calls 0.001 user 0.010 sys 35.290 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 230699008 mem 3.536 user 36.331 sys 2.496 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% @chr1:164000001, elapsed 0.1s, est remaining 2.1s, peak mem 204MB, user 0.4s, sys 2.3s, output queue size 29
progress 10% @chr2:78000001, elapsed 0.2s, est remaining 1.7s, peak mem 226MB, user 0.5s, sys 4.7s, output queue size 15
progress 15% @chr2:235000001, elapsed 0.3s, est remaining 1.6s, peak mem 253MB, user 0.7s, sys 7.0s, output queue size 3
progress 20% @chr3:154000001, elapsed 0.4s, est remaining 1.4s, peak mem 259MB, user 0.9s, sys 9.3s, output queue size 11
progress 25% @chr4:117000001, elapsed 0.4s, est remaining 1.3s, peak mem 262MB, user 1.1s, sys 11.6s, output queue size 17
progress 30% @chr5:86000001, elapsed 0.5s, est remaining 1.2s, peak mem 268MB, user 1.3s, sys 13.9s, output queue size 5
progress 35% @chr6:68000001, elapsed 0.6s, est remaining 1.1s, peak mem 279MB, user 1.5s, sys 16.2s, output queue size 4
progress 40% @chr7:60000001, elapsed 0.7s, est remaining 1.0s, peak mem 283MB, user 1.7s, sys 18.6s, output queue size 17
progress 45% @chr8:56000001, elapsed 0.8s, est remaining 0.9s, peak mem 286MB, user 1.8s, sys 20.9s, output queue size 21
progress 50% @chr9:74000001, elapsed 0.8s, est remaining 0.8s, peak mem 288MB, user 2.1s, sys 23.2s, output queue size 5
progress 55% @chr10:79000001, elapsed 0.9s, est remaining 0.8s, peak mem 291MB, user 2.3s, sys 25.7s, output queue size 16
progress 60% @chr11:123000001, elapsed 1.0s, est remaining 0.7s, peak mem 292MB, user 2.5s, sys 28.1s, output queue size 2
progress 65% @chr13:15000001, elapsed 1.1s, est remaining 0.6s, peak mem 295MB, user 2.7s, sys 30.5s, output queue size 2
progress 70% @chr14:62000001, elapsed 1.2s, est remaining 0.5s, peak mem 300MB, user 2.9s, sys 32.9s, output queue size 16
progress 75% @chr16:15000001, elapsed 1.3s, est remaining 0.4s, peak mem 303MB, user 3.0s, sys 35.5s, output queue size 14
progress 80% @chr17:74000001, elapsed 1.4s, est remaining 0.3s, peak mem 303MB, user 3.2s, sys 38.0s, output queue size 10
progress 85% @chr20:25000001, elapsed 1.4s, est remaining 0.3s, peak mem 307MB, user 3.3s, sys 40.6s, output queue size 12
progress 90% @chrX:35000001, elapsed 1.6s, est remaining 0.2s, peak mem 528MB, user 5.6s, sys 42.3s, output queue size 114
progress 95% @chrY:37000001, elapsed 1.8s, est remaining 0.1s, peak mem 541MB, user 7.0s, sys 44.0s, output queue size 276
progress 100% @chr21:41000001, elapsed 2.8s, est remaining 0.0s, peak mem 567MB, user 11.8s, 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 6.12.88
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 192
algo: Dedup
license: sentieon:Dedup=31
input file size: 49797077
reads: 1001320
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 23378 calls 0.015 user 0.005 sys 0.023 real
MateInfoByVcf::load: 23378 calls 3.599 user 0.689 sys 3.500 real
MateInfoByVcf::parse_events: 23378 calls 3.563 user 0.641 sys 3.392 real
advance: 3219322 calls 1.059 user 5.413 sys 7.261 real
calc: 3219322 calls 4.369 user 16.756 sys 21.350 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 0.003 user 0.002 sys 2.819 real
fetch: 3219322 calls 0.335 user 5.663 sys 6.142 real
find_pairEnds: 23378 calls 0.279 user 0.019 sys 0.337 real
idle: 2251 calls 0.206 user 0.188 sys 56.761 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 23378 calls 0.874 user 0.082 sys 1.328 real
vcfadvance: 23378 calls 0.008 user 0.075 sys 0.046 real
write: 3219322 calls 2.420 user 5.892 sys 7.827 real
overall: 594829312 mem 12.846 user 47.400 sys 3.841 real