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% @chr1:162000001, elapsed 0.1s, est remaining 2.5s, peak mem 81MB, user 0.1s, sys 3.4s, output queue size 2
progress 10% @chr2:72000001, elapsed 0.2s, est remaining 2.2s, peak mem 81MB, user 0.3s, sys 6.8s, output queue size 1
progress 15% @chr2:233000001, elapsed 0.4s, est remaining 2.1s, peak mem 81MB, user 0.4s, sys 10.3s, output queue size 2
progress 20% @chr3:152000001, elapsed 0.5s, est remaining 1.9s, peak mem 81MB, user 0.5s, sys 13.9s, output queue size 3
progress 25% @chr4:114000001, elapsed 0.6s, est remaining 1.8s, peak mem 81MB, user 0.6s, sys 17.4s, output queue size 1
progress 30% @chr5:87000001, elapsed 0.7s, est remaining 1.7s, peak mem 81MB, user 0.8s, sys 20.9s, output queue size 2
progress 35% @chr6:64000001, elapsed 0.8s, est remaining 1.6s, peak mem 81MB, user 0.9s, sys 24.4s, output queue size 1
progress 40% @chr7:54000001, elapsed 1.0s, est remaining 1.4s, peak mem 81MB, user 1.0s, sys 27.9s, output queue size 1
progress 45% @chr8:54000001, elapsed 1.1s, est remaining 1.3s, peak mem 81MB, user 1.2s, sys 31.4s, output queue size 3
progress 50% @chr9:72000001, elapsed 1.2s, est remaining 1.2s, peak mem 81MB, user 1.4s, sys 34.9s, output queue size 3
progress 55% @chr10:95000001, elapsed 1.3s, est remaining 1.1s, peak mem 81MB, user 1.5s, sys 38.4s, output queue size 7
progress 60% @chr11:121000001, elapsed 1.4s, est remaining 0.9s, peak mem 81MB, user 1.6s, sys 41.8s, output queue size 15
progress 65% @chr13:14000001, elapsed 1.5s, est remaining 0.8s, peak mem 81MB, user 1.8s, sys 45.2s, output queue size 3
progress 70% @chr14:58000001, elapsed 1.7s, est remaining 0.7s, peak mem 81MB, user 1.9s, sys 48.6s, output queue size 3
progress 75% @chr16:13000001, elapsed 1.8s, est remaining 0.6s, peak mem 81MB, user 2.1s, sys 52.0s, output queue size 6
progress 80% @chr17:81000001, elapsed 1.9s, est remaining 0.5s, peak mem 81MB, user 2.2s, sys 55.5s, output queue size 3
progress 85% @chr20:21000001, elapsed 2.0s, est remaining 0.4s, peak mem 81MB, user 2.4s, sys 58.9s, output queue size 1
progress 90% @chrX:31000001, elapsed 2.1s, est remaining 0.2s, peak mem 115MB, user 2.9s, sys 61.8s, output queue size 114
progress 95% @chrY:30000001, elapsed 2.3s, est remaining 0.1s, peak mem 145MB, user 3.3s, sys 65.2s, output queue size 276
progress 100% @chr21:41000001, elapsed 2.6s, est remaining 0.0s, peak mem 187MB, user 4.0s, sys 69.8s, 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: 49792993
reads: 1001320
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.031 user 0.003 sys 0.045 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.413 user 13.903 sys 15.793 real
calc: 3219322 calls 0.493 user 10.888 sys 11.866 real
done: 1 calls 0.031 user 0.003 sys 0.045 real
execute: 1 calls 0.002 user 0.002 sys 2.568 real
fetch: 3219322 calls 0.382 user 10.732 sys 11.771 real
idle: 75 calls 0.005 user 0.038 sys 35.980 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 231264256 mem 4.190 user 70.378 sys 3.625 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% @chr1:162000001, elapsed 0.1s, est remaining 2.0s, peak mem 189MB, user 0.4s, sys 2.2s, output queue size 30
progress 10% @chr2:75000001, elapsed 0.2s, est remaining 1.6s, peak mem 217MB, user 0.6s, sys 4.4s, output queue size 11
progress 15% @chr2:232000001, elapsed 0.3s, est remaining 1.5s, peak mem 240MB, user 0.9s, sys 6.6s, output queue size 34
progress 20% @chr3:154000001, elapsed 0.3s, est remaining 1.4s, peak mem 243MB, user 1.1s, sys 8.8s, output queue size 22
progress 25% @chr4:115000001, elapsed 0.4s, est remaining 1.3s, peak mem 253MB, user 1.4s, sys 11.0s, output queue size 4
progress 30% @chr5:89000001, elapsed 0.5s, est remaining 1.2s, peak mem 268MB, user 1.6s, sys 13.2s, output queue size 23
progress 35% @chr6:69000001, elapsed 0.6s, est remaining 1.1s, peak mem 276MB, user 1.8s, sys 15.4s, output queue size 18
progress 40% @chr7:56000001, elapsed 0.7s, est remaining 1.0s, peak mem 279MB, user 1.9s, sys 17.7s, output queue size 22
progress 45% @chr8:58000001, elapsed 0.7s, est remaining 0.9s, peak mem 289MB, user 2.1s, sys 19.9s, output queue size 12
progress 50% @chr9:73000001, elapsed 0.8s, est remaining 0.8s, peak mem 292MB, user 2.3s, sys 22.1s, output queue size 9
progress 55% @chr10:95000001, elapsed 0.9s, est remaining 0.7s, peak mem 294MB, user 2.5s, sys 24.3s, output queue size 3
progress 60% @chr11:122000001, elapsed 1.0s, est remaining 0.6s, peak mem 297MB, user 2.7s, sys 26.5s, output queue size 2
progress 65% @chr13:14000001, elapsed 1.0s, est remaining 0.6s, peak mem 300MB, user 2.9s, sys 28.9s, output queue size 1
progress 70% @chr14:63000001, elapsed 1.1s, est remaining 0.5s, peak mem 301MB, user 3.1s, sys 31.2s, output queue size 2
progress 75% @chr16:15000001, elapsed 1.2s, est remaining 0.4s, peak mem 303MB, user 3.3s, sys 33.5s, output queue size 9
progress 80% @chr18:1000001, elapsed 1.3s, est remaining 0.3s, peak mem 303MB, user 3.5s, sys 35.9s, output queue size 20
progress 85% @chr20:20000001, elapsed 1.4s, est remaining 0.2s, peak mem 306MB, user 3.8s, sys 38.3s, output queue size 2
progress 90% @chrX:40000001, elapsed 1.6s, est remaining 0.2s, peak mem 526MB, user 5.8s, sys 39.7s, output queue size 114
progress 95% @chrY:37000001, elapsed 1.7s, est remaining 0.1s, peak mem 544MB, user 7.5s, sys 40.9s, output queue size 276
progress 100% @chr21:41000001, elapsed 2.7s, est remaining 0.0s, peak mem 570MB, user 12.4s, sys 42.6s, 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: 49792993
reads: 1001320
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 23378 calls 0.009 user 0.002 sys 0.021 real
MateInfoByVcf::load: 23378 calls 3.857 user 0.656 sys 3.571 real
MateInfoByVcf::parse_events: 23378 calls 3.792 user 0.639 sys 3.468 real
advance: 3219322 calls 1.225 user 4.914 sys 6.886 real
calc: 3219322 calls 4.021 user 15.526 sys 20.173 real
done: 1 calls 0.000 user 0.001 sys 0.003 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.001 user 0.001 sys 2.717 real
fetch: 3219322 calls 0.330 user 4.814 sys 5.886 real
find_pairEnds: 23378 calls 0.241 user 0.023 sys 0.329 real
idle: 2088 calls 0.175 user 0.233 sys 56.960 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 23378 calls 0.852 user 0.086 sys 1.275 real
vcfadvance: 23378 calls 0.013 user 0.062 sys 0.029 real
write: 3219322 calls 2.121 user 5.295 sys 7.336 real
overall: 598147072 mem 13.392 user 43.777 sys 3.742 real