Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/98d30da47d782d1252ba78b260b714/HCC1395_BL.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/c2b74978999e79d68b10df4e48b8f5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/c2b74978999e79d68b10df4e48b8f5/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/98d30da47d782d1252ba78b260b714/HCC1395_BL.bai
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i HCC1395_BL.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info HCC1395_BL.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:156000001, elapsed 0.1s, est remaining 1.3s, peak mem 81MB, user 0.1s, sys 1.4s, output queue size 5
progress 10% @chr2:67000001, elapsed 0.1s, est remaining 1.1s, peak mem 81MB, user 0.2s, sys 3.3s, output queue size 6
progress 15% @chr2:230000001, elapsed 0.2s, est remaining 1.1s, peak mem 81MB, user 0.3s, sys 5.0s, output queue size 6
progress 20% @chr3:148000001, elapsed 0.2s, est remaining 1.0s, peak mem 81MB, user 0.4s, sys 6.8s, output queue size 6
progress 25% @chr4:110000001, elapsed 0.3s, est remaining 0.9s, peak mem 81MB, user 0.6s, sys 8.5s, output queue size 5
progress 30% @chr5:81000001, elapsed 0.4s, est remaining 0.9s, peak mem 81MB, user 0.7s, sys 10.3s, output queue size 6
progress 35% @chr6:60000001, elapsed 0.4s, est remaining 0.8s, peak mem 81MB, user 0.8s, sys 12.0s, output queue size 5
progress 40% @chr7:45000001, elapsed 0.5s, est remaining 0.7s, peak mem 81MB, user 1.0s, sys 13.7s, output queue size 10
progress 45% @chr8:52000001, elapsed 0.6s, est remaining 0.7s, peak mem 81MB, user 1.1s, sys 15.5s, output queue size 5
progress 50% @chr9:68000001, elapsed 0.6s, est remaining 0.6s, peak mem 81MB, user 1.2s, sys 17.2s, output queue size 5
progress 55% @chr10:91000001, elapsed 0.7s, est remaining 0.6s, peak mem 81MB, user 1.4s, sys 18.9s, output queue size 7
progress 60% @chr11:117000001, elapsed 0.7s, est remaining 0.5s, peak mem 81MB, user 1.5s, sys 20.6s, output queue size 6
progress 65% @chr13:9000001, elapsed 0.8s, est remaining 0.4s, peak mem 81MB, user 1.6s, sys 22.4s, output queue size 9
progress 70% @chr14:56000001, elapsed 0.9s, est remaining 0.4s, peak mem 81MB, user 1.8s, sys 24.1s, output queue size 5
progress 75% @chr16:7000001, elapsed 0.9s, est remaining 0.3s, peak mem 81MB, user 1.9s, sys 25.8s, output queue size 7
progress 80% @chr17:76000001, elapsed 1.0s, est remaining 0.2s, peak mem 81MB, user 2.0s, sys 27.6s, output queue size 9
progress 85% @chr20:15000001, elapsed 1.0s, est remaining 0.2s, peak mem 81MB, user 2.1s, sys 29.4s, output queue size 10
progress 90% @chrX:27000001, elapsed 1.1s, est remaining 0.1s, peak mem 120MB, user 2.6s, sys 30.9s, output queue size 114
progress 95% @chrY:25000001, elapsed 1.2s, est remaining 0.1s, peak mem 147MB, user 2.9s, sys 32.9s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.5s, est remaining 0.0s, peak mem 181MB, user 3.8s, sys 35.4s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31 max 192
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 50411662
reads: 1001089
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.008 user 0.032 sys 0.054 real
VcfLineRecordHelper::sort: 29 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.232 user 6.931 sys 8.789 real
calc: 3219322 calls 0.354 user 5.560 sys 6.146 real
done: 1 calls 0.008 user 0.032 sys 0.054 real
execute: 1 calls 0.001 user 0.001 sys 1.493 real
fetch: 3219322 calls 0.348 user 6.071 sys 6.145 real
idle: 75 calls 0.005 user 0.024 sys 36.711 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 233439232 mem 3.927 user 36.077 sys 2.558 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i HCC1395_BL.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info HCC1395_BL.md.score --metrics HCC1395_BL.md.metrics HCC1395_BL.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:162000001, elapsed 0.1s, est remaining 1.9s, peak mem 193MB, user 0.2s, sys 2.2s, output queue size 16
progress 10% @chr2:74000001, elapsed 0.2s, est remaining 1.5s, peak mem 214MB, user 0.5s, sys 4.1s, output queue size 11
progress 15% @chr2:233000001, elapsed 0.2s, est remaining 1.4s, peak mem 235MB, user 0.6s, sys 6.1s, output queue size 13
progress 20% @chr3:152000001, elapsed 0.3s, est remaining 1.2s, peak mem 252MB, user 0.9s, sys 8.0s, output queue size 9
progress 25% @chr4:116000001, elapsed 0.4s, est remaining 1.1s, peak mem 264MB, user 1.1s, sys 9.9s, output queue size 12
progress 30% @chr5:85000001, elapsed 0.4s, est remaining 1.0s, peak mem 267MB, user 1.3s, sys 11.8s, output queue size 6
progress 35% @chr6:65000001, elapsed 0.5s, est remaining 1.0s, peak mem 273MB, user 1.5s, sys 13.7s, output queue size 3
progress 40% @chr7:54000001, elapsed 0.6s, est remaining 0.9s, peak mem 279MB, user 1.7s, sys 15.6s, output queue size 1
progress 45% @chr8:58000001, elapsed 0.7s, est remaining 0.8s, peak mem 288MB, user 1.9s, sys 17.5s, output queue size 1
progress 50% @chr9:72000001, elapsed 0.7s, est remaining 0.7s, peak mem 289MB, user 2.1s, sys 19.5s, output queue size 1
progress 55% @chr10:94000001, elapsed 0.8s, est remaining 0.6s, peak mem 289MB, user 2.3s, sys 21.3s, output queue size 1
progress 60% @chr11:121000001, elapsed 0.9s, est remaining 0.6s, peak mem 291MB, user 2.4s, sys 23.2s, output queue size 2
progress 65% @chr13:14000001, elapsed 0.9s, est remaining 0.5s, peak mem 292MB, user 2.6s, sys 25.2s, output queue size 1
progress 70% @chr14:74000001, elapsed 1.0s, est remaining 0.4s, peak mem 294MB, user 2.8s, sys 27.5s, output queue size 2
progress 75% @chr16:11000001, elapsed 1.1s, est remaining 0.4s, peak mem 298MB, user 3.0s, sys 29.9s, output queue size 23
progress 80% @chr17:81000001, elapsed 1.2s, est remaining 0.3s, peak mem 301MB, user 3.2s, sys 32.3s, output queue size 4
progress 85% @chr20:19000001, elapsed 1.3s, est remaining 0.2s, peak mem 306MB, user 3.4s, sys 34.8s, output queue size 3
progress 90% @chrX:44000001, elapsed 1.4s, est remaining 0.2s, peak mem 525MB, user 5.2s, sys 35.9s, output queue size 114
progress 95% @chrY:40000001, elapsed 1.5s, est remaining 0.1s, peak mem 543MB, user 6.5s, sys 36.8s, output queue size 276
progress 100% @chr21:41000001, elapsed 2.8s, est remaining 0.0s, peak mem 573MB, user 12.7s, sys 38.3s, output queue size 3664
library HCC1395_BL:
chimeric_paired 873
duped 146553
duped_chimeric_paired 2
duped_paired 146548
duped_unpaired 5
optical_dup 4835
paired 999974
reads 1001089
secondary_supplementary 1097
unmapped 9
unpaired 9
optical dup clusters 4702, maxdup 7, total optical dup pairs 4835
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31 max 192
algo: Dedup
license: sentieon:Dedup=31
input file size: 50411662
reads: 1001089
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 25531 calls 0.000 user 0.010 sys 0.017 real
MateInfoByVcf::load: 25531 calls 4.405 user 0.498 sys 4.045 real
MateInfoByVcf::parse_events: 25531 calls 4.365 user 0.477 sys 3.956 real
advance: 3219322 calls 1.176 user 4.908 sys 6.260 real
calc: 3219322 calls 4.116 user 13.581 sys 18.566 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 0.001 user 0.001 sys 2.829 real
fetch: 3219322 calls 0.337 user 4.665 sys 5.043 real
find_pairEnds: 25531 calls 0.255 user 0.001 sys 0.358 real
idle: 1951 calls 0.069 user 0.094 sys 64.511 real
init: 1 calls 0.010 user 0.000 sys 0.007 real
markDup: 25531 calls 0.847 user 0.030 sys 1.333 real
vcfadvance: 25531 calls 0.014 user 0.109 sys 0.033 real
write: 3219322 calls 2.351 user 4.308 sys 7.043 real
overall: 601079808 mem 13.463 user 39.123 sys 3.861 real