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/62/afa349c96f8d89fea67eb351573717/HCC1395_BL.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/9bc2477a071584c0387d1c6464c441/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/9bc2477a071584c0387d1c6464c441/.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/62/afa349c96f8d89fea67eb351573717/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% @chr1:160000001, elapsed 0.1s, est remaining 1.7s, peak mem 81MB, user 0.1s, sys 2.2s, output queue size 1
progress 10% @chr2:73000001, elapsed 0.2s, est remaining 1.6s, peak mem 81MB, user 0.2s, sys 4.6s, output queue size 4
progress 15% @chr2:234000001, elapsed 0.3s, est remaining 1.4s, peak mem 81MB, user 0.3s, sys 7.0s, output queue size 15
progress 20% @chr3:152000001, elapsed 0.3s, est remaining 1.3s, peak mem 81MB, user 0.4s, sys 9.4s, output queue size 1
progress 25% @chr4:114000001, elapsed 0.4s, est remaining 1.3s, peak mem 81MB, user 0.6s, sys 11.8s, output queue size 1
progress 30% @chr5:85000001, elapsed 0.5s, est remaining 1.2s, peak mem 81MB, user 0.7s, sys 14.2s, output queue size 14
progress 35% @chr6:65000001, elapsed 0.6s, est remaining 1.1s, peak mem 81MB, user 0.9s, sys 16.6s, output queue size 2
progress 40% @chr7:58000001, elapsed 0.7s, est remaining 1.0s, peak mem 81MB, user 1.0s, sys 19.0s, output queue size 13
progress 45% @chr8:56000001, elapsed 0.7s, est remaining 0.9s, peak mem 81MB, user 1.1s, sys 21.4s, output queue size 1
progress 50% @chr9:73000001, elapsed 0.8s, est remaining 0.8s, peak mem 81MB, user 1.2s, sys 23.9s, output queue size 6
progress 55% @chr10:96000001, elapsed 0.9s, est remaining 0.7s, peak mem 81MB, user 1.3s, sys 26.3s, output queue size 1
progress 60% @chr11:123000001, elapsed 1.0s, est remaining 0.7s, peak mem 81MB, user 1.4s, sys 28.7s, output queue size 7
progress 65% @chr13:14000001, elapsed 1.1s, est remaining 0.6s, peak mem 81MB, user 1.5s, sys 31.1s, output queue size 1
progress 70% @chr14:60000001, elapsed 1.2s, est remaining 0.5s, peak mem 81MB, user 1.6s, sys 33.5s, output queue size 1
progress 75% @chr16:12000001, elapsed 1.2s, est remaining 0.4s, peak mem 81MB, user 1.8s, sys 35.7s, output queue size 1
progress 80% @chr17:82000001, elapsed 1.3s, est remaining 0.3s, peak mem 81MB, user 2.0s, sys 38.1s, output queue size 2
progress 85% @chr20:22000001, elapsed 1.4s, est remaining 0.2s, peak mem 81MB, user 2.2s, sys 40.3s, output queue size 15
progress 90% @chrX:31000001, elapsed 1.5s, est remaining 0.2s, peak mem 118MB, user 2.7s, sys 42.5s, output queue size 114
progress 95% @chrY:33000001, elapsed 1.6s, est remaining 0.1s, peak mem 147MB, user 3.0s, sys 45.0s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.9s, est remaining 0.0s, peak mem 187MB, user 3.7s, sys 48.7s, 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: 50411820
reads: 1001089
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.034 user 0.009 sys 0.048 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.240 user 9.620 sys 11.049 real
calc: 3219322 calls 0.319 user 7.280 sys 8.424 real
done: 1 calls 0.034 user 0.009 sys 0.048 real
execute: 1 calls 0.001 user 0.001 sys 1.895 real
fetch: 3219322 calls 0.334 user 7.885 sys 8.430 real
idle: 74 calls 0.010 user 0.019 sys 36.396 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 237572096 mem 3.870 user 49.331 sys 2.952 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% @chr1:160000001, elapsed 0.1s, est remaining 2.1s, peak mem 193MB, user 0.3s, sys 2.5s, output queue size 1
progress 10% @chr2:74000001, elapsed 0.2s, est remaining 1.7s, peak mem 223MB, user 0.5s, sys 4.8s, output queue size 1
progress 15% @chr2:233000001, elapsed 0.3s, est remaining 1.5s, peak mem 244MB, user 0.7s, sys 7.2s, output queue size 3
progress 20% @chr3:154000001, elapsed 0.4s, est remaining 1.4s, peak mem 256MB, user 0.9s, sys 9.5s, output queue size 1
progress 25% @chr4:114000001, elapsed 0.4s, est remaining 1.3s, peak mem 265MB, user 1.1s, sys 11.8s, output queue size 1
progress 30% @chr5:86000001, elapsed 0.5s, est remaining 1.2s, peak mem 268MB, user 1.3s, sys 14.0s, output queue size 1
progress 35% @chr6:64000001, elapsed 0.6s, est remaining 1.1s, peak mem 274MB, user 1.4s, sys 16.4s, output queue size 1
progress 40% @chr7:52000001, elapsed 0.7s, est remaining 1.0s, peak mem 283MB, user 1.6s, sys 18.7s, output queue size 3
progress 45% @chr8:56000001, elapsed 0.8s, est remaining 0.9s, peak mem 287MB, user 1.8s, sys 21.1s, output queue size 1
progress 50% @chr9:72000001, elapsed 0.8s, est remaining 0.8s, peak mem 292MB, user 2.0s, sys 23.5s, output queue size 4
progress 55% @chr10:94000001, elapsed 0.9s, est remaining 0.8s, peak mem 293MB, user 2.2s, sys 25.9s, output queue size 1
progress 60% @chr11:121000001, elapsed 1.0s, est remaining 0.7s, peak mem 295MB, user 2.4s, sys 28.2s, output queue size 2
progress 65% @chr13:14000001, elapsed 1.1s, est remaining 0.6s, peak mem 295MB, user 2.6s, sys 30.6s, output queue size 1
progress 70% @chr14:60000001, elapsed 1.2s, est remaining 0.5s, peak mem 298MB, user 2.8s, sys 33.0s, output queue size 1
progress 75% @chr16:9000001, elapsed 1.3s, est remaining 0.4s, peak mem 299MB, user 3.0s, sys 35.5s, output queue size 4
progress 80% @chr18:1, elapsed 1.4s, est remaining 0.3s, peak mem 299MB, user 3.2s, sys 37.9s, output queue size 21
progress 85% @chr20:21000001, elapsed 1.4s, est remaining 0.3s, peak mem 301MB, user 3.4s, sys 40.4s, output queue size 20
progress 90% @chrX:40000001, elapsed 1.6s, est remaining 0.2s, peak mem 535MB, user 5.5s, sys 41.7s, output queue size 114
progress 95% @chrY:39000001, elapsed 1.7s, est remaining 0.1s, peak mem 544MB, user 6.8s, sys 42.6s, output queue size 276
progress 100% @chr21:41000001, elapsed 2.8s, est remaining 0.0s, peak mem 563MB, user 12.6s, sys 44.2s, 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 6.12.83
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: 50411820
reads: 1001089
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 25531 calls 0.000 user 0.000 sys 0.022 real
MateInfoByVcf::load: 25531 calls 4.354 user 0.638 sys 3.922 real
MateInfoByVcf::parse_events: 25531 calls 4.294 user 0.604 sys 3.816 real
advance: 3219322 calls 1.193 user 5.585 sys 7.092 real
calc: 3219322 calls 3.906 user 15.896 sys 20.818 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 0.001 sys 2.893 real
fetch: 3219322 calls 0.417 user 5.393 sys 5.860 real
find_pairEnds: 25531 calls 0.189 user 0.000 sys 0.342 real
idle: 1772 calls 0.103 user 0.230 sys 60.545 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 25531 calls 0.748 user 0.058 sys 1.317 real
vcfadvance: 25531 calls 0.007 user 0.096 sys 0.037 real
write: 3219322 calls 2.277 user 5.072 sys 7.740 real
overall: 590995456 mem 13.516 user 45.470 sys 3.915 real