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/c7/994e54654f23b66345d4ccc004ecd0/Sig_18_Blood.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/5c7110ff47bdb871224ee1d5c4d1eb/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/5c7110ff47bdb871224ee1d5c4d1eb/.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/c7/994e54654f23b66345d4ccc004ecd0/Sig_18_Blood.bam
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Sig_18_Blood.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info Sig_18_Blood.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:163000001, elapsed 0.1s, est remaining 1.5s, peak mem 81MB, user 0.2s, sys 1.8s, output queue size 5
progress 10% @chr2:76000001, elapsed 0.2s, est remaining 1.4s, peak mem 81MB, user 0.3s, sys 3.8s, output queue size 12
progress 15% @chr2:236000001, elapsed 0.2s, est remaining 1.2s, peak mem 81MB, user 0.5s, sys 5.8s, output queue size 20
progress 20% @chr3:155000001, elapsed 0.3s, est remaining 1.2s, peak mem 81MB, user 0.6s, sys 7.9s, output queue size 13
progress 25% @chr4:116000001, elapsed 0.4s, est remaining 1.1s, peak mem 81MB, user 0.7s, sys 9.8s, output queue size 16
progress 30% @chr5:68000001, elapsed 0.4s, est remaining 1.0s, peak mem 81MB, user 0.9s, sys 11.9s, output queue size 19
progress 35% @chr6:65000001, elapsed 0.5s, est remaining 0.9s, peak mem 81MB, user 1.1s, sys 13.9s, output queue size 19
progress 40% @chr7:55000001, elapsed 0.6s, est remaining 0.9s, peak mem 81MB, user 1.3s, sys 15.9s, output queue size 21
progress 45% @chr8:35000001, elapsed 0.6s, est remaining 0.8s, peak mem 81MB, user 1.4s, sys 18.0s, output queue size 22
progress 50% @chr9:74000001, elapsed 0.7s, est remaining 0.7s, peak mem 81MB, user 1.6s, sys 20.0s, output queue size 23
progress 55% @chr10:94000001, elapsed 0.8s, est remaining 0.6s, peak mem 81MB, user 1.8s, sys 22.0s, output queue size 1
progress 60% @chr11:121000001, elapsed 0.9s, est remaining 0.6s, peak mem 81MB, user 2.0s, sys 24.0s, output queue size 3
progress 65% @chr13:16000001, elapsed 0.9s, est remaining 0.5s, peak mem 81MB, user 2.1s, sys 26.1s, output queue size 8
progress 70% @chr14:61000001, elapsed 1.0s, est remaining 0.4s, peak mem 81MB, user 2.2s, sys 28.2s, output queue size 4
progress 75% @chr16:12000001, elapsed 1.1s, est remaining 0.4s, peak mem 81MB, user 2.4s, sys 30.2s, output queue size 12
progress 80% @chr18:1000001, elapsed 1.1s, est remaining 0.3s, peak mem 81MB, user 2.6s, sys 32.3s, output queue size 20
progress 85% @chr20:22000001, elapsed 1.2s, est remaining 0.2s, peak mem 81MB, user 2.8s, sys 34.3s, output queue size 17
progress 90% @chrX:30000001, elapsed 1.3s, est remaining 0.1s, peak mem 123MB, user 3.4s, sys 36.1s, output queue size 114
progress 95% @chrY:33000001, elapsed 1.4s, est remaining 0.1s, peak mem 154MB, user 3.9s, sys 38.3s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.7s, est remaining 0.0s, peak mem 183MB, user 4.6s, sys 41.6s, 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: 51297613
reads: 1001133
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.024 user 0.013 sys 0.046 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.236 user 8.402 sys 9.713 real
calc: 3219322 calls 0.339 user 6.553 sys 7.120 real
done: 1 calls 0.024 user 0.013 sys 0.046 real
execute: 1 calls 0.000 user 0.000 sys 1.690 real
fetch: 3219322 calls 0.477 user 6.549 sys 7.141 real
idle: 73 calls 0.009 user 0.019 sys 36.302 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 234418176 mem 4.764 user 42.101 sys 2.755 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Sig_18_Blood.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info Sig_18_Blood.md.score --metrics Sig_18_Blood.md.metrics Sig_18_Blood.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:159000001, elapsed 0.1s, est remaining 2.7s, peak mem 187MB, user 0.3s, sys 3.5s, output queue size 27
progress 10% @chr2:74000001, elapsed 0.3s, est remaining 2.3s, peak mem 211MB, user 0.6s, sys 6.6s, output queue size 24
progress 15% @chr2:240000001, elapsed 0.4s, est remaining 2.1s, peak mem 230MB, user 0.8s, sys 9.7s, output queue size 19
progress 20% @chr3:153000001, elapsed 0.5s, est remaining 1.9s, peak mem 245MB, user 1.1s, sys 12.8s, output queue size 38
progress 25% @chr4:117000001, elapsed 0.6s, est remaining 1.8s, peak mem 251MB, user 1.3s, sys 16.0s, output queue size 34
progress 30% @chr5:87000001, elapsed 0.7s, est remaining 1.6s, peak mem 260MB, user 1.5s, sys 19.2s, output queue size 24
progress 35% @chr6:67000001, elapsed 0.8s, est remaining 1.5s, peak mem 265MB, user 1.8s, sys 22.4s, output queue size 28
progress 40% @chr7:56000001, elapsed 0.9s, est remaining 1.4s, peak mem 272MB, user 2.0s, sys 25.5s, output queue size 27
progress 45% @chr8:56000001, elapsed 1.0s, est remaining 1.3s, peak mem 275MB, user 2.2s, sys 28.8s, output queue size 1
progress 50% @chr9:73000001, elapsed 1.1s, est remaining 1.1s, peak mem 278MB, user 2.4s, sys 32.0s, output queue size 16
progress 55% @chr10:97000001, elapsed 1.2s, est remaining 1.0s, peak mem 280MB, user 2.7s, sys 35.2s, output queue size 1
progress 60% @chr11:121000001, elapsed 1.4s, est remaining 0.9s, peak mem 284MB, user 2.8s, sys 38.5s, output queue size 2
progress 65% @chr13:13000001, elapsed 1.5s, est remaining 0.8s, peak mem 286MB, user 3.0s, sys 41.8s, output queue size 2
progress 70% @chr14:62000001, elapsed 1.6s, est remaining 0.7s, peak mem 287MB, user 3.1s, sys 45.0s, output queue size 2
progress 75% @chr16:13000001, elapsed 1.7s, est remaining 0.6s, peak mem 287MB, user 3.3s, sys 48.2s, output queue size 6
progress 80% @chr17:79000001, elapsed 1.8s, est remaining 0.4s, peak mem 287MB, user 3.5s, sys 51.3s, output queue size 5
progress 85% @chr20:21000001, elapsed 1.9s, est remaining 0.3s, peak mem 287MB, user 3.7s, sys 54.4s, output queue size 12
progress 90% @chrX:39000001, elapsed 2.1s, est remaining 0.2s, peak mem 511MB, user 6.0s, sys 56.3s, output queue size 114
progress 95% @chrY:37000001, elapsed 2.2s, est remaining 0.1s, peak mem 537MB, user 7.9s, sys 57.9s, output queue size 271
progress 100% @chr21:41000001, elapsed 3.4s, est remaining 0.0s, peak mem 558MB, user 13.0s, sys 60.6s, output queue size 3664
library Sig_18_Blood:
chimeric_paired 1027
duped 115575
duped_chimeric_paired 2
duped_paired 115574
duped_unpaired 1
optical_dup 5956
paired 999968
reads 1001133
secondary_supplementary 1151
unmapped 7
unpaired 7
optical dup clusters 5759, maxdup 3, total optical dup pairs 5956
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: 51297613
reads: 1001133
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 26026 calls 0.022 user 0.016 sys 0.029 real
MateInfoByVcf::load: 26026 calls 4.389 user 0.811 sys 4.180 real
MateInfoByVcf::parse_events: 26026 calls 4.314 user 0.766 sys 4.043 real
advance: 3219322 calls 1.151 user 7.462 sys 9.196 real
calc: 3219322 calls 4.310 user 21.909 sys 26.840 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 0.004 sys 3.459 real
fetch: 3219322 calls 0.372 user 7.043 sys 8.059 real
find_pairEnds: 26026 calls 0.272 user 0.027 sys 0.351 real
idle: 1812 calls 0.103 user 0.204 sys 60.991 real
init: 1 calls 0.000 user 0.010 sys 0.006 real
markDup: 26026 calls 0.854 user 0.123 sys 1.356 real
vcfadvance: 26026 calls 0.013 user 0.113 sys 0.060 real
write: 3219322 calls 2.427 user 7.505 sys 9.891 real
overall: 585539584 mem 13.696 user 61.932 sys 4.473 real