Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/0819ac5d812f39181904900e2afec0/Sig_18_Blood.bai
  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/f4/e8f9452ffe2420eb8808ba1556b1dd/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/e8f9452ffe2420eb8808ba1556b1dd/.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/30/0819ac5d812f39181904900e2afec0/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% @chr1:164000001, elapsed 0.1s, est remaining 1.4s, peak mem 83MB, user 0.1s, sys 1.6s, output queue size 13
progress 10% @chr2:76000001, elapsed 0.1s, est remaining 1.3s, peak mem 83MB, user 0.3s, sys 3.6s, output queue size 23
progress 15% @chr2:238000001, elapsed 0.2s, est remaining 1.2s, peak mem 83MB, user 0.4s, sys 5.6s, output queue size 16
progress 20% @chr3:153000001, elapsed 0.3s, est remaining 1.1s, peak mem 83MB, user 0.5s, sys 7.5s, output queue size 1
progress 25% @chr4:100000001, elapsed 0.3s, est remaining 1.0s, peak mem 83MB, user 0.6s, sys 9.4s, output queue size 22
progress 30% @chr5:89000001, elapsed 0.4s, est remaining 0.9s, peak mem 83MB, user 0.8s, sys 11.2s, output queue size 23
progress 35% @chr6:70000001, elapsed 0.5s, est remaining 0.9s, peak mem 83MB, user 1.0s, sys 13.1s, output queue size 18
progress 40% @chr7:58000001, elapsed 0.5s, est remaining 0.8s, peak mem 83MB, user 1.2s, sys 15.0s, output queue size 13
progress 45% @chr8:56000001, elapsed 0.6s, est remaining 0.7s, peak mem 83MB, user 1.3s, sys 17.0s, output queue size 6
progress 50% @chr9:73000001, elapsed 0.7s, est remaining 0.7s, peak mem 83MB, user 1.5s, sys 18.9s, output queue size 1
progress 55% @chr10:96000001, elapsed 0.7s, est remaining 0.6s, peak mem 83MB, user 1.6s, sys 20.7s, output queue size 21
progress 60% @chr11:110000001, elapsed 0.8s, est remaining 0.5s, peak mem 83MB, user 1.8s, sys 22.6s, output queue size 13
progress 65% @chr13:17000001, elapsed 0.9s, est remaining 0.5s, peak mem 83MB, user 2.0s, sys 24.5s, output queue size 21
progress 70% @chr14:64000001, elapsed 0.9s, est remaining 0.4s, peak mem 83MB, user 2.1s, sys 26.4s, output queue size 23
progress 75% @chr16:16000001, elapsed 1.0s, est remaining 0.3s, peak mem 83MB, user 2.3s, sys 28.3s, output queue size 25
progress 80% @chr18:4000001, elapsed 1.1s, est remaining 0.3s, peak mem 83MB, user 2.4s, sys 30.2s, output queue size 17
progress 85% @chr20:25000001, elapsed 1.1s, est remaining 0.2s, peak mem 83MB, user 2.7s, sys 32.0s, output queue size 16
progress 90% @chrX:33000001, elapsed 1.2s, est remaining 0.1s, peak mem 148MB, user 3.4s, sys 33.6s, output queue size 114
progress 95% @chrY:31000001, elapsed 1.3s, est remaining 0.1s, peak mem 183MB, user 3.7s, sys 36.0s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.6s, est remaining 0.0s, peak mem 193MB, user 4.5s, sys 38.8s, 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 64
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 51298918
reads: 1001133
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.026 user 0.006 sys 0.045 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.441 user 7.075 sys 9.220 real
calc: 3219322 calls 0.368 user 6.117 sys 6.794 real
done: 1 calls 0.026 user 0.006 sys 0.045 real
execute: 1 calls 0.001 user 0.001 sys 1.564 real
fetch: 3219322 calls 0.411 user 5.946 sys 6.714 real
idle: 72 calls 0.003 user 0.014 sys 35.577 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 239366144 mem 4.596 user 39.227 sys 2.620 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% @chr1:163000001, elapsed 0.1s, est remaining 2.1s, peak mem 201MB, user 0.3s, sys 2.7s, output queue size 17
progress 10% @chr2:74000001, elapsed 0.2s, est remaining 1.8s, peak mem 231MB, user 0.5s, sys 5.5s, output queue size 3
progress 15% @chr2:234000001, elapsed 0.3s, est remaining 1.7s, peak mem 254MB, user 0.7s, sys 8.1s, output queue size 3
progress 20% @chr3:155000001, elapsed 0.4s, est remaining 1.6s, peak mem 262MB, user 0.8s, sys 10.8s, output queue size 16
progress 25% @chr4:114000001, elapsed 0.5s, est remaining 1.5s, peak mem 270MB, user 0.9s, sys 13.7s, output queue size 1
progress 30% @chr5:85000001, elapsed 0.6s, est remaining 1.4s, peak mem 282MB, user 1.1s, sys 16.4s, output queue size 6
progress 35% @chr6:66000001, elapsed 0.7s, est remaining 1.3s, peak mem 287MB, user 1.2s, sys 19.2s, output queue size 12
progress 40% @chr7:56000001, elapsed 0.8s, est remaining 1.1s, peak mem 293MB, user 1.3s, sys 21.9s, output queue size 13
progress 45% @chr8:57000001, elapsed 0.9s, est remaining 1.0s, peak mem 298MB, user 1.5s, sys 24.6s, output queue size 11
progress 50% @chr9:75000001, elapsed 0.9s, est remaining 0.9s, peak mem 306MB, user 1.6s, sys 27.2s, output queue size 8
progress 55% @chr10:94000001, elapsed 1.0s, est remaining 0.9s, peak mem 309MB, user 1.8s, sys 29.9s, output queue size 1
progress 60% @chr11:122000001, elapsed 1.1s, est remaining 0.8s, peak mem 311MB, user 1.9s, sys 32.8s, output queue size 13
progress 65% @chr13:16000001, elapsed 1.2s, est remaining 0.7s, peak mem 314MB, user 2.2s, sys 35.6s, output queue size 1
progress 70% @chr14:61000001, elapsed 1.3s, est remaining 0.6s, peak mem 316MB, user 2.4s, sys 38.1s, output queue size 12
progress 75% @chr16:12000001, elapsed 1.4s, est remaining 0.5s, peak mem 319MB, user 2.5s, sys 40.9s, output queue size 2
progress 80% @chr18:1000001, elapsed 1.5s, est remaining 0.4s, peak mem 319MB, user 2.6s, sys 43.6s, output queue size 17
progress 85% @chr20:24000001, elapsed 1.6s, est remaining 0.3s, peak mem 319MB, user 2.7s, sys 46.4s, output queue size 13
progress 90% @chrX:39000001, elapsed 1.8s, est remaining 0.2s, peak mem 533MB, user 4.5s, sys 47.7s, output queue size 114
progress 95% @chrY:42000001, elapsed 1.9s, est remaining 0.1s, peak mem 557MB, user 5.7s, sys 48.6s, output queue size 276
progress 100% @chr21:41000001, elapsed 2.8s, est remaining 0.0s, peak mem 588MB, user 11.4s, sys 50.2s, 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 6.12.88
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 64
algo: Dedup
license: sentieon:Dedup=31
input file size: 51298918
reads: 1001133
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 26026 calls 0.010 user 0.010 sys 0.022 real
MateInfoByVcf::load: 26026 calls 4.336 user 0.503 sys 3.873 real
MateInfoByVcf::parse_events: 26026 calls 4.255 user 0.471 sys 3.767 real
advance: 3219322 calls 1.081 user 5.959 sys 7.706 real
calc: 3219322 calls 3.567 user 18.882 sys 22.566 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 0.006 user 0.005 sys 2.856 real
fetch: 3219322 calls 0.357 user 6.113 sys 6.462 real
find_pairEnds: 26026 calls 0.237 user 0.009 sys 0.339 real
idle: 2052 calls 0.426 user 0.178 sys 54.580 real
init: 1 calls 0.000 user 0.000 sys 0.006 real
markDup: 26026 calls 0.655 user 0.054 sys 1.278 real
vcfadvance: 26026 calls 0.006 user 0.116 sys 0.034 real
write: 3219322 calls 2.071 user 6.601 sys 8.134 real
overall: 617009152 mem 13.013 user 50.890 sys 3.873 real