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/ca/68a43b6e6c5d7eaee35b841b56afd3/Sig_18_Blood.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/bbf3839dfd2c68f28e02f3d64e69ad/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/bbf3839dfd2c68f28e02f3d64e69ad/.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/ca/68a43b6e6c5d7eaee35b841b56afd3/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 1.3s, peak mem 81MB, user 0.1s, sys 1.7s, output queue size 43
progress 10% @chr2:75000001, elapsed 0.1s, est remaining 1.2s, peak mem 81MB, user 0.3s, sys 3.4s, output queue size 31
progress 15% @chr2:234000001, elapsed 0.2s, est remaining 1.1s, peak mem 81MB, user 0.5s, sys 5.2s, output queue size 26
progress 20% @chr3:154000001, elapsed 0.3s, est remaining 1.0s, peak mem 81MB, user 0.6s, sys 7.0s, output queue size 4
progress 25% @chr4:115000001, elapsed 0.3s, est remaining 1.0s, peak mem 81MB, user 0.7s, sys 8.8s, output queue size 8
progress 30% @chr5:84000001, elapsed 0.4s, est remaining 0.9s, peak mem 81MB, user 0.8s, sys 10.7s, output queue size 2
progress 35% @chr6:64000001, elapsed 0.5s, est remaining 0.8s, peak mem 81MB, user 0.9s, sys 12.6s, output queue size 1
progress 40% @chr7:81000001, elapsed 0.5s, est remaining 0.8s, peak mem 81MB, user 1.0s, sys 15.1s, output queue size 20
progress 45% @chr8:50000001, elapsed 0.7s, est remaining 0.8s, peak mem 81MB, user 1.2s, sys 18.8s, output queue size 22
progress 50% @chr9:65000001, elapsed 0.8s, est remaining 0.8s, peak mem 81MB, user 1.3s, sys 22.5s, output queue size 8
progress 55% @chr10:63000001, elapsed 0.9s, est remaining 0.8s, peak mem 81MB, user 1.4s, sys 26.3s, output queue size 32
progress 60% @chr12:13000001, elapsed 1.0s, est remaining 0.7s, peak mem 81MB, user 1.6s, sys 30.1s, output queue size 7
progress 65% @chr13:9000001, elapsed 1.2s, est remaining 0.6s, peak mem 81MB, user 1.8s, sys 33.8s, output queue size 26
progress 70% @chr14:88000001, elapsed 1.3s, est remaining 0.6s, peak mem 81MB, user 2.0s, sys 37.6s, output queue size 12
progress 75% @chr16:7000001, elapsed 1.4s, est remaining 0.5s, peak mem 81MB, user 2.2s, sys 41.5s, output queue size 10
progress 80% @chr17:79000001, elapsed 1.6s, est remaining 0.4s, peak mem 81MB, user 2.4s, sys 45.3s, output queue size 25
progress 85% @chr20:10000001, elapsed 1.7s, est remaining 0.3s, peak mem 81MB, user 2.6s, sys 49.7s, output queue size 12
progress 90% @chrX:23000001, elapsed 1.9s, est remaining 0.2s, peak mem 102MB, user 3.1s, sys 53.6s, output queue size 114
progress 95% @chrY:21000001, elapsed 2.1s, est remaining 0.1s, peak mem 129MB, user 3.5s, sys 59.4s, output queue size 271
progress 100% @chr21:41000001, elapsed 2.5s, est remaining 0.0s, peak mem 160MB, user 4.4s, sys 67.0s, 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 384
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 51298920
reads: 1001133
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.014 user 0.025 sys 0.049 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.400 user 13.908 sys 15.693 real
calc: 3219322 calls 0.448 user 10.432 sys 10.868 real
done: 1 calls 0.014 user 0.025 sys 0.049 real
execute: 1 calls 0.001 user 0.001 sys 2.493 real
fetch: 3219322 calls 0.288 user 11.134 sys 10.778 real
idle: 85 calls 0.006 user 0.026 sys 36.099 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 209543168 mem 4.496 user 67.727 sys 3.553 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 2.2s, peak mem 168MB, user 0.2s, sys 2.8s, output queue size 13
progress 10% @chr2:73000001, elapsed 0.2s, est remaining 1.8s, peak mem 186MB, user 0.4s, sys 5.3s, output queue size 18
progress 15% @chr2:232000001, elapsed 0.3s, est remaining 1.6s, peak mem 207MB, user 0.7s, sys 7.8s, output queue size 13
progress 20% @chr3:152000001, elapsed 0.4s, est remaining 1.5s, peak mem 213MB, user 0.9s, sys 10.2s, output queue size 18
progress 25% @chr4:115000001, elapsed 0.5s, est remaining 1.4s, peak mem 228MB, user 1.1s, sys 12.6s, output queue size 4
progress 30% @chr5:86000001, elapsed 0.5s, est remaining 1.3s, peak mem 240MB, user 1.3s, sys 15.0s, output queue size 16
progress 35% @chr6:66000001, elapsed 0.6s, est remaining 1.2s, peak mem 243MB, user 1.4s, sys 17.5s, output queue size 12
progress 40% @chr7:56000001, elapsed 0.7s, est remaining 1.1s, peak mem 258MB, user 1.7s, sys 19.9s, output queue size 21
progress 45% @chr8:57000001, elapsed 0.8s, est remaining 1.0s, peak mem 261MB, user 1.9s, sys 22.3s, output queue size 6
progress 50% @chr9:73000001, elapsed 0.9s, est remaining 0.9s, peak mem 270MB, user 2.1s, sys 24.7s, output queue size 15
progress 55% @chr10:96000001, elapsed 1.0s, est remaining 0.8s, peak mem 270MB, user 2.2s, sys 27.2s, output queue size 19
progress 60% @chr11:123000001, elapsed 1.1s, est remaining 0.7s, peak mem 270MB, user 2.5s, sys 29.6s, output queue size 9
progress 65% @chr13:15000001, elapsed 1.1s, est remaining 0.6s, peak mem 270MB, user 2.7s, sys 32.1s, output queue size 12
progress 70% @chr14:57000001, elapsed 1.3s, est remaining 0.5s, peak mem 276MB, user 2.9s, sys 35.5s, output queue size 9
progress 75% @chr16:7000001, elapsed 1.4s, est remaining 0.5s, peak mem 276MB, user 3.2s, sys 40.7s, output queue size 27
progress 80% @chr17:76000001, elapsed 1.7s, est remaining 0.4s, peak mem 279MB, user 3.6s, sys 46.4s, output queue size 30
progress 85% @chr20:46000001, elapsed 1.9s, est remaining 0.3s, peak mem 279MB, user 3.8s, sys 53.0s, output queue size 28
progress 90% @chrX:44000001, elapsed 2.2s, est remaining 0.2s, peak mem 507MB, user 6.7s, sys 57.4s, output queue size 114
progress 95% @chrY:52000001, elapsed 2.5s, est remaining 0.1s, peak mem 519MB, user 10.5s, sys 62.8s, output queue size 247
progress 100% @chr21:41000001, elapsed 3.5s, est remaining 0.0s, peak mem 540MB, user 13.6s, sys 68.8s, 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 384
algo: Dedup
license: sentieon:Dedup=31
input file size: 51298920
reads: 1001133
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 26026 calls 0.002 user 0.013 sys 0.055 real
MateInfoByVcf::load: 26026 calls 4.431 user 1.106 sys 4.454 real
MateInfoByVcf::parse_events: 26026 calls 4.365 user 1.035 sys 4.212 real
advance: 3219322 calls 1.072 user 8.528 sys 10.439 real
calc: 3219322 calls 4.513 user 24.621 sys 30.106 real
done: 1 calls 0.000 user 0.000 sys 0.004 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.000 user 0.001 sys 3.550 real
fetch: 3219322 calls 0.338 user 8.041 sys 8.892 real
find_pairEnds: 26026 calls 0.215 user 0.021 sys 0.383 real
idle: 1036 calls 0.046 user 0.183 sys 55.091 real
init: 1 calls 0.000 user 0.010 sys 0.006 real
markDup: 26026 calls 0.840 user 0.219 sys 1.562 real
vcfadvance: 26026 calls 0.029 user 0.135 sys 0.114 real
write: 3219322 calls 2.610 user 8.775 sys 10.860 real
overall: 566337536 mem 14.051 user 70.408 sys 4.564 real