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/54/a7303060a903dfb63bf56292651d1a/Sig_18_Blood.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/d26cef4d95a19b3f51aacdd1b33bad/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/d26cef4d95a19b3f51aacdd1b33bad/.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/54/a7303060a903dfb63bf56292651d1a/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% @chr1:162000001, elapsed 0.1s, est remaining 1.6s, peak mem 78MB, user 0.2s, sys 1.9s, output queue size 14
progress 10% @chr2:77000001, elapsed 0.2s, est remaining 1.5s, peak mem 78MB, user 0.5s, sys 4.1s, output queue size 11
progress 15% @chr2:225000001, elapsed 0.2s, est remaining 1.4s, peak mem 78MB, user 0.6s, sys 6.3s, output queue size 10
progress 20% @chr3:153000001, elapsed 0.3s, est remaining 1.3s, peak mem 78MB, user 0.8s, sys 8.5s, output queue size 24
progress 25% @chr4:105000001, elapsed 0.4s, est remaining 1.2s, peak mem 78MB, user 1.1s, sys 10.7s, output queue size 20
progress 30% @chr5:76000001, elapsed 0.5s, est remaining 1.1s, peak mem 78MB, user 1.3s, sys 12.9s, output queue size 10
progress 35% @chr6:65000001, elapsed 0.6s, est remaining 1.0s, peak mem 78MB, user 1.5s, sys 15.1s, output queue size 33
progress 40% @chr7:54000001, elapsed 0.6s, est remaining 0.9s, peak mem 78MB, user 1.6s, sys 17.4s, output queue size 29
progress 45% @chr8:60000001, elapsed 0.7s, est remaining 0.9s, peak mem 78MB, user 1.7s, sys 19.7s, output queue size 23
progress 50% @chr9:73000001, elapsed 0.8s, est remaining 0.8s, peak mem 78MB, user 1.9s, sys 22.0s, output queue size 23
progress 55% @chr10:88000001, elapsed 0.9s, est remaining 0.7s, peak mem 78MB, user 2.1s, sys 24.4s, output queue size 7
progress 60% @chr11:120000001, elapsed 1.0s, est remaining 0.7s, peak mem 78MB, user 2.3s, sys 28.1s, output queue size 15
progress 65% @chr13:10000001, elapsed 1.1s, est remaining 0.6s, peak mem 78MB, user 2.5s, sys 31.7s, output queue size 14
progress 70% @chr14:57000001, elapsed 1.3s, est remaining 0.5s, peak mem 78MB, user 2.7s, sys 35.3s, output queue size 12
progress 75% @chr16:5000001, elapsed 1.4s, est remaining 0.5s, peak mem 78MB, user 2.9s, sys 39.3s, output queue size 24
progress 80% @chr18:25000001, elapsed 1.6s, est remaining 0.4s, peak mem 78MB, user 3.0s, sys 44.2s, output queue size 25
progress 85% @chr19:50000001, elapsed 1.7s, est remaining 0.3s, peak mem 78MB, user 3.3s, sys 49.5s, output queue size 31
progress 90% @chrX:46000001, elapsed 2.0s, est remaining 0.2s, peak mem 81MB, user 3.8s, sys 54.5s, output queue size 114
progress 95% @chrY:20000001, elapsed 2.2s, est remaining 0.1s, peak mem 111MB, user 4.2s, sys 59.8s, output queue size 276
progress 100% @chr21:41000001, elapsed 2.7s, est remaining 0.0s, peak mem 161MB, user 5.2s, sys 69.7s, 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: 51298916
reads: 1001133
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.024 user 0.016 sys 0.050 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.362 user 17.551 sys 18.796 real
calc: 3219322 calls 0.527 user 11.115 sys 9.815 real
done: 1 calls 0.024 user 0.016 sys 0.050 real
execute: 1 calls 0.006 user 0.004 sys 2.677 real
fetch: 3219322 calls 0.415 user 11.454 sys 9.882 real
idle: 73 calls 0.012 user 0.037 sys 38.028 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 209960960 mem 5.309 user 70.277 sys 3.745 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% @chr1:160000001, elapsed 0.1s, est remaining 2.6s, peak mem 165MB, user 0.3s, sys 3.4s, output queue size 1
progress 10% @chr2:58000001, elapsed 0.2s, est remaining 2.2s, peak mem 189MB, user 0.5s, sys 6.4s, output queue size 15
progress 15% @chr2:234000001, elapsed 0.3s, est remaining 2.0s, peak mem 216MB, user 0.7s, sys 9.4s, output queue size 6
progress 20% @chr3:153000001, elapsed 0.4s, est remaining 1.8s, peak mem 225MB, user 1.1s, sys 12.3s, output queue size 2
progress 25% @chr4:115000001, elapsed 0.6s, est remaining 1.7s, peak mem 240MB, user 1.3s, sys 15.2s, output queue size 12
progress 30% @chr5:87000001, elapsed 0.7s, est remaining 1.5s, peak mem 255MB, user 1.4s, sys 18.3s, output queue size 12
progress 35% @chr6:65000001, elapsed 0.8s, est remaining 1.4s, peak mem 258MB, user 1.6s, sys 21.2s, output queue size 7
progress 40% @chr7:55000001, elapsed 0.9s, est remaining 1.3s, peak mem 261MB, user 1.8s, sys 24.2s, output queue size 6
progress 45% @chr8:46000001, elapsed 1.0s, est remaining 1.2s, peak mem 264MB, user 1.9s, sys 27.2s, output queue size 11
progress 50% @chr9:73000001, elapsed 1.1s, est remaining 1.1s, peak mem 270MB, user 2.2s, sys 30.1s, output queue size 6
progress 55% @chr10:95000001, elapsed 1.2s, est remaining 1.0s, peak mem 270MB, user 2.5s, sys 33.0s, output queue size 3
progress 60% @chr11:122000001, elapsed 1.3s, est remaining 0.8s, peak mem 273MB, user 2.6s, sys 35.9s, output queue size 14
progress 65% @chr13:14000001, elapsed 1.4s, est remaining 0.7s, peak mem 273MB, user 2.8s, sys 38.9s, output queue size 8
progress 70% @chr14:56000001, elapsed 1.6s, est remaining 0.7s, peak mem 273MB, user 3.1s, sys 44.0s, output queue size 21
progress 75% @chr16:26000001, elapsed 1.8s, est remaining 0.6s, peak mem 276MB, user 3.3s, sys 51.4s, output queue size 13
progress 80% @chr18:3000001, elapsed 2.0s, est remaining 0.5s, peak mem 276MB, user 3.6s, sys 58.6s, output queue size 9
progress 85% @chr20:27000001, elapsed 2.3s, est remaining 0.4s, peak mem 276MB, user 3.9s, sys 65.7s, output queue size 8
progress 90% @chrX:29000001, elapsed 2.7s, est remaining 0.3s, peak mem 498MB, user 7.3s, sys 70.7s, output queue size 114
progress 95% @chrY:34000001, elapsed 2.9s, est remaining 0.2s, peak mem 510MB, user 10.5s, sys 76.3s, output queue size 271
progress 100% @chr21:41000001, elapsed 3.9s, est remaining 0.0s, peak mem 519MB, user 14.0s, sys 83.7s, 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: 51298916
reads: 1001133
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 26026 calls 0.000 user 0.030 sys 0.066 real
MateInfoByVcf::load: 26026 calls 4.635 user 1.450 sys 4.916 real
MateInfoByVcf::parse_events: 26026 calls 4.573 user 1.308 sys 4.613 real
advance: 3219322 calls 1.178 user 10.570 sys 12.298 real
calc: 3219322 calls 4.574 user 29.475 sys 35.358 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 0.005 user 0.001 sys 3.921 real
fetch: 3219322 calls 0.297 user 10.539 sys 10.625 real
find_pairEnds: 26026 calls 0.150 user 0.042 sys 0.399 real
idle: 940 calls 0.039 user 0.224 sys 51.555 real
init: 1 calls 0.008 user 0.000 sys 0.006 real
markDup: 26026 calls 0.780 user 0.227 sys 1.644 real
vcfadvance: 26026 calls 0.010 user 0.117 sys 0.132 real
write: 3219322 calls 2.749 user 9.471 sys 12.411 real
overall: 547438592 mem 14.412 user 85.040 sys 4.951 real