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/66/14f3b26a78a63f2f79ab48791b0f80/Sig_18_Blood.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/25dc077a00a8ba972f2936f02d2b56/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/25dc077a00a8ba972f2936f02d2b56/.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/66/14f3b26a78a63f2f79ab48791b0f80/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% @chr1:161000001, elapsed 0.1s, est remaining 1.3s, peak mem 78MB, user 0.2s, sys 1.4s, output queue size 4
progress 10% @chr2:72000001, elapsed 0.1s, est remaining 1.1s, peak mem 78MB, user 0.3s, sys 3.2s, output queue size 1
progress 15% @chr2:234000001, elapsed 0.2s, est remaining 1.1s, peak mem 78MB, user 0.5s, sys 4.9s, output queue size 8
progress 20% @chr3:154000001, elapsed 0.3s, est remaining 1.1s, peak mem 78MB, user 0.6s, sys 7.4s, output queue size 6
progress 25% @chr4:115000001, elapsed 0.4s, est remaining 1.1s, peak mem 78MB, user 0.9s, sys 10.2s, output queue size 24
progress 30% @chr5:83000001, elapsed 0.5s, est remaining 1.1s, peak mem 78MB, user 1.0s, sys 13.0s, output queue size 14
progress 35% @chr6:62000001, elapsed 0.6s, est remaining 1.1s, peak mem 78MB, user 1.1s, sys 15.9s, output queue size 9
progress 40% @chr7:50000001, elapsed 0.7s, est remaining 1.0s, peak mem 78MB, user 1.3s, sys 18.7s, output queue size 5
progress 45% @chr8:75000001, elapsed 0.8s, est remaining 0.9s, peak mem 78MB, user 1.6s, sys 21.5s, output queue size 5
progress 50% @chr9:93000001, elapsed 0.9s, est remaining 0.9s, peak mem 78MB, user 1.8s, sys 24.2s, output queue size 22
progress 55% @chr10:92000001, elapsed 1.0s, est remaining 0.8s, peak mem 78MB, user 2.0s, sys 27.0s, output queue size 17
progress 60% @chr11:123000001, elapsed 1.1s, est remaining 0.7s, peak mem 78MB, user 2.2s, sys 29.8s, output queue size 18
progress 65% @chr13:4000001, elapsed 1.2s, est remaining 0.6s, peak mem 78MB, user 2.5s, sys 33.6s, output queue size 13
progress 70% @chr14:52000001, elapsed 1.4s, est remaining 0.6s, peak mem 78MB, user 2.7s, sys 38.3s, output queue size 24
progress 75% @chr16:36000001, elapsed 1.5s, est remaining 0.5s, peak mem 78MB, user 2.9s, sys 43.3s, output queue size 14
progress 80% @chr17:53000001, elapsed 1.7s, est remaining 0.4s, peak mem 78MB, user 3.1s, sys 48.3s, output queue size 31
progress 85% @chr19:40000001, elapsed 1.9s, est remaining 0.3s, peak mem 78MB, user 3.3s, sys 53.6s, output queue size 41
progress 90% @chrX:27000001, elapsed 2.1s, est remaining 0.2s, peak mem 105MB, user 4.0s, sys 58.9s, output queue size 114
progress 95% @chrY:50000001, elapsed 2.4s, est remaining 0.1s, peak mem 135MB, user 4.3s, sys 66.1s, output queue size 271
progress 100% @chr21:41000001, elapsed 2.8s, est remaining 0.0s, peak mem 164MB, user 5.1s, sys 74.1s, 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: 51298918
reads: 1001133
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.031 user 0.012 sys 0.048 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.387 user 16.433 sys 17.725 real
calc: 3219322 calls 0.271 user 11.819 sys 11.493 real
done: 1 calls 0.031 user 0.012 sys 0.048 real
execute: 1 calls 0.001 user 0.010 sys 2.783 real
fetch: 3219322 calls 0.375 user 12.556 sys 11.639 real
idle: 78 calls 0.004 user 0.012 sys 37.396 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 212889600 mem 5.241 user 74.631 sys 3.846 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 174MB, user 0.4s, sys 2.5s, output queue size 2
progress 10% @chr2:76000001, elapsed 0.2s, est remaining 1.8s, peak mem 192MB, user 0.7s, sys 4.8s, output queue size 12
progress 15% @chr2:237000001, elapsed 0.3s, est remaining 1.6s, peak mem 207MB, user 1.0s, sys 7.1s, output queue size 20
progress 20% @chr3:152000001, elapsed 0.4s, est remaining 1.5s, peak mem 228MB, user 1.2s, sys 9.6s, output queue size 12
progress 25% @chr4:117000001, elapsed 0.4s, est remaining 1.3s, peak mem 237MB, user 1.4s, sys 11.9s, output queue size 16
progress 30% @chr5:88000001, elapsed 0.5s, est remaining 1.2s, peak mem 252MB, user 1.5s, sys 14.3s, output queue size 22
progress 35% @chr6:58000001, elapsed 0.6s, est remaining 1.1s, peak mem 258MB, user 1.7s, sys 16.8s, output queue size 20
progress 40% @chr7:57000001, elapsed 0.7s, est remaining 1.0s, peak mem 267MB, user 1.9s, sys 19.1s, output queue size 19
progress 45% @chr8:33000001, elapsed 0.8s, est remaining 1.0s, peak mem 273MB, user 2.2s, sys 21.4s, output queue size 24
progress 50% @chr9:73000001, elapsed 0.9s, est remaining 0.9s, peak mem 276MB, user 2.5s, sys 23.7s, output queue size 22
progress 55% @chr10:97000001, elapsed 0.9s, est remaining 0.8s, peak mem 276MB, user 2.7s, sys 26.0s, output queue size 14
progress 60% @chr11:123000001, elapsed 1.0s, est remaining 0.7s, peak mem 279MB, user 2.9s, sys 28.4s, output queue size 24
progress 65% @chr13:15000001, elapsed 1.1s, est remaining 0.6s, peak mem 279MB, user 3.2s, sys 30.8s, output queue size 9
progress 70% @chr14:61000001, elapsed 1.2s, est remaining 0.5s, peak mem 282MB, user 3.4s, sys 33.0s, output queue size 3
progress 75% @chr16:15000001, elapsed 1.3s, est remaining 0.4s, peak mem 285MB, user 3.6s, sys 35.4s, output queue size 3
progress 80% @chr17:78000001, elapsed 1.4s, est remaining 0.4s, peak mem 285MB, user 3.8s, sys 39.1s, output queue size 16
progress 85% @chr20:21000001, elapsed 1.6s, est remaining 0.3s, peak mem 288MB, user 4.1s, sys 44.8s, output queue size 32
progress 90% @chrX:36000001, elapsed 1.9s, est remaining 0.2s, peak mem 513MB, user 7.1s, sys 48.3s, output queue size 114
progress 95% @chrY:24000001, elapsed 2.1s, est remaining 0.1s, peak mem 534MB, user 10.2s, sys 51.3s, output queue size 271
progress 100% @chr21:41000001, elapsed 3.2s, est remaining 0.0s, peak mem 561MB, user 14.3s, sys 57.0s, 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: 51298918
reads: 1001133
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 26026 calls 0.010 user 0.012 sys 0.046 real
MateInfoByVcf::load: 26026 calls 4.676 user 0.963 sys 4.447 real
MateInfoByVcf::parse_events: 26026 calls 4.625 user 0.908 sys 4.237 real
advance: 3219322 calls 1.199 user 7.079 sys 8.644 real
calc: 3219322 calls 4.545 user 19.609 sys 25.630 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 3.283 real
fetch: 3219322 calls 0.471 user 6.899 sys 7.620 real
find_pairEnds: 26026 calls 0.207 user 0.010 sys 0.378 real
idle: 1231 calls 0.126 user 0.234 sys 58.502 real
init: 1 calls 0.009 user 0.001 sys 0.006 real
markDup: 26026 calls 0.813 user 0.118 sys 1.449 real
vcfadvance: 26026 calls 0.019 user 0.118 sys 0.062 real
write: 3219322 calls 2.542 user 6.918 sys 9.206 real
overall: 588357632 mem 15.100 user 58.070 sys 4.304 real