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/52/281ee71efc853676d7c901b1be3fac/Sig_18_Blood.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/08e6b3f65b7a9c67907262130bdda1/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/08e6b3f65b7a9c67907262130bdda1/.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/52/281ee71efc853676d7c901b1be3fac/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 1.3s, peak mem 81MB, user 0.2s, sys 1.5s, output queue size 18
progress 10% @chr2:74000001, elapsed 0.1s, est remaining 1.2s, peak mem 81MB, user 0.3s, sys 3.2s, output queue size 13
progress 15% @chr2:235000001, elapsed 0.2s, est remaining 1.1s, peak mem 81MB, user 0.4s, sys 4.9s, output queue size 21
progress 20% @chr3:156000001, elapsed 0.3s, est remaining 1.0s, peak mem 81MB, user 0.5s, sys 6.7s, output queue size 14
progress 25% @chr4:117000001, elapsed 0.3s, est remaining 0.9s, peak mem 81MB, user 0.6s, sys 8.4s, output queue size 17
progress 30% @chr5:87000001, elapsed 0.4s, est remaining 0.9s, peak mem 81MB, user 0.8s, sys 10.1s, output queue size 20
progress 35% @chr6:66000001, elapsed 0.4s, est remaining 0.8s, peak mem 81MB, user 0.9s, sys 11.9s, output queue size 17
progress 40% @chr7:55000001, elapsed 0.5s, est remaining 0.7s, peak mem 81MB, user 1.0s, sys 13.6s, output queue size 21
progress 45% @chr8:58000001, elapsed 0.6s, est remaining 0.7s, peak mem 81MB, user 1.2s, sys 15.4s, output queue size 18
progress 50% @chr9:72000001, elapsed 0.6s, est remaining 0.6s, peak mem 81MB, user 1.4s, sys 17.0s, output queue size 20
progress 55% @chr10:96000001, elapsed 0.7s, est remaining 0.5s, peak mem 81MB, user 1.5s, sys 18.8s, output queue size 1
progress 60% @chr11:100000001, elapsed 0.7s, est remaining 0.5s, peak mem 81MB, user 1.6s, sys 20.5s, output queue size 23
progress 65% @chr13:15000001, elapsed 0.8s, est remaining 0.4s, peak mem 81MB, user 1.7s, sys 22.2s, output queue size 19
progress 70% @chr14:61000001, elapsed 0.9s, est remaining 0.4s, peak mem 81MB, user 1.9s, sys 23.9s, output queue size 13
progress 75% @chr16:13000001, elapsed 0.9s, est remaining 0.3s, peak mem 81MB, user 2.1s, sys 25.6s, output queue size 9
progress 80% @chr18:1, elapsed 1.0s, est remaining 0.2s, peak mem 81MB, user 2.3s, sys 27.3s, output queue size 9
progress 85% @chr20:22000001, elapsed 1.0s, est remaining 0.2s, peak mem 81MB, user 2.4s, sys 29.1s, output queue size 5
progress 90% @chrX:31000001, elapsed 1.1s, est remaining 0.1s, peak mem 117MB, user 2.9s, sys 30.7s, output queue size 114
progress 95% @chrY:53000001, elapsed 1.3s, est remaining 0.1s, peak mem 150MB, user 3.4s, sys 33.4s, output queue size 271
progress 100% @chr21:41000001, elapsed 1.6s, est remaining 0.0s, peak mem 169MB, user 4.1s, sys 38.4s, 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 0.032 user 0.015 sys 0.061 real
VcfLineRecordHelper::sort: 30 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.360 user 7.331 sys 9.459 real
calc: 3219322 calls 0.373 user 6.197 sys 6.848 real
done: 1 calls 0.032 user 0.015 sys 0.061 real
execute: 1 calls 0.000 user 0.011 sys 1.558 real
fetch: 3219322 calls 0.382 user 6.291 sys 6.811 real
idle: 79 calls 0.004 user 0.018 sys 35.583 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 224739328 mem 4.337 user 39.157 sys 2.624 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 165MB, user 0.2s, sys 2.7s, output queue size 7
progress 10% @chr2:75000001, elapsed 0.2s, est remaining 1.7s, peak mem 192MB, user 0.4s, sys 5.0s, output queue size 19
progress 15% @chr2:235000001, elapsed 0.3s, est remaining 1.6s, peak mem 216MB, user 0.7s, sys 7.3s, output queue size 13
progress 20% @chr3:131000001, elapsed 0.4s, est remaining 1.4s, peak mem 225MB, user 0.9s, sys 9.6s, output queue size 22
progress 25% @chr4:116000001, elapsed 0.4s, est remaining 1.3s, peak mem 249MB, user 1.1s, sys 11.9s, output queue size 8
progress 30% @chr5:87000001, elapsed 0.5s, est remaining 1.2s, peak mem 258MB, user 1.4s, sys 14.1s, output queue size 11
progress 35% @chr6:66000001, elapsed 0.6s, est remaining 1.1s, peak mem 261MB, user 1.6s, sys 16.4s, output queue size 21
progress 40% @chr7:57000001, elapsed 0.7s, est remaining 1.0s, peak mem 264MB, user 1.9s, sys 18.7s, output queue size 14
progress 45% @chr8:58000001, elapsed 0.8s, est remaining 0.9s, peak mem 267MB, user 2.1s, sys 21.0s, output queue size 19
progress 50% @chr9:74000001, elapsed 0.8s, est remaining 0.8s, peak mem 270MB, user 2.3s, sys 23.3s, output queue size 19
progress 55% @chr10:96000001, elapsed 0.9s, est remaining 0.8s, peak mem 270MB, user 2.5s, sys 25.6s, output queue size 16
progress 60% @chr11:123000001, elapsed 1.0s, est remaining 0.7s, peak mem 270MB, user 2.6s, sys 28.0s, output queue size 20
progress 65% @chr13:15000001, elapsed 1.1s, est remaining 0.6s, peak mem 273MB, user 2.8s, sys 30.5s, output queue size 22
progress 70% @chr14:61000001, elapsed 1.2s, est remaining 0.5s, peak mem 273MB, user 3.0s, sys 32.9s, output queue size 1
progress 75% @chr16:14000001, elapsed 1.3s, est remaining 0.4s, peak mem 273MB, user 3.1s, sys 35.3s, output queue size 26
progress 80% @chr17:80000001, elapsed 1.4s, est remaining 0.3s, peak mem 273MB, user 3.4s, sys 39.2s, output queue size 20
progress 85% @chr20:23000001, elapsed 1.5s, est remaining 0.3s, peak mem 273MB, user 3.6s, sys 42.5s, output queue size 11
progress 90% @chrX:42000001, elapsed 1.7s, est remaining 0.2s, peak mem 504MB, user 5.3s, sys 43.9s, output queue size 114
progress 95% @chrY:35000001, elapsed 1.8s, est remaining 0.1s, peak mem 528MB, user 7.4s, sys 45.3s, output queue size 271
progress 100% @chr21:41000001, elapsed 3.0s, est remaining 0.0s, peak mem 543MB, user 12.9s, sys 49.0s, 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: 51298916
reads: 1001133
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 26026 calls 0.000 user 0.006 sys 0.029 real
MateInfoByVcf::load: 26026 calls 4.357 user 0.761 sys 4.184 real
MateInfoByVcf::parse_events: 26026 calls 4.286 user 0.718 sys 4.046 real
advance: 3219322 calls 1.300 user 5.757 sys 7.599 real
calc: 3219322 calls 4.105 user 17.632 sys 22.370 real
done: 1 calls 0.000 user 0.002 sys 0.004 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.004 user 0.004 sys 3.091 real
fetch: 3219322 calls 0.361 user 5.956 sys 6.492 real
find_pairEnds: 26026 calls 0.204 user 0.028 sys 0.354 real
idle: 1544 calls 0.099 user 0.182 sys 61.413 real
init: 1 calls 0.000 user 0.000 sys 0.006 real
markDup: 26026 calls 0.825 user 0.070 sys 1.336 real
vcfadvance: 26026 calls 0.008 user 0.092 sys 0.050 real
write: 3219322 calls 2.247 user 6.008 sys 8.166 real
overall: 569466880 mem 13.644 user 50.369 sys 4.117 real