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/3f/dd224e96ab9502f4ebfc54a5703226/HCC1395_BL.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/bc5e7b7f2c48b2e51fd97162601462/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/bc5e7b7f2c48b2e51fd97162601462/.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/3f/dd224e96ab9502f4ebfc54a5703226/HCC1395_BL.bai
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i HCC1395_BL.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info HCC1395_BL.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:157000001, elapsed 0.1s, est remaining 2.5s, peak mem 78MB, user 0.2s, sys 3.4s, output queue size 4
progress 10% @chr2:72000001, elapsed 0.3s, est remaining 2.3s, peak mem 78MB, user 0.3s, sys 7.0s, output queue size 1
progress 15% @chr2:238000001, elapsed 0.4s, est remaining 2.1s, peak mem 78MB, user 0.5s, sys 10.6s, output queue size 2
progress 20% @chr3:154000001, elapsed 0.5s, est remaining 2.0s, peak mem 78MB, user 0.6s, sys 14.2s, output queue size 2
progress 25% @chr4:118000001, elapsed 0.6s, est remaining 1.8s, peak mem 78MB, user 0.7s, sys 17.7s, output queue size 1
progress 30% @chr5:82000001, elapsed 0.7s, est remaining 1.7s, peak mem 78MB, user 0.9s, sys 21.2s, output queue size 4
progress 35% @chr6:59000001, elapsed 0.9s, est remaining 1.6s, peak mem 78MB, user 1.0s, sys 24.9s, output queue size 8
progress 40% @chr7:79000001, elapsed 1.1s, est remaining 1.6s, peak mem 78MB, user 1.2s, sys 30.9s, output queue size 13
progress 45% @chr8:80000001, elapsed 1.3s, est remaining 1.6s, peak mem 78MB, user 1.5s, sys 37.4s, output queue size 13
progress 50% @chr9:90000001, elapsed 1.5s, est remaining 1.5s, peak mem 78MB, user 1.8s, sys 43.8s, output queue size 10
progress 55% @chr10:114000001, elapsed 1.7s, est remaining 1.4s, peak mem 78MB, user 2.0s, sys 50.0s, output queue size 10
progress 60% @chr12:7000001, elapsed 1.9s, est remaining 1.3s, peak mem 78MB, user 2.2s, sys 56.2s, output queue size 11
progress 65% @chr13:5000001, elapsed 2.1s, est remaining 1.1s, peak mem 78MB, user 2.4s, sys 62.3s, output queue size 11
progress 70% @chr14:48000001, elapsed 2.3s, est remaining 1.0s, peak mem 78MB, user 2.7s, sys 68.4s, output queue size 13
progress 75% @chr15:101000001, elapsed 2.5s, est remaining 0.8s, peak mem 78MB, user 2.9s, sys 74.7s, output queue size 14
progress 80% @chr17:75000001, elapsed 2.7s, est remaining 0.7s, peak mem 78MB, user 3.1s, sys 81.1s, output queue size 11
progress 85% @chr20:5000001, elapsed 3.0s, est remaining 0.5s, peak mem 78MB, user 3.4s, sys 87.5s, output queue size 22
progress 90% @chrX:43000001, elapsed 3.2s, est remaining 0.4s, peak mem 96MB, user 4.0s, sys 92.8s, output queue size 114
progress 95% @chr21:38000001, elapsed 3.5s, est remaining 0.2s, peak mem 135MB, user 4.5s, sys 100.4s, output queue size 276
progress 100% @chr21:41000001, elapsed 3.9s, est remaining 0.0s, peak mem 173MB, user 5.3s, sys 109.8s, 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 384
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 50411659
reads: 1001089
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.023 user 0.012 sys 0.048 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.315 user 23.047 sys 24.521 real
calc: 3219322 calls 0.474 user 17.685 sys 17.781 real
done: 1 calls 0.023 user 0.012 sys 0.048 real
execute: 1 calls 0.001 user 0.005 sys 3.905 real
fetch: 3219322 calls 0.373 user 17.252 sys 17.821 real
idle: 82 calls 0.010 user 0.026 sys 35.967 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 218996736 mem 5.385 user 110.453 sys 4.969 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i HCC1395_BL.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info HCC1395_BL.md.score --metrics HCC1395_BL.md.metrics HCC1395_BL.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:161000001, elapsed 0.1s, est remaining 2.4s, peak mem 168MB, user 0.3s, sys 3.1s, output queue size 14
progress 10% @chr2:70000001, elapsed 0.2s, est remaining 2.0s, peak mem 189MB, user 0.5s, sys 6.0s, output queue size 8
progress 15% @chr2:235000001, elapsed 0.3s, est remaining 1.8s, peak mem 216MB, user 0.8s, sys 8.7s, output queue size 14
progress 20% @chr3:154000001, elapsed 0.4s, est remaining 1.7s, peak mem 231MB, user 1.1s, sys 11.3s, output queue size 12
progress 25% @chr4:110000001, elapsed 0.5s, est remaining 1.5s, peak mem 243MB, user 1.3s, sys 14.0s, output queue size 5
progress 30% @chr5:86000001, elapsed 0.6s, est remaining 1.4s, peak mem 243MB, user 1.5s, sys 16.8s, output queue size 4
progress 35% @chr6:92000001, elapsed 0.7s, est remaining 1.4s, peak mem 249MB, user 1.7s, sys 20.4s, output queue size 21
progress 40% @chr7:56000001, elapsed 0.9s, est remaining 1.3s, peak mem 255MB, user 2.0s, sys 24.3s, output queue size 2
progress 45% @chr8:61000001, elapsed 1.0s, est remaining 1.2s, peak mem 258MB, user 2.2s, sys 27.1s, output queue size 27
progress 50% @chr9:72000001, elapsed 1.1s, est remaining 1.1s, peak mem 261MB, user 2.4s, sys 29.9s, output queue size 11
progress 55% @chr10:95000001, elapsed 1.3s, est remaining 1.0s, peak mem 261MB, user 2.6s, sys 35.0s, output queue size 11
progress 60% @chr11:120000001, elapsed 1.5s, est remaining 1.0s, peak mem 261MB, user 3.0s, sys 41.2s, output queue size 15
progress 65% @chr13:15000001, elapsed 1.6s, est remaining 0.8s, peak mem 261MB, user 3.1s, sys 44.6s, output queue size 4
progress 70% @chr14:54000001, elapsed 1.8s, est remaining 0.8s, peak mem 261MB, user 3.4s, sys 49.4s, output queue size 15
progress 75% @chr15:98000001, elapsed 2.0s, est remaining 0.7s, peak mem 264MB, user 3.7s, sys 56.9s, output queue size 29
progress 80% @chr17:80000001, elapsed 2.3s, est remaining 0.6s, peak mem 264MB, user 4.1s, sys 64.5s, output queue size 15
progress 85% @chr20:7000001, elapsed 2.5s, est remaining 0.4s, peak mem 264MB, user 4.3s, sys 72.1s, output queue size 24
progress 90% @chrX:35000001, elapsed 2.9s, est remaining 0.3s, peak mem 456MB, user 7.3s, sys 77.0s, output queue size 114
progress 95% @chrY:15000001, elapsed 3.1s, est remaining 0.2s, peak mem 471MB, user 11.0s, sys 82.6s, output queue size 271
progress 100% @chr21:41000001, elapsed 4.2s, est remaining 0.0s, peak mem 486MB, user 14.6s, sys 89.4s, output queue size 3664
library HCC1395_BL:
chimeric_paired 873
duped 146553
duped_chimeric_paired 2
duped_paired 146548
duped_unpaired 5
optical_dup 4835
paired 999974
reads 1001089
secondary_supplementary 1097
unmapped 9
unpaired 9
optical dup clusters 4702, maxdup 7, total optical dup pairs 4835
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: 50411659
reads: 1001089
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 25531 calls 0.001 user 0.021 sys 0.060 real
MateInfoByVcf::load: 25531 calls 4.449 user 1.252 sys 4.636 real
MateInfoByVcf::parse_events: 25531 calls 4.369 user 1.139 sys 4.368 real
advance: 3219322 calls 1.341 user 11.207 sys 13.227 real
calc: 3219322 calls 4.833 user 32.374 sys 38.076 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 0.003 user 0.000 sys 4.244 real
fetch: 3219322 calls 0.509 user 10.795 sys 11.370 real
find_pairEnds: 25531 calls 0.123 user 0.038 sys 0.393 real
idle: 1018 calls 0.045 user 0.126 sys 53.458 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 25531 calls 0.905 user 0.246 sys 1.695 real
vcfadvance: 25531 calls 0.019 user 0.105 sys 0.168 real
write: 3219322 calls 2.631 user 11.463 sys 13.359 real
overall: 509698048 mem 15.165 user 90.663 sys 5.239 real