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/09/33bfa0cf2b5490ffed2a2569edbe9c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/5cce749784a4d4a78ef8b942d6127c/Sig_18_tissue.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/33bfa0cf2b5490ffed2a2569edbe9c/.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/a5/5cce749784a4d4a78ef8b942d6127c/Sig_18_tissue.bai
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Sig_18_tissue.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info Sig_18_tissue.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:155000001, elapsed 0.1s, est remaining 1.2s, peak mem 81MB, user 0.2s, sys 1.4s, output queue size 28
progress 10% @chr2:75000001, elapsed 0.1s, est remaining 1.1s, peak mem 81MB, user 0.4s, sys 3.0s, output queue size 34
progress 15% @chr2:235000001, elapsed 0.2s, est remaining 1.1s, peak mem 81MB, user 0.6s, sys 4.7s, output queue size 21
progress 20% @chr3:170000001, elapsed 0.3s, est remaining 1.1s, peak mem 81MB, user 0.7s, sys 7.5s, output queue size 18
progress 25% @chr4:106000001, elapsed 0.4s, est remaining 1.2s, peak mem 81MB, user 0.9s, sys 11.0s, output queue size 9
progress 30% @chr5:106000001, elapsed 0.6s, est remaining 1.3s, peak mem 81MB, user 1.0s, sys 15.7s, output queue size 15
progress 35% @chr6:64000001, elapsed 0.7s, est remaining 1.3s, peak mem 81MB, user 1.2s, sys 20.4s, output queue size 6
progress 40% @chr7:72000001, elapsed 0.9s, est remaining 1.3s, peak mem 81MB, user 1.4s, sys 24.8s, output queue size 7
progress 45% @chr8:53000001, elapsed 1.0s, est remaining 1.3s, peak mem 81MB, user 1.6s, sys 29.3s, output queue size 7
progress 50% @chr9:63000001, elapsed 1.2s, est remaining 1.2s, peak mem 81MB, user 1.8s, sys 34.0s, output queue size 10
progress 55% @chr10:93000001, elapsed 1.3s, est remaining 1.1s, peak mem 81MB, user 2.0s, sys 38.4s, output queue size 7
progress 60% @chr11:119000001, elapsed 1.5s, est remaining 1.0s, peak mem 81MB, user 2.2s, sys 42.8s, output queue size 25
progress 65% @chr13:33000001, elapsed 1.6s, est remaining 0.9s, peak mem 81MB, user 2.5s, sys 47.4s, output queue size 22
progress 70% @chr14:53000001, elapsed 1.8s, est remaining 0.8s, peak mem 81MB, user 2.8s, sys 52.2s, output queue size 9
progress 75% @chr16:6000001, elapsed 2.0s, est remaining 0.7s, peak mem 81MB, user 3.0s, sys 57.1s, output queue size 16
progress 80% @chr17:79000001, elapsed 2.1s, est remaining 0.5s, peak mem 81MB, user 3.3s, sys 61.7s, output queue size 7
progress 85% @chr20:20000001, elapsed 2.3s, est remaining 0.4s, peak mem 81MB, user 3.4s, sys 66.6s, output queue size 4
progress 90% @chrX:30000001, elapsed 2.5s, est remaining 0.3s, peak mem 105MB, user 4.1s, sys 71.2s, output queue size 114
progress 95% @chrY:32000001, elapsed 2.7s, est remaining 0.1s, peak mem 132MB, user 4.4s, sys 77.4s, output queue size 271
progress 100% @chr21:41000001, elapsed 3.1s, est remaining 0.0s, peak mem 156MB, user 5.3s, sys 84.6s, 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: 49121344
reads: 1001838
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.016 user 0.024 sys 0.051 real
VcfLineRecordHelper::sort: 29 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.470 user 17.836 sys 19.448 real
calc: 3219322 calls 0.483 user 13.946 sys 13.712 real
done: 1 calls 0.016 user 0.024 sys 0.051 real
execute: 1 calls 0.001 user 0.001 sys 3.114 real
fetch: 3219322 calls 0.375 user 13.814 sys 13.692 real
idle: 80 calls 0.001 user 0.007 sys 36.490 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 213962752 mem 5.395 user 85.292 sys 4.180 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Sig_18_tissue.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info Sig_18_tissue.md.score --metrics Sig_18_tissue.md.metrics Sig_18_tissue.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:147000001, elapsed 0.3s, est remaining 6.2s, peak mem 174MB, user 0.4s, sys 8.4s, output queue size 14
progress 10% @chr2:67000001, elapsed 0.6s, est remaining 5.3s, peak mem 195MB, user 0.7s, sys 16.6s, output queue size 9
progress 15% @chr2:230000001, elapsed 0.9s, est remaining 4.9s, peak mem 216MB, user 1.1s, sys 24.5s, output queue size 5
progress 20% @chr3:151000001, elapsed 1.1s, est remaining 4.5s, peak mem 225MB, user 1.4s, sys 32.4s, output queue size 8
progress 25% @chr4:113000001, elapsed 1.4s, est remaining 4.2s, peak mem 231MB, user 1.7s, sys 40.4s, output queue size 7
progress 30% @chr5:85000001, elapsed 1.7s, est remaining 3.9s, peak mem 237MB, user 2.1s, sys 48.4s, output queue size 1
progress 35% @chr6:57000001, elapsed 1.9s, est remaining 3.6s, peak mem 240MB, user 2.4s, sys 56.3s, output queue size 8
progress 40% @chr7:35000001, elapsed 2.2s, est remaining 3.3s, peak mem 249MB, user 2.9s, sys 63.9s, output queue size 22
progress 45% @chr8:67000001, elapsed 2.4s, est remaining 3.0s, peak mem 249MB, user 3.2s, sys 71.4s, output queue size 19
progress 50% @chr9:84000001, elapsed 2.7s, est remaining 2.7s, peak mem 249MB, user 3.6s, sys 78.9s, output queue size 17
progress 55% @chr10:75000001, elapsed 3.0s, est remaining 2.4s, peak mem 249MB, user 4.0s, sys 86.6s, output queue size 20
progress 60% @chr11:127000001, elapsed 3.2s, est remaining 2.2s, peak mem 255MB, user 4.4s, sys 94.6s, output queue size 20
progress 65% @chr12:132000001, elapsed 3.5s, est remaining 1.9s, peak mem 258MB, user 4.7s, sys 102.6s, output queue size 17
progress 70% @chr14:67000001, elapsed 3.8s, est remaining 1.6s, peak mem 261MB, user 5.1s, sys 110.7s, output queue size 11
progress 75% @chr16:17000001, elapsed 4.1s, est remaining 1.4s, peak mem 264MB, user 5.4s, sys 119.0s, output queue size 16
progress 80% @chr18:6000001, elapsed 4.3s, est remaining 1.1s, peak mem 264MB, user 5.6s, sys 126.7s, output queue size 19
progress 85% @chr20:30000001, elapsed 4.6s, est remaining 0.8s, peak mem 267MB, user 5.9s, sys 134.4s, output queue size 11
progress 90% @chrX:41000001, elapsed 5.0s, est remaining 0.6s, peak mem 426MB, user 9.1s, sys 139.6s, output queue size 114
progress 95% @chrY:33000001, elapsed 5.3s, est remaining 0.3s, peak mem 438MB, user 13.1s, sys 146.6s, output queue size 247
progress 100% @chr21:41000001, elapsed 6.1s, est remaining 0.0s, peak mem 447MB, user 16.1s, sys 154.4s, output queue size 3664
library Sig_18_tissue:
chimeric_paired 1886
duped 84376
duped_chimeric_paired 8
duped_paired 84374
duped_unpaired 2
optical_dup 3799
paired 999968
reads 1001834
secondary_supplementary 1858
unmapped 8
unpaired 4
optical dup clusters 3695, maxdup 3, total optical dup pairs 3799
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: 49121344
reads: 1001838
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 28282 calls 0.009 user 0.030 sys 0.091 real
MateInfoByVcf::load: 28282 calls 4.628 user 1.758 sys 5.163 real
MateInfoByVcf::parse_events: 28282 calls 4.556 user 1.576 sys 4.729 real
advance: 3219322 calls 1.473 user 20.490 sys 21.196 real
calc: 3219322 calls 5.125 user 58.205 sys 65.084 real
done: 1 calls 0.000 user 0.000 sys 0.004 real
exec_no_coor: 1 calls 0.000 user 0.008 sys 0.012 real
execute: 1 calls 0.002 user 0.000 sys 6.161 real
fetch: 3219323 calls 0.450 user 19.836 sys 14.071 real
find_pairEnds: 28282 calls 0.314 user 0.097 sys 0.455 real
idle: 843 calls 0.026 user 0.098 sys 46.820 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 28282 calls 0.899 user 0.471 sys 1.999 real
vcfadvance: 28282 calls 0.035 user 0.200 sys 0.264 real
write: 3219323 calls 2.489 user 18.742 sys 22.065 real
overall: 468869120 mem 16.588 user 155.641 sys 7.169 real