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/85/4009f8e4e38d24d0dcfb31a137bd0e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/e460bed37cb1c18d33aade2c80b261/Sig_18_tissue.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/4009f8e4e38d24d0dcfb31a137bd0e/.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/ff/e460bed37cb1c18d33aade2c80b261/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% @chr1:163000001, elapsed 0.1s, est remaining 1.7s, peak mem 78MB, user 0.2s, sys 2.2s, output queue size 10
progress 10% @chr2:61000001, elapsed 0.2s, est remaining 1.6s, peak mem 78MB, user 0.3s, sys 4.7s, output queue size 12
progress 15% @chr2:238000001, elapsed 0.3s, est remaining 1.5s, peak mem 78MB, user 0.4s, sys 7.1s, output queue size 14
progress 20% @chr3:137000001, elapsed 0.3s, est remaining 1.4s, peak mem 78MB, user 0.5s, sys 9.6s, output queue size 16
progress 25% @chr4:115000001, elapsed 0.4s, est remaining 1.3s, peak mem 78MB, user 0.7s, sys 12.0s, output queue size 6
progress 30% @chr5:87000001, elapsed 0.5s, est remaining 1.2s, peak mem 78MB, user 0.8s, sys 14.3s, output queue size 18
progress 35% @chr6:66000001, elapsed 0.6s, est remaining 1.1s, peak mem 78MB, user 1.0s, sys 16.8s, output queue size 8
progress 40% @chr7:56000001, elapsed 0.7s, est remaining 1.0s, peak mem 78MB, user 1.1s, sys 19.2s, output queue size 16
progress 45% @chr8:57000001, elapsed 0.8s, est remaining 0.9s, peak mem 78MB, user 1.2s, sys 21.7s, output queue size 6
progress 50% @chr9:52000001, elapsed 0.8s, est remaining 0.8s, peak mem 78MB, user 1.4s, sys 24.1s, output queue size 21
progress 55% @chr10:94000001, elapsed 0.9s, est remaining 0.8s, peak mem 78MB, user 1.5s, sys 26.5s, output queue size 7
progress 60% @chr11:123000001, elapsed 1.0s, est remaining 0.7s, peak mem 78MB, user 1.6s, sys 28.9s, output queue size 15
progress 65% @chr13:5000001, elapsed 1.1s, est remaining 0.6s, peak mem 78MB, user 1.8s, sys 32.0s, output queue size 10
progress 70% @chr14:86000001, elapsed 1.3s, est remaining 0.6s, peak mem 78MB, user 1.9s, sys 36.7s, output queue size 22
progress 75% @chr15:86000001, elapsed 1.5s, est remaining 0.5s, peak mem 78MB, user 2.2s, sys 42.2s, output queue size 29
progress 80% @chr18:22000001, elapsed 1.6s, est remaining 0.4s, peak mem 78MB, user 2.4s, sys 47.5s, output queue size 17
progress 85% @chr20:11000001, elapsed 1.8s, est remaining 0.3s, peak mem 78MB, user 2.6s, sys 52.9s, output queue size 11
progress 90% @chrX:40000001, elapsed 2.0s, est remaining 0.2s, peak mem 96MB, user 3.4s, sys 57.2s, output queue size 114
progress 95% @chrY:23000001, elapsed 2.3s, est remaining 0.1s, peak mem 123MB, user 3.6s, sys 62.9s, output queue size 276
progress 100% @chr21:41000001, elapsed 2.6s, est remaining 0.0s, peak mem 153MB, user 4.4s, sys 70.7s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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 0.017 user 0.019 sys 0.046 real
VcfLineRecordHelper::sort: 30 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.518 user 15.767 sys 16.882 real
calc: 3219322 calls 0.368 user 11.352 sys 11.289 real
done: 1 calls 0.017 user 0.019 sys 0.046 real
execute: 1 calls 0.000 user 0.001 sys 2.622 real
fetch: 3219322 calls 0.404 user 10.891 sys 11.295 real
idle: 71 calls 0.008 user 0.014 sys 35.944 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 210862080 mem 4.601 user 71.408 sys 3.683 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% @chr1:162000001, elapsed 0.2s, est remaining 3.7s, peak mem 183MB, user 0.5s, sys 4.4s, output queue size 56
progress 10% @chr2:69000001, elapsed 0.4s, est remaining 3.2s, peak mem 210MB, user 1.0s, sys 8.9s, output queue size 54
progress 15% @chr3:15000001, elapsed 0.5s, est remaining 2.9s, peak mem 228MB, user 1.3s, sys 13.6s, output queue size 16
progress 20% @chr3:148000001, elapsed 0.7s, est remaining 2.7s, peak mem 243MB, user 1.6s, sys 18.2s, output queue size 33
progress 25% @chr4:91000001, elapsed 0.8s, est remaining 2.5s, peak mem 255MB, user 1.9s, sys 22.8s, output queue size 24
progress 30% @chr5:112000001, elapsed 1.0s, est remaining 2.3s, peak mem 258MB, user 2.2s, sys 27.4s, output queue size 12
progress 35% @chr6:66000001, elapsed 1.2s, est remaining 2.1s, peak mem 264MB, user 2.5s, sys 32.1s, output queue size 7
progress 40% @chr7:79000001, elapsed 1.4s, est remaining 2.0s, peak mem 267MB, user 2.8s, sys 37.6s, output queue size 31
progress 45% @chr8:44000001, elapsed 1.5s, est remaining 1.9s, peak mem 270MB, user 3.2s, sys 43.5s, output queue size 13
progress 50% @chr9:86000001, elapsed 1.7s, est remaining 1.7s, peak mem 270MB, user 3.5s, sys 49.3s, output queue size 26
progress 55% @chr10:89000001, elapsed 1.9s, est remaining 1.6s, peak mem 270MB, user 3.7s, sys 55.4s, output queue size 6
progress 60% @chr11:119000001, elapsed 2.2s, est remaining 1.4s, peak mem 273MB, user 4.0s, sys 61.8s, output queue size 6
progress 65% @chr13:13000001, elapsed 2.4s, est remaining 1.3s, peak mem 273MB, user 4.4s, sys 68.2s, output queue size 26
progress 70% @chr14:59000001, elapsed 2.6s, est remaining 1.1s, peak mem 273MB, user 4.7s, sys 74.5s, output queue size 21
progress 75% @chr16:21000001, elapsed 2.8s, est remaining 0.9s, peak mem 273MB, user 4.9s, sys 81.0s, output queue size 11
progress 80% @chr18:6000001, elapsed 3.0s, est remaining 0.8s, peak mem 273MB, user 5.3s, sys 87.4s, output queue size 4
progress 85% @chr20:28000001, elapsed 3.3s, est remaining 0.6s, peak mem 273MB, user 5.5s, sys 93.8s, output queue size 5
progress 90% @chrX:33000001, elapsed 3.6s, est remaining 0.4s, peak mem 468MB, user 8.9s, sys 98.4s, output queue size 114
progress 95% @chrY:34000001, elapsed 3.8s, est remaining 0.2s, peak mem 486MB, user 11.8s, sys 104.3s, output queue size 247
progress 100% @chr21:41000001, elapsed 4.7s, est remaining 0.0s, peak mem 498MB, user 14.7s, sys 111.2s, 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 6.12.83
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 0.024 user 0.076 sys 0.075 real
MateInfoByVcf::load: 28282 calls 4.319 user 1.222 sys 4.405 real
MateInfoByVcf::parse_events: 28282 calls 4.254 user 0.981 sys 4.081 real
advance: 3219322 calls 1.310 user 13.831 sys 16.023 real
calc: 3219322 calls 4.695 user 40.788 sys 46.018 real
done: 1 calls 0.000 user 0.000 sys 0.005 real
exec_no_coor: 1 calls 0.000 user 0.001 sys 0.002 real
execute: 1 calls 0.003 user 0.001 sys 4.798 real
fetch: 3219323 calls 0.412 user 12.870 sys 13.843 real
find_pairEnds: 28282 calls 0.229 user 0.039 sys 0.396 real
idle: 987 calls 0.049 user 0.252 sys 50.570 real
init: 1 calls 0.010 user 0.000 sys 0.007 real
markDup: 28282 calls 0.854 user 0.260 sys 1.633 real
vcfadvance: 28282 calls 0.013 user 0.106 sys 0.157 real
write: 3219323 calls 2.323 user 14.272 sys 15.857 real
overall: 522289152 mem 15.161 user 112.338 sys 5.830 real