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/92/216e4670e79f5e1bc0609a846a7a3b/Sig_18_Blood.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/d2f581f0b34a6613ec7cf9c4a975c8/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/d2f581f0b34a6613ec7cf9c4a975c8/.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/92/216e4670e79f5e1bc0609a846a7a3b/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% @chr1:133000001, elapsed 0.1s, est remaining 2.5s, peak mem 78MB, user 0.2s, sys 3.2s, output queue size 28
progress 10% @chr2:65000001, elapsed 0.3s, est remaining 2.3s, peak mem 78MB, user 0.4s, sys 6.7s, output queue size 22
progress 15% @chr3:14000001, elapsed 0.4s, est remaining 2.4s, peak mem 78MB, user 0.6s, sys 11.7s, output queue size 20
progress 20% @chr3:176000001, elapsed 0.6s, est remaining 2.4s, peak mem 78MB, user 0.8s, sys 16.7s, output queue size 29
progress 25% @chr4:107000001, elapsed 0.8s, est remaining 2.3s, peak mem 78MB, user 1.0s, sys 21.8s, output queue size 25
progress 30% @chr5:111000001, elapsed 0.9s, est remaining 2.2s, peak mem 78MB, user 1.2s, sys 26.9s, output queue size 28
progress 35% @chr6:59000001, elapsed 1.1s, est remaining 2.1s, peak mem 78MB, user 1.5s, sys 31.9s, output queue size 26
progress 40% @chr7:66000001, elapsed 1.3s, est remaining 2.0s, peak mem 78MB, user 1.7s, sys 37.8s, output queue size 18
progress 45% @chr8:69000001, elapsed 1.5s, est remaining 1.8s, peak mem 78MB, user 1.9s, sys 42.9s, output queue size 18
progress 50% @chr9:69000001, elapsed 1.7s, est remaining 1.7s, peak mem 78MB, user 2.2s, sys 48.2s, output queue size 4
progress 55% @chr10:100000001, elapsed 1.8s, est remaining 1.5s, peak mem 78MB, user 2.3s, sys 53.5s, output queue size 9
progress 60% @chr11:107000001, elapsed 2.0s, est remaining 1.3s, peak mem 78MB, user 2.6s, sys 58.7s, output queue size 16
progress 65% @chr13:19000001, elapsed 2.2s, est remaining 1.2s, peak mem 78MB, user 3.0s, sys 64.1s, output queue size 6
progress 70% @chr14:50000001, elapsed 2.4s, est remaining 1.0s, peak mem 78MB, user 3.3s, sys 69.6s, output queue size 11
progress 75% @chr16:17000001, elapsed 2.6s, est remaining 0.9s, peak mem 78MB, user 3.4s, sys 75.3s, output queue size 7
progress 80% @chr18:2000001, elapsed 2.8s, est remaining 0.7s, peak mem 78MB, user 3.6s, sys 80.8s, output queue size 7
progress 85% @chr20:9000001, elapsed 2.9s, est remaining 0.5s, peak mem 78MB, user 3.9s, sys 86.3s, output queue size 13
progress 90% @chrX:30000001, elapsed 3.2s, est remaining 0.4s, peak mem 111MB, user 4.6s, sys 91.4s, output queue size 114
progress 95% @chrY:30000001, elapsed 3.4s, est remaining 0.2s, peak mem 135MB, user 5.0s, sys 96.9s, output queue size 276
progress 100% @chr21:41000001, elapsed 3.8s, est remaining 0.0s, peak mem 171MB, user 5.9s, sys 105.1s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 51298915
reads: 1001133
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.034 user 0.002 sys 0.049 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.180 user 21.562 sys 22.736 real
calc: 3219322 calls 0.423 user 17.100 sys 16.763 real
done: 1 calls 0.034 user 0.002 sys 0.049 real
execute: 1 calls 0.001 user 0.010 sys 3.759 real
fetch: 3219322 calls 0.393 user 17.515 sys 16.693 real
idle: 74 calls 0.004 user 0.023 sys 35.250 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 219373568 mem 6.044 user 105.813 sys 4.824 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% @chr1:160000001, elapsed 0.2s, est remaining 2.9s, peak mem 171MB, user 0.3s, sys 3.7s, output queue size 7
progress 10% @chr2:74000001, elapsed 0.3s, est remaining 2.4s, peak mem 192MB, user 0.7s, sys 6.9s, output queue size 20
progress 15% @chr2:225000001, elapsed 0.4s, est remaining 2.2s, peak mem 222MB, user 1.0s, sys 10.2s, output queue size 10
progress 20% @chr3:153000001, elapsed 0.5s, est remaining 2.0s, peak mem 234MB, user 1.2s, sys 13.5s, output queue size 6
progress 25% @chr4:99000001, elapsed 0.7s, est remaining 2.1s, peak mem 243MB, user 1.5s, sys 18.8s, output queue size 29
progress 30% @chr5:60000001, elapsed 1.0s, est remaining 2.3s, peak mem 249MB, user 1.8s, sys 26.9s, output queue size 26
progress 35% @chr6:58000001, elapsed 1.2s, est remaining 2.3s, peak mem 249MB, user 2.1s, sys 34.9s, output queue size 25
progress 40% @chr7:44000001, elapsed 1.5s, est remaining 2.3s, peak mem 258MB, user 2.4s, sys 43.5s, output queue size 11
progress 45% @chr8:69000001, elapsed 1.8s, est remaining 2.2s, peak mem 258MB, user 2.6s, sys 51.6s, output queue size 12
progress 50% @chr9:62000001, elapsed 2.1s, est remaining 2.1s, peak mem 261MB, user 2.9s, sys 59.4s, output queue size 11
progress 55% @chr10:93000001, elapsed 2.3s, est remaining 1.9s, peak mem 261MB, user 3.2s, sys 67.2s, output queue size 8
progress 60% @chr11:119000001, elapsed 2.6s, est remaining 1.7s, peak mem 261MB, user 3.5s, sys 74.9s, output queue size 4
progress 65% @chr13:12000001, elapsed 2.8s, est remaining 1.5s, peak mem 261MB, user 3.7s, sys 82.5s, output queue size 3
progress 70% @chr14:62000001, elapsed 3.1s, est remaining 1.3s, peak mem 261MB, user 4.1s, sys 90.4s, output queue size 23
progress 75% @chr16:12000001, elapsed 3.4s, est remaining 1.1s, peak mem 261MB, user 4.4s, sys 98.5s, output queue size 5
progress 80% @chr18:8000001, elapsed 3.6s, est remaining 0.9s, peak mem 261MB, user 4.6s, sys 106.5s, output queue size 5
progress 85% @chr20:18000001, elapsed 3.9s, est remaining 0.7s, peak mem 264MB, user 5.0s, sys 114.2s, output queue size 4
progress 90% @chrX:35000001, elapsed 4.3s, est remaining 0.5s, peak mem 471MB, user 8.4s, sys 120.0s, output queue size 114
progress 95% @chrY:24000001, elapsed 4.6s, est remaining 0.2s, peak mem 477MB, user 12.3s, sys 127.0s, output queue size 240
progress 100% @chr21:41000001, elapsed 5.6s, est remaining 0.0s, peak mem 492MB, user 15.1s, sys 134.4s, 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: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: Dedup
license: sentieon:Dedup=31
input file size: 51298915
reads: 1001133
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 26026 calls 0.009 user 0.060 sys 0.078 real
MateInfoByVcf::load: 26026 calls 4.462 user 1.575 sys 4.891 real
MateInfoByVcf::parse_events: 26026 calls 4.354 user 1.338 sys 4.521 real
advance: 3219322 calls 1.219 user 18.201 sys 18.107 real
calc: 3219322 calls 4.889 user 49.897 sys 55.073 real
done: 1 calls 0.000 user 0.000 sys 0.005 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.003 user 0.004 sys 5.616 real
fetch: 3219322 calls 0.378 user 17.085 sys 13.584 real
find_pairEnds: 26026 calls 0.206 user 0.048 sys 0.417 real
idle: 938 calls 0.042 user 0.132 sys 51.629 real
init: 1 calls 0.000 user 0.000 sys 0.006 real
markDup: 26026 calls 0.904 user 0.280 sys 1.668 real
vcfadvance: 26026 calls 0.018 user 0.157 sys 0.204 real
write: 3219322 calls 2.532 user 15.115 sys 19.326 real
overall: 516055040 mem 15.610 user 135.507 sys 6.632 real