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/0b/ef823722485ec760d22085e440f7e5/Sig_18_Blood.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/1522110040efeb211ec882b01ba433/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/1522110040efeb211ec882b01ba433/.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/0b/ef823722485ec760d22085e440f7e5/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% @chr1:165000001, elapsed 0.1s, est remaining 1.9s, peak mem 78MB, user 0.1s, sys 2.4s, output queue size 23
progress 10% @chr2:81000001, elapsed 0.2s, est remaining 1.8s, peak mem 78MB, user 0.3s, sys 5.2s, output queue size 17
progress 15% @chr2:212000001, elapsed 0.3s, est remaining 1.6s, peak mem 78MB, user 0.5s, sys 7.8s, output queue size 23
progress 20% @chr3:163000001, elapsed 0.4s, est remaining 1.5s, peak mem 78MB, user 0.6s, sys 10.6s, output queue size 23
progress 25% @chr4:122000001, elapsed 0.5s, est remaining 1.4s, peak mem 78MB, user 0.8s, sys 13.3s, output queue size 21
progress 30% @chr5:92000001, elapsed 0.6s, est remaining 1.3s, peak mem 78MB, user 1.0s, sys 15.9s, output queue size 25
progress 35% @chr6:72000001, elapsed 0.7s, est remaining 1.2s, peak mem 78MB, user 1.2s, sys 18.6s, output queue size 22
progress 40% @chr7:56000001, elapsed 0.8s, est remaining 1.1s, peak mem 78MB, user 1.4s, sys 21.3s, output queue size 24
progress 45% @chr8:61000001, elapsed 0.8s, est remaining 1.0s, peak mem 78MB, user 1.5s, sys 24.0s, output queue size 21
progress 50% @chr9:78000001, elapsed 0.9s, est remaining 0.9s, peak mem 78MB, user 1.7s, sys 26.7s, output queue size 25
progress 55% @chr10:101000001, elapsed 1.0s, est remaining 0.8s, peak mem 78MB, user 1.9s, sys 29.3s, output queue size 20
progress 60% @chr11:122000001, elapsed 1.1s, est remaining 0.7s, peak mem 78MB, user 2.0s, sys 32.0s, output queue size 10
progress 65% @chr12:120000001, elapsed 1.2s, est remaining 0.7s, peak mem 78MB, user 2.2s, sys 34.6s, output queue size 32
progress 70% @chr14:69000001, elapsed 1.3s, est remaining 0.6s, peak mem 78MB, user 2.3s, sys 37.3s, output queue size 24
progress 75% @chr15:72000001, elapsed 1.4s, est remaining 0.5s, peak mem 78MB, user 2.5s, sys 40.3s, output queue size 43
progress 80% @chr17:78000001, elapsed 1.6s, est remaining 0.4s, peak mem 78MB, user 2.8s, sys 44.7s, output queue size 44
progress 85% @chr20:15000001, elapsed 1.7s, est remaining 0.3s, peak mem 78MB, user 3.1s, sys 48.8s, output queue size 31
progress 90% @chrX:28000001, elapsed 1.9s, est remaining 0.2s, peak mem 84MB, user 3.7s, sys 52.4s, output queue size 114
progress 95% @chrY:25000001, elapsed 2.1s, est remaining 0.1s, peak mem 120MB, user 4.2s, sys 57.2s, output queue size 276
progress 100% @chr21:41000001, elapsed 2.5s, est remaining 0.0s, peak mem 168MB, user 5.1s, sys 65.9s, 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: 51298916
reads: 1001133
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.015 user 0.023 sys 0.049 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.479 user 14.472 sys 16.436 real
calc: 3219322 calls 0.363 user 10.512 sys 10.817 real
done: 1 calls 0.015 user 0.023 sys 0.049 real
execute: 1 calls 0.002 user 0.009 sys 2.507 real
fetch: 3219322 calls 0.385 user 9.955 sys 10.858 real
idle: 79 calls 0.015 user 0.036 sys 36.802 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 220270592 mem 5.255 user 66.493 sys 3.561 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% @chr1:161000001, elapsed 0.1s, est remaining 2.0s, peak mem 168MB, user 0.3s, sys 2.3s, output queue size 11
progress 10% @chr2:77000001, elapsed 0.2s, est remaining 1.7s, peak mem 189MB, user 0.6s, sys 4.5s, output queue size 22
progress 15% @chr2:237000001, elapsed 0.3s, est remaining 1.5s, peak mem 222MB, user 1.0s, sys 6.6s, output queue size 17
progress 20% @chr3:153000001, elapsed 0.3s, est remaining 1.4s, peak mem 231MB, user 1.2s, sys 8.7s, output queue size 9
progress 25% @chr4:114000001, elapsed 0.4s, est remaining 1.3s, peak mem 243MB, user 1.5s, sys 10.9s, output queue size 9
progress 30% @chr5:87000001, elapsed 0.5s, est remaining 1.2s, peak mem 252MB, user 1.7s, sys 13.0s, output queue size 9
progress 35% @chr6:65000001, elapsed 0.6s, est remaining 1.1s, peak mem 252MB, user 2.0s, sys 15.2s, output queue size 12
progress 40% @chr7:56000001, elapsed 0.7s, est remaining 1.0s, peak mem 264MB, user 2.2s, sys 17.4s, output queue size 18
progress 45% @chr8:58000001, elapsed 0.7s, est remaining 0.9s, peak mem 267MB, user 2.5s, sys 19.3s, output queue size 7
progress 50% @chr9:73000001, elapsed 0.8s, est remaining 0.8s, peak mem 267MB, user 2.8s, sys 21.5s, output queue size 17
progress 55% @chr10:96000001, elapsed 0.9s, est remaining 0.7s, peak mem 267MB, user 3.0s, sys 23.7s, output queue size 22
progress 60% @chr11:121000001, elapsed 1.0s, est remaining 0.6s, peak mem 270MB, user 3.3s, sys 26.0s, output queue size 14
progress 65% @chr13:16000001, elapsed 1.0s, est remaining 0.6s, peak mem 273MB, user 3.6s, sys 28.1s, output queue size 15
progress 70% @chr14:87000001, elapsed 1.1s, est remaining 0.5s, peak mem 279MB, user 3.8s, sys 30.4s, output queue size 6
progress 75% @chr16:7000001, elapsed 1.3s, est remaining 0.4s, peak mem 279MB, user 4.2s, sys 34.6s, output queue size 6
progress 80% @chr17:51000001, elapsed 1.4s, est remaining 0.4s, peak mem 279MB, user 4.6s, sys 38.8s, output queue size 33
progress 85% @chr20:17000001, elapsed 1.6s, est remaining 0.3s, peak mem 279MB, user 4.9s, sys 43.2s, output queue size 13
progress 90% @chrX:29000001, elapsed 1.9s, est remaining 0.2s, peak mem 513MB, user 7.6s, sys 46.7s, output queue size 114
progress 95% @chrY:20000001, elapsed 2.1s, est remaining 0.1s, peak mem 525MB, user 11.2s, sys 51.3s, output queue size 240
progress 100% @chr21:41000001, elapsed 3.3s, est remaining 0.0s, peak mem 534MB, user 14.2s, sys 57.4s, 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: 51298916
reads: 1001133
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 26026 calls 0.020 user 0.020 sys 0.050 real
MateInfoByVcf::load: 26026 calls 3.873 user 1.002 sys 4.186 real
MateInfoByVcf::parse_events: 26026 calls 3.816 user 0.822 sys 3.954 real
advance: 3219322 calls 1.077 user 6.683 sys 8.513 real
calc: 3219322 calls 4.869 user 20.859 sys 26.231 real
done: 1 calls 0.000 user 0.000 sys 0.003 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.002 user 0.002 sys 3.302 real
fetch: 3219322 calls 0.466 user 7.247 sys 6.904 real
find_pairEnds: 26026 calls 0.207 user 0.052 sys 0.376 real
idle: 1139 calls 0.059 user 0.112 sys 58.698 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 26026 calls 0.974 user 0.224 sys 1.424 real
vcfadvance: 26026 calls 0.011 user 0.108 sys 0.100 real
write: 3219322 calls 2.588 user 6.721 sys 9.615 real
overall: 560095232 mem 14.768 user 58.464 sys 4.324 real