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/ba/64a6bea760832d59a43a4ef754f9ac/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/002c9d93b140c61a56685cacacb7c2/Sig_18_tissue.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/64a6bea760832d59a43a4ef754f9ac/.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/64/002c9d93b140c61a56685cacacb7c2/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% @chr1:162000001, elapsed 0.1s, est remaining 1.3s, peak mem 81MB, user 0.2s, sys 1.5s, output queue size 14
progress 10% @chr2:72000001, elapsed 0.1s, est remaining 1.1s, peak mem 81MB, user 0.3s, sys 3.1s, output queue size 22
progress 15% @chr2:235000001, elapsed 0.2s, est remaining 1.1s, peak mem 81MB, user 0.5s, sys 4.9s, output queue size 11
progress 20% @chr3:154000001, elapsed 0.2s, est remaining 1.0s, peak mem 81MB, user 0.6s, sys 6.5s, output queue size 22
progress 25% @chr4:115000001, elapsed 0.3s, est remaining 0.9s, peak mem 81MB, user 0.8s, sys 8.2s, output queue size 4
progress 30% @chr5:87000001, elapsed 0.4s, est remaining 0.9s, peak mem 81MB, user 0.9s, sys 9.8s, output queue size 8
progress 35% @chr6:65000001, elapsed 0.4s, est remaining 0.8s, peak mem 81MB, user 1.1s, sys 11.5s, output queue size 3
progress 40% @chr7:55000001, elapsed 0.5s, est remaining 0.7s, peak mem 81MB, user 1.2s, sys 13.3s, output queue size 3
progress 45% @chr8:56000001, elapsed 0.5s, est remaining 0.7s, peak mem 81MB, user 1.3s, sys 15.0s, output queue size 1
progress 50% @chr9:72000001, elapsed 0.6s, est remaining 0.6s, peak mem 81MB, user 1.5s, sys 16.6s, output queue size 4
progress 55% @chr10:94000001, elapsed 0.7s, est remaining 0.5s, peak mem 81MB, user 1.6s, sys 18.3s, output queue size 1
progress 60% @chr11:122000001, elapsed 0.7s, est remaining 0.5s, peak mem 81MB, user 1.7s, sys 20.1s, output queue size 2
progress 65% @chr12:125000001, elapsed 0.8s, est remaining 0.4s, peak mem 81MB, user 1.8s, sys 21.8s, output queue size 24
progress 70% @chr14:35000001, elapsed 0.8s, est remaining 0.4s, peak mem 81MB, user 2.0s, sys 23.5s, output queue size 26
progress 75% @chr16:13000001, elapsed 0.9s, est remaining 0.3s, peak mem 81MB, user 2.1s, sys 25.3s, output queue size 21
progress 80% @chr18:1000001, elapsed 1.0s, est remaining 0.2s, peak mem 81MB, user 2.2s, sys 27.0s, output queue size 25
progress 85% @chr20:24000001, elapsed 1.0s, est remaining 0.2s, peak mem 81MB, user 2.4s, sys 28.7s, output queue size 21
progress 90% @chrX:29000001, elapsed 1.1s, est remaining 0.1s, peak mem 127MB, user 2.9s, sys 30.1s, output queue size 114
progress 95% @chrY:30000001, elapsed 1.2s, est remaining 0.1s, peak mem 156MB, user 3.2s, sys 32.2s, output queue size 271
progress 100% @chr21:41000001, elapsed 1.4s, est remaining 0.0s, peak mem 172MB, user 3.8s, sys 34.5s, 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 192
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 49119623
reads: 1001838
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.032 user 0.008 sys 0.050 real
VcfLineRecordHelper::sort: 30 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.382 user 6.710 sys 8.484 real
calc: 3219322 calls 0.362 user 5.595 sys 6.032 real
done: 1 calls 0.032 user 0.008 sys 0.050 real
execute: 1 calls 0.002 user 0.002 sys 1.441 real
fetch: 3219322 calls 0.314 user 5.315 sys 5.918 real
idle: 72 calls 0.002 user 0.009 sys 36.271 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 231129088 mem 3.919 user 35.039 sys 2.504 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% @chr1:155000001, elapsed 0.1s, est remaining 2.0s, peak mem 205MB, user 0.3s, sys 2.5s, output queue size 6
progress 10% @chr2:73000001, elapsed 0.2s, est remaining 1.7s, peak mem 232MB, user 0.6s, sys 4.8s, output queue size 1
progress 15% @chr2:233000001, elapsed 0.3s, est remaining 1.6s, peak mem 252MB, user 0.9s, sys 7.2s, output queue size 2
progress 20% @chr3:152000001, elapsed 0.4s, est remaining 1.4s, peak mem 265MB, user 1.1s, sys 9.5s, output queue size 3
progress 25% @chr4:113000001, elapsed 0.4s, est remaining 1.3s, peak mem 276MB, user 1.4s, sys 11.9s, output queue size 2
progress 30% @chr5:86000001, elapsed 0.5s, est remaining 1.2s, peak mem 282MB, user 1.7s, sys 14.2s, output queue size 1
progress 35% @chr6:66000001, elapsed 0.6s, est remaining 1.1s, peak mem 286MB, user 2.0s, sys 16.5s, output queue size 4
progress 40% @chr7:55000001, elapsed 0.7s, est remaining 1.0s, peak mem 291MB, user 2.2s, sys 18.9s, output queue size 2
progress 45% @chr8:59000001, elapsed 0.8s, est remaining 1.0s, peak mem 295MB, user 2.4s, sys 21.3s, output queue size 5
progress 50% @chr9:75000001, elapsed 0.9s, est remaining 0.9s, peak mem 300MB, user 2.7s, sys 23.7s, output queue size 13
progress 55% @chr10:95000001, elapsed 1.0s, est remaining 0.8s, peak mem 301MB, user 3.0s, sys 26.0s, output queue size 15
progress 60% @chr11:122000001, elapsed 1.0s, est remaining 0.7s, peak mem 304MB, user 3.3s, sys 28.2s, output queue size 12
progress 65% @chr13:17000001, elapsed 1.1s, est remaining 0.6s, peak mem 304MB, user 3.6s, sys 30.6s, output queue size 18
progress 70% @chr14:61000001, elapsed 1.2s, est remaining 0.5s, peak mem 307MB, user 3.9s, sys 33.0s, output queue size 22
progress 75% @chr16:11000001, elapsed 1.3s, est remaining 0.4s, peak mem 307MB, user 4.1s, sys 35.5s, output queue size 2
progress 80% @chr18:1, elapsed 1.4s, est remaining 0.3s, peak mem 309MB, user 4.3s, sys 38.1s, output queue size 23
progress 85% @chr20:22000001, elapsed 1.5s, est remaining 0.3s, peak mem 310MB, user 4.6s, sys 40.6s, output queue size 8
progress 90% @chrX:40000001, elapsed 1.7s, est remaining 0.2s, peak mem 525MB, user 6.8s, sys 41.9s, output queue size 114
progress 95% @chrY:34000001, elapsed 1.8s, est remaining 0.1s, peak mem 540MB, user 9.3s, sys 43.0s, output queue size 248
progress 100% @chr21:41000001, elapsed 2.9s, est remaining 0.0s, peak mem 555MB, user 13.4s, sys 45.0s, 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 192
algo: Dedup
license: sentieon:Dedup=31
input file size: 49119623
reads: 1001838
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 28282 calls 0.000 user 0.020 sys 0.025 real
MateInfoByVcf::load: 28282 calls 4.276 user 0.694 sys 3.732 real
MateInfoByVcf::parse_events: 28282 calls 4.257 user 0.631 sys 3.618 real
advance: 3219322 calls 1.212 user 5.331 sys 7.143 real
calc: 3219322 calls 3.970 user 16.096 sys 21.009 real
done: 1 calls 0.000 user 0.001 sys 0.003 real
exec_no_coor: 1 calls 0.000 user 0.007 sys 0.003 real
execute: 1 calls 0.004 user 0.004 sys 2.901 real
fetch: 3219323 calls 0.362 user 5.547 sys 5.784 real
find_pairEnds: 28282 calls 0.159 user 0.012 sys 0.329 real
idle: 1558 calls 0.086 user 0.133 sys 59.486 real
init: 1 calls 0.000 user 0.000 sys 0.006 real
markDup: 28282 calls 0.663 user 0.093 sys 1.241 real
vcfadvance: 28282 calls 0.012 user 0.059 sys 0.039 real
write: 3219323 calls 2.109 user 5.352 sys 7.524 real
overall: 582074368 mem 14.062 user 46.308 sys 3.923 real