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/6e/8467a0f89a3b28cafdce3f1ccefdce/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/1bc8e9d0dbe55a859b75d4ca3ea17c/Sig_18_tissue.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/8467a0f89a3b28cafdce3f1ccefdce/.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/5f/1bc8e9d0dbe55a859b75d4ca3ea17c/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% @chr1:164000001, elapsed 0.1s, est remaining 1.4s, peak mem 81MB, user 0.2s, sys 1.5s, output queue size 9
progress 10% @chr2:75000001, elapsed 0.1s, est remaining 1.2s, peak mem 81MB, user 0.3s, sys 3.3s, output queue size 14
progress 15% @chr2:237000001, elapsed 0.2s, est remaining 1.1s, peak mem 81MB, user 0.5s, sys 5.1s, output queue size 12
progress 20% @chr3:156000001, elapsed 0.3s, est remaining 1.0s, peak mem 81MB, user 0.6s, sys 6.9s, output queue size 17
progress 25% @chr4:117000001, elapsed 0.3s, est remaining 1.0s, peak mem 81MB, user 0.7s, sys 8.7s, output queue size 14
progress 30% @chr5:89000001, elapsed 0.4s, est remaining 0.9s, peak mem 81MB, user 0.9s, sys 10.5s, output queue size 17
progress 35% @chr6:65000001, elapsed 0.4s, est remaining 0.8s, peak mem 81MB, user 1.0s, sys 12.3s, output queue size 18
progress 40% @chr7:57000001, elapsed 0.5s, est remaining 0.8s, peak mem 81MB, user 1.2s, sys 14.1s, output queue size 19
progress 45% @chr8:59000001, elapsed 0.6s, est remaining 0.7s, peak mem 81MB, user 1.4s, sys 15.8s, output queue size 19
progress 50% @chr9:75000001, elapsed 0.6s, est remaining 0.6s, peak mem 81MB, user 1.5s, sys 17.6s, output queue size 20
progress 55% @chr10:74000001, elapsed 0.7s, est remaining 0.6s, peak mem 81MB, user 1.7s, sys 19.4s, output queue size 21
progress 60% @chr11:123000001, elapsed 0.8s, est remaining 0.5s, peak mem 81MB, user 1.8s, sys 21.2s, output queue size 23
progress 65% @chr13:15000001, elapsed 0.8s, est remaining 0.4s, peak mem 81MB, user 2.0s, sys 23.0s, output queue size 23
progress 70% @chr14:61000001, elapsed 0.9s, est remaining 0.4s, peak mem 81MB, user 2.1s, sys 24.9s, output queue size 4
progress 75% @chr16:13000001, elapsed 1.0s, est remaining 0.3s, peak mem 81MB, user 2.2s, sys 26.8s, output queue size 4
progress 80% @chr18:1, elapsed 1.0s, est remaining 0.3s, peak mem 81MB, user 2.3s, sys 28.6s, output queue size 5
progress 85% @chr20:22000001, elapsed 1.1s, est remaining 0.2s, peak mem 81MB, user 2.5s, sys 30.4s, output queue size 8
progress 90% @chrX:25000001, elapsed 1.2s, est remaining 0.1s, peak mem 108MB, user 3.1s, sys 32.7s, output queue size 114
progress 95% @chrY:25000001, elapsed 1.4s, est remaining 0.1s, peak mem 135MB, user 3.6s, sys 36.5s, output queue size 271
progress 100% @chr21:41000001, elapsed 1.7s, est remaining 0.0s, peak mem 162MB, user 4.3s, sys 41.4s, 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: 49121349
reads: 1001838
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.032 user 0.006 sys 0.050 real
VcfLineRecordHelper::sort: 29 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.387 user 8.727 sys 10.416 real
calc: 3219322 calls 0.306 user 6.468 sys 6.860 real
done: 1 calls 0.032 user 0.006 sys 0.050 real
execute: 1 calls 0.003 user 0.006 sys 1.678 real
fetch: 3219322 calls 0.307 user 6.716 sys 6.892 real
idle: 79 calls 0.004 user 0.018 sys 36.343 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 217120768 mem 4.431 user 41.828 sys 2.738 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% @chr1:164000001, elapsed 0.1s, est remaining 2.0s, peak mem 183MB, user 0.2s, sys 2.4s, output queue size 14
progress 10% @chr2:76000001, elapsed 0.2s, est remaining 1.7s, peak mem 207MB, user 0.4s, sys 4.7s, output queue size 15
progress 15% @chr2:236000001, elapsed 0.3s, est remaining 1.5s, peak mem 237MB, user 0.6s, sys 6.9s, output queue size 23
progress 20% @chr3:154000001, elapsed 0.3s, est remaining 1.4s, peak mem 255MB, user 0.8s, sys 9.1s, output queue size 24
progress 25% @chr4:116000001, elapsed 0.4s, est remaining 1.3s, peak mem 261MB, user 1.1s, sys 11.4s, output queue size 3
progress 30% @chr5:89000001, elapsed 0.5s, est remaining 1.2s, peak mem 267MB, user 1.2s, sys 13.8s, output queue size 25
progress 35% @chr6:66000001, elapsed 0.6s, est remaining 1.1s, peak mem 270MB, user 1.4s, sys 16.2s, output queue size 19
progress 40% @chr7:74000001, elapsed 0.7s, est remaining 1.1s, peak mem 273MB, user 1.7s, sys 20.2s, output queue size 20
progress 45% @chr8:36000001, elapsed 0.9s, est remaining 1.1s, peak mem 276MB, user 2.0s, sys 25.4s, output queue size 21
progress 50% @chr9:67000001, elapsed 1.1s, est remaining 1.1s, peak mem 276MB, user 2.5s, sys 30.7s, output queue size 14
progress 55% @chr10:91000001, elapsed 1.3s, est remaining 1.1s, peak mem 276MB, user 2.9s, sys 36.5s, output queue size 27
progress 60% @chr11:92000001, elapsed 1.6s, est remaining 1.0s, peak mem 276MB, user 3.2s, sys 43.5s, output queue size 31
progress 65% @chr13:7000001, elapsed 1.8s, est remaining 1.0s, peak mem 276MB, user 3.5s, sys 50.9s, output queue size 26
progress 70% @chr14:68000001, elapsed 2.0s, est remaining 0.9s, peak mem 276MB, user 3.7s, sys 57.8s, output queue size 11
progress 75% @chr16:16000001, elapsed 2.3s, est remaining 0.8s, peak mem 276MB, user 4.0s, sys 64.9s, output queue size 4
progress 80% @chr17:75000001, elapsed 2.5s, est remaining 0.6s, peak mem 276MB, user 4.3s, sys 71.9s, output queue size 9
progress 85% @chr20:32000001, elapsed 2.7s, est remaining 0.5s, peak mem 276MB, user 4.6s, sys 78.8s, output queue size 13
progress 90% @chr21:32000001, elapsed 3.1s, est remaining 0.3s, peak mem 471MB, user 8.3s, sys 84.1s, output queue size 109
progress 95% @chrY:26000001, elapsed 3.4s, est remaining 0.2s, peak mem 486MB, user 11.1s, sys 90.4s, output queue size 240
progress 100% @chr21:41000001, elapsed 4.3s, est remaining 0.0s, peak mem 492MB, user 13.6s, sys 97.9s, 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: 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: 49121349
reads: 1001838
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 28282 calls 0.021 user 0.094 sys 0.081 real
MateInfoByVcf::load: 28282 calls 4.101 user 1.623 sys 4.441 real
MateInfoByVcf::parse_events: 28282 calls 4.056 user 1.346 sys 4.093 real
advance: 3219322 calls 1.052 user 11.882 sys 14.040 real
calc: 3219322 calls 4.601 user 34.435 sys 40.744 real
done: 1 calls 0.000 user 0.000 sys 0.004 real
exec_no_coor: 1 calls 0.000 user 0.003 sys 0.000 real
execute: 1 calls 0.005 user 0.002 sys 4.330 real
fetch: 3219323 calls 0.390 user 11.922 sys 11.888 real
find_pairEnds: 28282 calls 0.247 user 0.044 sys 0.406 real
idle: 940 calls 0.076 user 0.118 sys 49.435 real
init: 1 calls 0.009 user 0.001 sys 0.006 real
markDup: 28282 calls 0.884 user 0.303 sys 1.667 real
vcfadvance: 28282 calls 0.020 user 0.131 sys 0.247 real
write: 3219323 calls 2.311 user 11.628 sys 14.206 real
overall: 516055040 mem 14.178 user 99.292 sys 5.333 real