Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/5d2d2a40ebfadd6cf387c9473e6514/.command.sh
  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/4e/19e0f78a1955194ba78e24cc650e5b/Sig_18_tissue.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/5d2d2a40ebfadd6cf387c9473e6514/.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/4e/19e0f78a1955194ba78e24cc650e5b/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% @chr1:158000001, elapsed 0.1s, est remaining 1.4s, peak mem 81MB, user 0.1s, sys 1.6s, output queue size 10
progress 10% @chr2:74000001, elapsed 0.1s, est remaining 1.3s, peak mem 81MB, user 0.3s, sys 3.5s, output queue size 3
progress 15% @chr2:236000001, elapsed 0.2s, est remaining 1.1s, peak mem 81MB, user 0.5s, sys 5.3s, output queue size 26
progress 20% @chr3:156000001, elapsed 0.3s, est remaining 1.1s, peak mem 81MB, user 0.6s, sys 7.2s, output queue size 13
progress 25% @chr4:118000001, elapsed 0.3s, est remaining 1.0s, peak mem 81MB, user 0.7s, sys 9.1s, output queue size 5
progress 30% @chr5:88000001, elapsed 0.4s, est remaining 0.9s, peak mem 81MB, user 0.8s, sys 10.9s, output queue size 13
progress 35% @chr6:67000001, elapsed 0.5s, est remaining 0.9s, peak mem 81MB, user 1.0s, sys 12.8s, output queue size 13
progress 40% @chr7:56000001, elapsed 0.5s, est remaining 0.8s, peak mem 81MB, user 1.2s, sys 14.6s, output queue size 25
progress 45% @chr8:32000001, elapsed 0.6s, est remaining 0.7s, peak mem 81MB, user 1.3s, sys 16.5s, output queue size 25
progress 50% @chr9:49000001, elapsed 0.7s, est remaining 0.7s, peak mem 81MB, user 1.4s, sys 18.4s, output queue size 24
progress 55% @chr10:97000001, elapsed 0.7s, est remaining 0.6s, peak mem 81MB, user 1.5s, sys 20.2s, output queue size 17
progress 60% @chr11:122000001, elapsed 0.8s, est remaining 0.5s, peak mem 81MB, user 1.7s, sys 22.2s, output queue size 17
progress 65% @chr13:14000001, elapsed 0.9s, est remaining 0.5s, peak mem 81MB, user 1.8s, sys 24.0s, output queue size 1
progress 70% @chr14:62000001, elapsed 0.9s, est remaining 0.4s, peak mem 81MB, user 1.9s, sys 26.0s, output queue size 3
progress 75% @chr16:14000001, elapsed 1.0s, est remaining 0.3s, peak mem 81MB, user 2.1s, sys 27.8s, output queue size 5
progress 80% @chr18:1000001, elapsed 1.1s, est remaining 0.3s, peak mem 81MB, user 2.3s, sys 29.7s, output queue size 18
progress 85% @chr20:22000001, elapsed 1.1s, est remaining 0.2s, peak mem 81MB, user 2.4s, sys 31.7s, output queue size 10
progress 90% @chrX:30000001, elapsed 1.2s, est remaining 0.1s, peak mem 126MB, user 3.1s, sys 33.6s, output queue size 114
progress 95% @chrY:31000001, elapsed 1.3s, est remaining 0.1s, peak mem 156MB, user 3.5s, sys 36.1s, output queue size 271
progress 100% @chr21:41000001, elapsed 1.6s, est remaining 0.0s, peak mem 169MB, user 4.2s, sys 38.7s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
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: 49121613
reads: 1001838
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.024 user 0.016 sys 0.047 real
VcfLineRecordHelper::sort: 30 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.421 user 7.673 sys 9.121 real
calc: 3219322 calls 0.299 user 6.451 sys 6.704 real
done: 1 calls 0.024 user 0.016 sys 0.047 real
execute: 1 calls 0.002 user 0.002 sys 1.571 real
fetch: 3219322 calls 0.438 user 6.162 sys 6.653 real
idle: 76 calls 0.003 user 0.009 sys 35.863 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 227991552 mem 4.329 user 39.238 sys 2.631 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 0.1s, est remaining 2.7s, peak mem 202MB, user 0.2s, sys 3.4s, output queue size 10
progress 10% @chr2:72000001, elapsed 0.2s, est remaining 2.2s, peak mem 235MB, user 0.4s, sys 6.6s, output queue size 2
progress 15% @chr2:233000001, elapsed 0.4s, est remaining 2.0s, peak mem 253MB, user 0.6s, sys 9.7s, output queue size 2
progress 20% @chr3:152000001, elapsed 0.5s, est remaining 1.8s, peak mem 259MB, user 0.9s, sys 12.7s, output queue size 1
progress 25% @chr4:116000001, elapsed 0.6s, est remaining 1.7s, peak mem 268MB, user 1.1s, sys 15.6s, output queue size 12
progress 30% @chr5:87000001, elapsed 0.7s, est remaining 1.6s, peak mem 275MB, user 1.4s, sys 18.6s, output queue size 2
progress 35% @chr6:67000001, elapsed 0.8s, est remaining 1.4s, peak mem 287MB, user 1.6s, sys 21.7s, output queue size 6
progress 40% @chr7:54000001, elapsed 0.9s, est remaining 1.3s, peak mem 287MB, user 1.9s, sys 24.7s, output queue size 2
progress 45% @chr8:56000001, elapsed 1.0s, est remaining 1.2s, peak mem 290MB, user 2.1s, sys 27.8s, output queue size 1
progress 50% @chr9:73000001, elapsed 1.1s, est remaining 1.1s, peak mem 292MB, user 2.3s, sys 30.9s, output queue size 8
progress 55% @chr10:95000001, elapsed 1.2s, est remaining 1.0s, peak mem 293MB, user 2.6s, sys 33.8s, output queue size 13
progress 60% @chr11:123000001, elapsed 1.3s, est remaining 0.9s, peak mem 293MB, user 2.9s, sys 36.7s, output queue size 7
progress 65% @chr13:16000001, elapsed 1.4s, est remaining 0.8s, peak mem 295MB, user 3.1s, sys 39.8s, output queue size 3
progress 70% @chr14:60000001, elapsed 1.5s, est remaining 0.6s, peak mem 296MB, user 3.4s, sys 42.7s, output queue size 1
progress 75% @chr16:13000001, elapsed 1.6s, est remaining 0.5s, peak mem 296MB, user 3.6s, sys 45.8s, output queue size 6
progress 80% @chr17:82000001, elapsed 1.7s, est remaining 0.4s, peak mem 296MB, user 3.7s, sys 48.9s, output queue size 2
progress 85% @chr20:10000001, elapsed 1.8s, est remaining 0.3s, peak mem 296MB, user 3.9s, sys 52.0s, output queue size 12
progress 90% @chrX:39000001, elapsed 2.0s, est remaining 0.2s, peak mem 502MB, user 6.2s, sys 53.7s, output queue size 114
progress 95% @chrY:33000001, elapsed 2.2s, est remaining 0.1s, peak mem 522MB, user 9.1s, sys 55.5s, output queue size 248
progress 100% @chr21:41000001, elapsed 3.3s, est remaining 0.0s, peak mem 536MB, user 12.9s, sys 58.3s, 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: 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: 49121613
reads: 1001838
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 28282 calls 0.000 user 0.020 sys 0.035 real
MateInfoByVcf::load: 28282 calls 4.196 user 0.905 sys 3.898 real
MateInfoByVcf::parse_events: 28282 calls 4.178 user 0.832 sys 3.745 real
advance: 3219322 calls 1.369 user 7.459 sys 8.917 real
calc: 3219322 calls 3.848 user 21.396 sys 25.631 real
done: 1 calls 0.000 user 0.000 sys 0.004 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.005 user 0.005 sys 3.314 real
fetch: 3219323 calls 0.459 user 6.493 sys 7.674 real
find_pairEnds: 28282 calls 0.176 user 0.007 sys 0.343 real
idle: 1522 calls 0.068 user 0.165 sys 59.531 real
init: 1 calls 0.000 user 0.000 sys 0.006 real
markDup: 28282 calls 0.668 user 0.102 sys 1.322 real
vcfadvance: 28282 calls 0.008 user 0.083 sys 0.061 real
write: 3219323 calls 2.136 user 7.349 sys 9.090 real
overall: 562364416 mem 13.532 user 59.469 sys 4.335 real