Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/00d03dfeed4e2185bbbc3d3721b34c/.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/9c/9ad596bb02a328b0faf55ade1659a2/Sig_18_tissue.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/00d03dfeed4e2185bbbc3d3721b34c/.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/9c/9ad596bb02a328b0faf55ade1659a2/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 17
progress 10% @chr2:74000001, elapsed 0.1s, est remaining 1.2s, peak mem 81MB, user 0.3s, sys 3.3s, output queue size 12
progress 15% @chr2:235000001, elapsed 0.2s, est remaining 1.1s, peak mem 81MB, user 0.4s, sys 5.0s, output queue size 16
progress 20% @chr3:154000001, elapsed 0.3s, est remaining 1.2s, peak mem 81MB, user 0.6s, sys 8.1s, output queue size 6
progress 25% @chr4:108000001, elapsed 0.4s, est remaining 1.3s, peak mem 81MB, user 0.7s, sys 11.6s, output queue size 7
progress 30% @chr5:111000001, elapsed 0.5s, est remaining 1.3s, peak mem 81MB, user 1.0s, sys 15.1s, output queue size 15
progress 35% @chr6:58000001, elapsed 0.7s, est remaining 1.2s, peak mem 81MB, user 1.2s, sys 18.7s, output queue size 7
progress 40% @chr7:42000001, elapsed 0.8s, est remaining 1.2s, peak mem 81MB, user 1.4s, sys 22.2s, output queue size 16
progress 45% @chr8:52000001, elapsed 0.9s, est remaining 1.1s, peak mem 81MB, user 1.7s, sys 25.7s, output queue size 31
progress 50% @chr9:86000001, elapsed 1.0s, est remaining 1.0s, peak mem 81MB, user 1.9s, sys 29.4s, output queue size 13
progress 55% @chr10:87000001, elapsed 1.2s, est remaining 1.0s, peak mem 81MB, user 2.0s, sys 34.0s, output queue size 8
progress 60% @chr12:6000001, elapsed 1.3s, est remaining 0.9s, peak mem 81MB, user 2.1s, sys 38.7s, output queue size 24
progress 65% @chr13:10000001, elapsed 1.5s, est remaining 0.8s, peak mem 81MB, user 2.3s, sys 43.6s, output queue size 8
progress 70% @chr14:56000001, elapsed 1.7s, est remaining 0.7s, peak mem 81MB, user 2.5s, sys 48.4s, output queue size 5
progress 75% @chr16:13000001, elapsed 1.8s, est remaining 0.6s, peak mem 81MB, user 2.6s, sys 53.3s, output queue size 6
progress 80% @chr18:1, elapsed 2.0s, est remaining 0.5s, peak mem 81MB, user 2.8s, sys 58.1s, output queue size 25
progress 85% @chr20:20000001, elapsed 2.2s, est remaining 0.4s, peak mem 81MB, user 2.9s, sys 63.1s, output queue size 14
progress 90% @chrX:31000001, elapsed 2.4s, est remaining 0.3s, peak mem 111MB, user 3.6s, sys 67.8s, output queue size 114
progress 95% @chrY:26000001, elapsed 2.6s, est remaining 0.1s, peak mem 135MB, user 3.9s, sys 74.0s, output queue size 271
progress 100% @chr21:41000001, elapsed 2.9s, est remaining 0.0s, peak mem 156MB, user 4.7s, sys 81.1s, 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 384
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 49121348
reads: 1001838
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.029 user 0.011 sys 0.047 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.432 user 16.910 sys 18.430 real
calc: 3219322 calls 0.471 user 13.080 sys 13.124 real
done: 1 calls 0.029 user 0.011 sys 0.047 real
execute: 1 calls 0.002 user 0.007 sys 2.937 real
fetch: 3219322 calls 0.342 user 13.534 sys 13.116 real
idle: 78 calls 0.001 user 0.012 sys 35.164 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 207773696 mem 4.818 user 81.870 sys 4.002 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 2.1s, peak mem 186MB, user 0.3s, sys 2.6s, output queue size 10
progress 10% @chr2:60000001, elapsed 0.2s, est remaining 2.2s, peak mem 210MB, user 0.6s, sys 5.7s, output queue size 26
progress 15% @chr2:222000001, elapsed 0.5s, est remaining 2.7s, peak mem 237MB, user 1.0s, sys 12.7s, output queue size 22
progress 20% @chr3:150000001, elapsed 0.7s, est remaining 2.9s, peak mem 246MB, user 1.2s, sys 19.8s, output queue size 35
progress 25% @chr4:141000001, elapsed 1.0s, est remaining 2.9s, peak mem 249MB, user 1.5s, sys 27.0s, output queue size 27
progress 30% @chr5:110000001, elapsed 1.2s, est remaining 2.8s, peak mem 258MB, user 1.8s, sys 34.1s, output queue size 13
progress 35% @chr6:87000001, elapsed 1.4s, est remaining 2.7s, peak mem 258MB, user 2.2s, sys 41.3s, output queue size 33
progress 40% @chr7:47000001, elapsed 1.7s, est remaining 2.5s, peak mem 264MB, user 2.4s, sys 48.8s, output queue size 21
progress 45% @chr8:34000001, elapsed 1.9s, est remaining 2.4s, peak mem 264MB, user 2.7s, sys 56.3s, output queue size 28
progress 50% @chr9:70000001, elapsed 2.2s, est remaining 2.2s, peak mem 267MB, user 3.1s, sys 64.0s, output queue size 16
progress 55% @chr10:96000001, elapsed 2.5s, est remaining 2.0s, peak mem 267MB, user 3.4s, sys 71.4s, output queue size 20
progress 60% @chr11:122000001, elapsed 2.7s, est remaining 1.8s, peak mem 267MB, user 3.7s, sys 79.1s, output queue size 3
progress 65% @chr13:20000001, elapsed 3.0s, est remaining 1.6s, peak mem 270MB, user 4.1s, sys 86.5s, output queue size 6
progress 70% @chr14:69000001, elapsed 3.2s, est remaining 1.4s, peak mem 276MB, user 4.3s, sys 94.2s, output queue size 6
progress 75% @chr16:21000001, elapsed 3.5s, est remaining 1.2s, peak mem 279MB, user 4.6s, sys 101.6s, output queue size 9
progress 80% @chr18:5000001, elapsed 3.7s, est remaining 0.9s, peak mem 279MB, user 4.9s, sys 108.9s, output queue size 21
progress 85% @chr20:30000001, elapsed 3.9s, est remaining 0.7s, peak mem 279MB, user 5.2s, sys 116.0s, output queue size 15
progress 90% @chrX:32000001, elapsed 4.4s, est remaining 0.5s, peak mem 465MB, user 9.0s, sys 122.2s, output queue size 114
progress 95% @chrY:26000001, elapsed 4.7s, est remaining 0.2s, peak mem 474MB, user 12.1s, sys 129.1s, output queue size 247
progress 100% @chr21:41000001, elapsed 5.6s, est remaining 0.0s, peak mem 486MB, user 15.2s, sys 137.1s, 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 384
algo: Dedup
license: sentieon:Dedup=31
input file size: 49121348
reads: 1001838
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 28282 calls 0.003 user 0.054 sys 0.091 real
MateInfoByVcf::load: 28282 calls 4.419 user 1.765 sys 4.895 real
MateInfoByVcf::parse_events: 28282 calls 4.360 user 1.516 sys 4.479 real
advance: 3219322 calls 1.318 user 18.041 sys 19.401 real
calc: 3219322 calls 4.900 user 50.851 sys 56.356 real
done: 1 calls 0.000 user 0.000 sys 0.004 real
exec_no_coor: 1 calls 0.000 user 0.007 sys 0.000 real
execute: 1 calls 0.006 user 0.004 sys 5.683 real
fetch: 3219323 calls 0.358 user 16.535 sys 15.317 real
find_pairEnds: 28282 calls 0.234 user 0.099 sys 0.435 real
idle: 954 calls 0.021 user 0.096 sys 51.057 real
init: 1 calls 0.000 user 0.000 sys 0.006 real
markDup: 28282 calls 0.893 user 0.451 sys 1.908 real
vcfadvance: 28282 calls 0.020 user 0.151 sys 0.335 real
write: 3219323 calls 2.734 user 17.569 sys 19.132 real
overall: 509689856 mem 15.661 user 138.412 sys 6.708 real