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/ab/115b64305d060833379ba5675af81f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/da68d50c834af5dc5a0c657f919527/Sig_18_tissue.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/115b64305d060833379ba5675af81f/.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/4c/da68d50c834af5dc5a0c657f919527/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 0.2s, est remaining 4.0s, peak mem 78MB, user 0.3s, sys 4.9s, output queue size 31
progress 10% @chr2:83000001, elapsed 0.4s, est remaining 3.5s, peak mem 78MB, user 0.7s, sys 10.6s, output queue size 36
progress 15% @chr2:227000001, elapsed 0.6s, est remaining 3.3s, peak mem 78MB, user 0.9s, sys 16.0s, output queue size 27
progress 20% @chr3:170000001, elapsed 0.8s, est remaining 3.1s, peak mem 78MB, user 1.2s, sys 21.3s, output queue size 36
progress 25% @chr4:108000001, elapsed 0.9s, est remaining 2.8s, peak mem 78MB, user 1.5s, sys 26.9s, output queue size 23
progress 30% @chr5:86000001, elapsed 1.1s, est remaining 2.6s, peak mem 78MB, user 1.8s, sys 32.3s, output queue size 29
progress 35% @chr6:30000001, elapsed 1.3s, est remaining 2.4s, peak mem 78MB, user 2.0s, sys 37.5s, output queue size 35
progress 40% @chr7:64000001, elapsed 1.5s, est remaining 2.2s, peak mem 78MB, user 2.2s, sys 43.2s, output queue size 16
progress 45% @chr8:43000001, elapsed 1.7s, est remaining 2.1s, peak mem 78MB, user 2.5s, sys 48.6s, output queue size 31
progress 50% @chr9:40000001, elapsed 1.9s, est remaining 1.9s, peak mem 78MB, user 2.7s, sys 54.0s, output queue size 33
progress 55% @chr10:71000001, elapsed 2.0s, est remaining 1.7s, peak mem 78MB, user 3.1s, sys 59.3s, output queue size 35
progress 60% @chr11:114000001, elapsed 2.2s, est remaining 1.5s, peak mem 78MB, user 3.3s, sys 64.6s, output queue size 34
progress 65% @chr13:8000001, elapsed 2.4s, est remaining 1.3s, peak mem 78MB, user 3.6s, sys 70.0s, output queue size 32
progress 70% @chr14:71000001, elapsed 2.6s, est remaining 1.1s, peak mem 78MB, user 3.8s, sys 75.1s, output queue size 21
progress 75% @chr16:21000001, elapsed 2.8s, est remaining 0.9s, peak mem 78MB, user 4.1s, sys 80.3s, output queue size 28
progress 80% @chr18:4000001, elapsed 2.9s, est remaining 0.7s, peak mem 78MB, user 4.3s, sys 85.5s, output queue size 24
progress 85% @chr20:8000001, elapsed 3.1s, est remaining 0.5s, peak mem 78MB, user 4.5s, sys 90.7s, output queue size 28
progress 90% @chrX:29000001, elapsed 3.4s, est remaining 0.4s, peak mem 93MB, user 5.2s, sys 95.8s, output queue size 114
progress 95% @chrY:30000001, elapsed 3.6s, est remaining 0.2s, peak mem 129MB, user 5.6s, sys 103.3s, output queue size 271
progress 100% @chr21:41000001, elapsed 4.0s, est remaining 0.0s, peak mem 156MB, user 6.2s, sys 111.8s, 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: 49121345
reads: 1001838
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.031 user 0.010 sys 0.049 real
VcfLineRecordHelper::sort: 30 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.504 user 25.601 sys 24.002 real
calc: 3219322 calls 0.265 user 20.667 sys 13.887 real
done: 1 calls 0.031 user 0.010 sys 0.049 real
execute: 1 calls 0.001 user 0.002 sys 3.991 real
fetch: 3219322 calls 0.185 user 20.818 sys 13.957 real
idle: 83 calls 0.007 user 0.017 sys 35.403 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 214065152 mem 6.346 user 112.331 sys 5.049 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% @chr1:166000001, elapsed 0.1s, est remaining 2.3s, peak mem 183MB, user 0.3s, sys 2.9s, output queue size 12
progress 10% @chr2:76000001, elapsed 0.2s, est remaining 2.0s, peak mem 210MB, user 0.5s, sys 5.5s, output queue size 15
progress 15% @chr2:237000001, elapsed 0.3s, est remaining 1.7s, peak mem 228MB, user 0.8s, sys 8.1s, output queue size 24
progress 20% @chr3:154000001, elapsed 0.4s, est remaining 1.6s, peak mem 243MB, user 1.1s, sys 10.7s, output queue size 13
progress 25% @chr4:116000001, elapsed 0.5s, est remaining 1.5s, peak mem 249MB, user 1.3s, sys 13.2s, output queue size 11
progress 30% @chr5:89000001, elapsed 0.6s, est remaining 1.4s, peak mem 258MB, user 1.6s, sys 15.8s, output queue size 14
progress 35% @chr6:67000001, elapsed 0.7s, est remaining 1.2s, peak mem 258MB, user 1.7s, sys 18.4s, output queue size 19
progress 40% @chr7:55000001, elapsed 0.8s, est remaining 1.1s, peak mem 264MB, user 1.9s, sys 21.0s, output queue size 19
progress 45% @chr8:58000001, elapsed 0.9s, est remaining 1.0s, peak mem 264MB, user 2.2s, sys 23.6s, output queue size 8
progress 50% @chr9:65000001, elapsed 1.0s, est remaining 1.0s, peak mem 267MB, user 2.5s, sys 28.0s, output queue size 30
progress 55% @chr10:94000001, elapsed 1.2s, est remaining 1.0s, peak mem 267MB, user 2.8s, sys 33.0s, output queue size 18
progress 60% @chr11:123000001, elapsed 1.3s, est remaining 0.9s, peak mem 270MB, user 3.0s, sys 36.9s, output queue size 8
progress 65% @chr13:14000001, elapsed 1.4s, est remaining 0.8s, peak mem 273MB, user 3.2s, sys 39.5s, output queue size 17
progress 70% @chr14:87000001, elapsed 1.6s, est remaining 0.7s, peak mem 276MB, user 3.5s, sys 44.4s, output queue size 23
progress 75% @chr16:6000001, elapsed 1.8s, est remaining 0.6s, peak mem 276MB, user 3.7s, sys 49.6s, output queue size 16
progress 80% @chr17:58000001, elapsed 1.9s, est remaining 0.5s, peak mem 276MB, user 4.0s, sys 54.8s, output queue size 26
progress 85% @chr20:8000001, elapsed 2.1s, est remaining 0.4s, peak mem 276MB, user 4.2s, sys 60.2s, output queue size 29
progress 90% @chrX:32000001, elapsed 2.4s, est remaining 0.3s, peak mem 486MB, user 6.9s, sys 64.2s, output queue size 114
progress 95% @chrY:21000001, elapsed 2.7s, est remaining 0.1s, peak mem 492MB, user 10.5s, sys 69.5s, output queue size 240
progress 100% @chr21:41000001, elapsed 3.7s, est remaining 0.0s, peak mem 501MB, user 13.4s, sys 76.0s, 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 6.12.88
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: 49121345
reads: 1001838
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 28282 calls 0.028 user 0.038 sys 0.060 real
MateInfoByVcf::load: 28282 calls 4.035 user 1.056 sys 4.071 real
MateInfoByVcf::parse_events: 28282 calls 3.975 user 0.916 sys 3.809 real
advance: 3219322 calls 1.116 user 9.768 sys 11.129 real
calc: 3219322 calls 4.357 user 27.602 sys 32.571 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 0.002 user 0.001 sys 3.708 real
fetch: 3219323 calls 0.340 user 8.614 sys 9.293 real
find_pairEnds: 28282 calls 0.158 user 0.017 sys 0.378 real
idle: 996 calls 0.043 user 0.104 sys 53.607 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 28282 calls 0.768 user 0.167 sys 1.431 real
vcfadvance: 28282 calls 0.012 user 0.093 sys 0.129 real
write: 3219323 calls 2.414 user 9.237 sys 11.558 real
overall: 525422592 mem 13.915 user 77.148 sys 4.726 real