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/75/0d3ebec96b16ea3cbbed40ad085a9f/HCC1395_BL.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/7136949d40d953659fd7a38775cd98/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/7136949d40d953659fd7a38775cd98/.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/75/0d3ebec96b16ea3cbbed40ad085a9f/HCC1395_BL.bai
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i HCC1395_BL.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info HCC1395_BL.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 1.6s, output queue size 6
progress 10% @chr2:71000001, elapsed 0.1s, est remaining 1.2s, peak mem 81MB, user 0.4s, sys 3.4s, output queue size 2
progress 15% @chr2:233000001, elapsed 0.2s, est remaining 1.1s, peak mem 81MB, user 0.7s, sys 5.1s, output queue size 2
progress 20% @chr3:154000001, elapsed 0.3s, est remaining 1.1s, peak mem 81MB, user 0.9s, sys 6.8s, output queue size 1
progress 25% @chr4:115000001, elapsed 0.3s, est remaining 1.0s, peak mem 81MB, user 1.2s, sys 8.5s, output queue size 4
progress 30% @chr5:87000001, elapsed 0.4s, est remaining 0.9s, peak mem 81MB, user 1.4s, sys 10.3s, output queue size 16
progress 35% @chr6:65000001, elapsed 0.5s, est remaining 0.8s, peak mem 81MB, user 1.6s, sys 12.0s, output queue size 8
progress 40% @chr7:55000001, elapsed 0.5s, est remaining 0.8s, peak mem 81MB, user 1.9s, sys 13.6s, output queue size 13
progress 45% @chr8:58000001, elapsed 0.6s, est remaining 0.7s, peak mem 81MB, user 2.3s, sys 15.3s, output queue size 19
progress 50% @chr9:75000001, elapsed 0.6s, est remaining 0.6s, peak mem 81MB, user 2.5s, sys 17.0s, output queue size 22
progress 55% @chr10:96000001, elapsed 0.7s, est remaining 0.6s, peak mem 81MB, user 2.9s, sys 18.7s, output queue size 2
progress 60% @chr11:122000001, elapsed 0.8s, est remaining 0.5s, peak mem 81MB, user 3.1s, sys 20.4s, output queue size 22
progress 65% @chr13:15000001, elapsed 0.8s, est remaining 0.5s, peak mem 81MB, user 3.4s, sys 22.1s, output queue size 18
progress 70% @chr14:63000001, elapsed 0.9s, est remaining 0.4s, peak mem 81MB, user 3.6s, sys 23.9s, output queue size 15
progress 75% @chr16:10000001, elapsed 1.0s, est remaining 0.3s, peak mem 81MB, user 3.9s, sys 25.7s, output queue size 13
progress 80% @chr18:1, elapsed 1.0s, est remaining 0.3s, peak mem 81MB, user 4.3s, sys 27.3s, output queue size 8
progress 85% @chr20:22000001, elapsed 1.1s, est remaining 0.2s, peak mem 81MB, user 4.3s, sys 29.4s, output queue size 2
progress 90% @chrX:32000001, elapsed 1.2s, est remaining 0.1s, peak mem 118MB, user 4.9s, sys 31.0s, output queue size 114
progress 95% @chrY:31000001, elapsed 1.3s, est remaining 0.1s, peak mem 147MB, user 5.2s, sys 33.3s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.6s, est remaining 0.0s, peak mem 187MB, user 5.8s, sys 36.4s, 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: 50411643
reads: 1001089
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.031 user 0.001 sys 0.044 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.201 user 7.640 sys 9.075 real
calc: 3219322 calls 0.271 user 5.792 sys 6.109 real
done: 1 calls 0.031 user 0.001 sys 0.044 real
execute: 1 calls 0.001 user 0.010 sys 1.565 real
fetch: 3219322 calls 0.434 user 5.747 sys 6.029 real
idle: 75 calls 0.017 user 0.026 sys 36.466 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 235917312 mem 6.002 user 36.908 sys 2.629 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i HCC1395_BL.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info HCC1395_BL.md.score --metrics HCC1395_BL.md.metrics HCC1395_BL.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:160000001, elapsed 0.1s, est remaining 2.0s, peak mem 195MB, user 0.4s, sys 2.5s, output queue size 20
progress 10% @chr2:76000001, elapsed 0.2s, est remaining 1.7s, peak mem 223MB, user 0.7s, sys 4.8s, output queue size 14
progress 15% @chr2:235000001, elapsed 0.3s, est remaining 1.6s, peak mem 249MB, user 0.9s, sys 7.1s, output queue size 11
progress 20% @chr3:154000001, elapsed 0.4s, est remaining 1.4s, peak mem 261MB, user 1.1s, sys 9.4s, output queue size 16
progress 25% @chr4:117000001, elapsed 0.4s, est remaining 1.3s, peak mem 264MB, user 1.3s, sys 11.8s, output queue size 17
progress 30% @chr5:87000001, elapsed 0.5s, est remaining 1.2s, peak mem 270MB, user 1.6s, sys 14.0s, output queue size 17
progress 35% @chr6:65000001, elapsed 0.6s, est remaining 1.1s, peak mem 283MB, user 1.8s, sys 16.3s, output queue size 23
progress 40% @chr7:57000001, elapsed 0.7s, est remaining 1.0s, peak mem 289MB, user 2.0s, sys 18.6s, output queue size 21
progress 45% @chr8:37000001, elapsed 0.8s, est remaining 0.9s, peak mem 291MB, user 2.2s, sys 20.9s, output queue size 20
progress 50% @chr9:74000001, elapsed 0.8s, est remaining 0.8s, peak mem 292MB, user 2.5s, sys 23.2s, output queue size 22
progress 55% @chr10:94000001, elapsed 0.9s, est remaining 0.8s, peak mem 295MB, user 2.6s, sys 25.6s, output queue size 22
progress 60% @chr11:122000001, elapsed 1.0s, est remaining 0.7s, peak mem 298MB, user 2.8s, sys 28.0s, output queue size 23
progress 65% @chr13:16000001, elapsed 1.1s, est remaining 0.6s, peak mem 304MB, user 3.0s, sys 30.5s, output queue size 14
progress 70% @chr14:61000001, elapsed 1.2s, est remaining 0.5s, peak mem 307MB, user 3.3s, sys 32.9s, output queue size 20
progress 75% @chr16:14000001, elapsed 1.3s, est remaining 0.4s, peak mem 309MB, user 3.6s, sys 35.2s, output queue size 6
progress 80% @chr18:1, elapsed 1.4s, est remaining 0.3s, peak mem 310MB, user 3.8s, sys 37.7s, output queue size 3
progress 85% @chr20:22000001, elapsed 1.4s, est remaining 0.3s, peak mem 310MB, user 4.0s, sys 40.2s, output queue size 12
progress 90% @chrX:41000001, elapsed 1.6s, est remaining 0.2s, peak mem 535MB, user 5.9s, sys 41.5s, output queue size 114
progress 95% @chrY:39000001, elapsed 1.7s, est remaining 0.1s, peak mem 555MB, user 7.4s, sys 42.6s, output queue size 276
progress 100% @chr21:41000001, elapsed 2.9s, est remaining 0.0s, peak mem 583MB, user 12.9s, sys 44.4s, output queue size 3664
library HCC1395_BL:
chimeric_paired 873
duped 146553
duped_chimeric_paired 2
duped_paired 146548
duped_unpaired 5
optical_dup 4835
paired 999974
reads 1001089
secondary_supplementary 1097
unmapped 9
unpaired 9
optical dup clusters 4702, maxdup 7, total optical dup pairs 4835
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: 50411643
reads: 1001089
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 25531 calls 0.000 user 0.002 sys 0.022 real
MateInfoByVcf::load: 25531 calls 4.224 user 0.665 sys 3.842 real
MateInfoByVcf::parse_events: 25531 calls 4.187 user 0.643 sys 3.740 real
advance: 3219322 calls 1.223 user 5.385 sys 7.044 real
calc: 3219322 calls 4.194 user 15.828 sys 20.846 real
done: 1 calls 0.000 user 0.000 sys 0.003 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.002 user 0.001 sys 2.898 real
fetch: 3219322 calls 0.419 user 5.302 sys 6.042 real
find_pairEnds: 25531 calls 0.207 user 0.040 sys 0.326 real
idle: 1816 calls 0.113 user 0.184 sys 60.469 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 25531 calls 0.796 user 0.067 sys 1.258 real
vcfadvance: 25531 calls 0.013 user 0.073 sys 0.027 real
write: 3219322 calls 2.353 user 5.518 sys 7.655 real
overall: 612126720 mem 13.755 user 45.552 sys 3.920 real