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/cf/a6c88bdadde1e682b342af6ce922ac/HCC1395_BL.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/67e80fd959906794093fa1156b5149/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/67e80fd959906794093fa1156b5149/.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/cf/a6c88bdadde1e682b342af6ce922ac/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% @chr1:158000001, elapsed 0.1s, est remaining 1.4s, peak mem 81MB, user 0.2s, sys 1.5s, output queue size 3
progress 10% @chr2:71000001, elapsed 0.1s, est remaining 1.3s, peak mem 81MB, user 0.4s, sys 3.5s, output queue size 4
progress 15% @chr2:237000001, elapsed 0.2s, est remaining 1.2s, peak mem 81MB, user 0.5s, sys 5.4s, output queue size 9
progress 20% @chr3:130000001, elapsed 0.3s, est remaining 1.1s, peak mem 81MB, user 0.7s, sys 7.3s, output queue size 23
progress 25% @chr4:115000001, elapsed 0.3s, est remaining 1.0s, peak mem 81MB, user 0.9s, sys 9.2s, output queue size 17
progress 30% @chr5:88000001, elapsed 0.4s, est remaining 1.0s, peak mem 81MB, user 1.1s, sys 11.0s, output queue size 30
progress 35% @chr6:68000001, elapsed 0.5s, est remaining 0.9s, peak mem 81MB, user 1.3s, sys 13.0s, output queue size 30
progress 40% @chr7:56000001, elapsed 0.5s, est remaining 0.8s, peak mem 81MB, user 1.5s, sys 14.8s, output queue size 44
progress 45% @chr8:60000001, elapsed 0.6s, est remaining 0.8s, peak mem 81MB, user 1.7s, sys 17.0s, output queue size 7
progress 50% @chr9:75000001, elapsed 0.7s, est remaining 0.7s, peak mem 81MB, user 1.9s, sys 19.7s, output queue size 12
progress 55% @chr10:94000001, elapsed 0.8s, est remaining 0.7s, peak mem 81MB, user 2.2s, sys 22.4s, output queue size 2
progress 60% @chr11:123000001, elapsed 0.9s, est remaining 0.6s, peak mem 81MB, user 2.5s, sys 25.0s, output queue size 8
progress 65% @chr13:6000001, elapsed 1.0s, est remaining 0.5s, peak mem 81MB, user 2.8s, sys 27.6s, output queue size 13
progress 70% @chr14:64000001, elapsed 1.1s, est remaining 0.5s, peak mem 81MB, user 3.0s, sys 30.1s, output queue size 9
progress 75% @chr16:16000001, elapsed 1.2s, est remaining 0.4s, peak mem 81MB, user 3.2s, sys 32.5s, output queue size 6
progress 80% @chr17:74000001, elapsed 1.3s, est remaining 0.3s, peak mem 81MB, user 3.4s, sys 34.9s, output queue size 10
progress 85% @chr20:21000001, elapsed 1.3s, est remaining 0.2s, peak mem 81MB, user 3.6s, sys 36.9s, output queue size 17
progress 90% @chrX:25000001, elapsed 1.4s, est remaining 0.2s, peak mem 115MB, user 4.2s, sys 38.8s, output queue size 114
progress 95% @chrY:37000001, elapsed 1.5s, est remaining 0.1s, peak mem 148MB, user 4.6s, sys 41.3s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.9s, est remaining 0.0s, peak mem 187MB, user 5.4s, sys 45.0s, 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: 50411660
reads: 1001089
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.017 user 0.022 sys 0.043 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.576 user 9.210 sys 10.790 real
calc: 3219322 calls 0.588 user 7.370 sys 7.753 real
done: 1 calls 0.017 user 0.022 sys 0.043 real
execute: 1 calls 0.001 user 0.002 sys 1.864 real
fetch: 3219322 calls 0.413 user 6.751 sys 7.752 real
idle: 74 calls 0.010 user 0.021 sys 37.473 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 238530560 mem 5.551 user 45.608 sys 2.924 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.
No more license available for sentieon:Dedup
No more license available for sentieon:Dedup
No more license available for sentieon:Dedup
No more license available for sentieon:Dedup
No more license available for sentieon:Dedup
No more license available for sentieon:Dedup
No more license available for sentieon:Dedup
No more license available for sentieon:Dedup
No more license available for sentieon:Dedup
No more license available for sentieon:Dedup
No more license available for sentieon:Dedup
No more license available for sentieon:Dedup
No more license available for sentieon:Dedup
No more license available for sentieon:Dedup
No more license available for sentieon:Dedup
No more license available for sentieon:Dedup
No more license available for sentieon:Dedup
No more license available for sentieon:Dedup
No more license available for sentieon:Dedup
No more license available for sentieon:Dedup
No more license available for sentieon:Dedup
progress 5% @chr1:162000001, elapsed 1080.4s, est remaining 20527.0s, peak mem 190MB, user 0.4s, sys 5.4s, output queue size 2
progress 10% @chr2:71000001, elapsed 1080.5s, est remaining 9724.8s, peak mem 218MB, user 0.7s, sys 10.5s, output queue size 2
progress 15% @chr2:233000001, elapsed 1080.7s, est remaining 6124.0s, peak mem 241MB, user 1.0s, sys 15.5s, output queue size 2
progress 20% @chr3:153000001, elapsed 1080.9s, est remaining 4323.5s, peak mem 251MB, user 1.3s, sys 20.5s, output queue size 1
progress 25% @chr4:113000001, elapsed 1081.1s, est remaining 3243.2s, peak mem 263MB, user 1.7s, sys 25.4s, output queue size 4
progress 30% @chr5:86000001, elapsed 1081.2s, est remaining 2522.9s, peak mem 268MB, user 2.0s, sys 30.4s, output queue size 7
progress 35% @chr6:62000001, elapsed 1081.4s, est remaining 2008.3s, peak mem 275MB, user 2.2s, sys 35.4s, output queue size 3
progress 40% @chr7:54000001, elapsed 1081.6s, est remaining 1622.3s, peak mem 277MB, user 2.5s, sys 40.4s, output queue size 1
progress 45% @chr8:58000001, elapsed 1081.7s, est remaining 1322.1s, peak mem 281MB, user 2.7s, sys 45.4s, output queue size 1
progress 50% @chr9:72000001, elapsed 1081.9s, est remaining 1081.9s, peak mem 284MB, user 2.9s, sys 50.3s, output queue size 1
progress 55% @chr10:97000001, elapsed 1082.1s, est remaining 885.3s, peak mem 286MB, user 3.1s, sys 55.2s, output queue size 7
progress 60% @chr11:122000001, elapsed 1082.2s, est remaining 721.5s, peak mem 290MB, user 3.3s, sys 60.2s, output queue size 4
progress 65% @chr13:13000001, elapsed 1082.4s, est remaining 582.8s, peak mem 293MB, user 3.7s, sys 65.0s, output queue size 4
progress 70% @chr14:52000001, elapsed 1082.6s, est remaining 464.0s, peak mem 296MB, user 4.1s, sys 69.7s, output queue size 9
progress 75% @chr16:13000001, elapsed 1082.7s, est remaining 360.9s, peak mem 299MB, user 4.4s, sys 74.6s, output queue size 3
progress 80% @chr18:1, elapsed 1082.9s, est remaining 270.7s, peak mem 302MB, user 4.7s, sys 79.4s, output queue size 3
progress 85% @chr20:16000001, elapsed 1083.1s, est remaining 191.1s, peak mem 304MB, user 5.0s, sys 84.2s, output queue size 6
progress 90% @chrX:37000001, elapsed 1083.3s, est remaining 120.4s, peak mem 535MB, user 7.9s, sys 86.5s, output queue size 114
progress 95% @chrY:34000001, elapsed 1083.5s, est remaining 57.0s, peak mem 554MB, user 11.0s, sys 89.0s, output queue size 271
progress 100% @chr21:41000001, elapsed 1084.3s, est remaining 0.0s, peak mem 575MB, user 15.9s, sys 92.9s, 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 6.12.88
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: 50411660
reads: 1001089
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 25531 calls 0.013 user 0.006 sys 0.041 real
MateInfoByVcf::load: 25531 calls 5.268 user 0.878 sys 4.830 real
MateInfoByVcf::parse_events: 25531 calls 5.176 user 0.808 sys 4.644 real
advance: 3219322 calls 1.465 user 11.482 sys 13.548 real
calc: 3219322 calls 4.811 user 33.514 sys 39.595 real
done: 1 calls 0.004 user 0.000 sys 0.005 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.002 user 0.001 sys 1084.364 real
fetch: 3219322 calls 0.560 user 10.982 sys 11.922 real
find_pairEnds: 25531 calls 0.258 user 0.011 sys 0.420 real
idle: 1519 calls 0.574 user 0.299 sys 47.840 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 25531 calls 1.123 user 0.097 sys 1.683 real
vcfadvance: 25531 calls 0.010 user 0.115 sys 0.046 real
write: 3219322 calls 2.375 user 11.785 sys 13.676 real
overall: 602947584 mem 17.361 user 94.518 sys 1085.376 real