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/39/bd1f289e8991118c4d4fa5b1d09054/HCC1395_BL.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/5e14d3c54516fce231a15f3d7307d2/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/5e14d3c54516fce231a15f3d7307d2/.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/39/bd1f289e8991118c4d4fa5b1d09054/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% @chr1:162000001, elapsed 0.1s, est remaining 1.6s, peak mem 78MB, user 0.2s, sys 1.9s, output queue size 25
progress 10% @chr2:75000001, elapsed 0.2s, est remaining 1.5s, peak mem 78MB, user 0.3s, sys 4.2s, output queue size 12
progress 15% @chr2:210000001, elapsed 0.2s, est remaining 1.4s, peak mem 78MB, user 0.6s, sys 6.4s, output queue size 25
progress 20% @chr3:153000001, elapsed 0.3s, est remaining 1.3s, peak mem 78MB, user 0.7s, sys 8.7s, output queue size 11
progress 25% @chr4:116000001, elapsed 0.4s, est remaining 1.2s, peak mem 78MB, user 0.8s, sys 10.9s, output queue size 13
progress 30% @chr5:86000001, elapsed 0.5s, est remaining 1.1s, peak mem 78MB, user 1.1s, sys 13.1s, output queue size 7
progress 35% @chr6:63000001, elapsed 0.6s, est remaining 1.0s, peak mem 78MB, user 1.2s, sys 15.3s, output queue size 3
progress 40% @chr7:54000001, elapsed 0.6s, est remaining 0.9s, peak mem 78MB, user 1.4s, sys 17.6s, output queue size 1
progress 45% @chr8:60000001, elapsed 0.7s, est remaining 0.9s, peak mem 78MB, user 1.6s, sys 19.8s, output queue size 3
progress 50% @chr9:73000001, elapsed 0.8s, est remaining 0.8s, peak mem 78MB, user 1.7s, sys 22.1s, output queue size 1
progress 55% @chr10:87000001, elapsed 0.9s, est remaining 0.7s, peak mem 78MB, user 1.9s, sys 24.9s, output queue size 8
progress 60% @chr11:120000001, elapsed 1.0s, est remaining 0.7s, peak mem 78MB, user 2.2s, sys 28.2s, output queue size 12
progress 65% @chr13:13000001, elapsed 1.1s, est remaining 0.6s, peak mem 78MB, user 2.4s, sys 31.5s, output queue size 22
progress 70% @chr14:58000001, elapsed 1.2s, est remaining 0.5s, peak mem 78MB, user 2.5s, sys 34.9s, output queue size 17
progress 75% @chr16:10000001, elapsed 1.3s, est remaining 0.4s, peak mem 78MB, user 2.8s, sys 38.1s, output queue size 15
progress 80% @chr17:82000001, elapsed 1.5s, est remaining 0.4s, peak mem 78MB, user 3.0s, sys 41.4s, output queue size 10
progress 85% @chr20:44000001, elapsed 1.6s, est remaining 0.3s, peak mem 78MB, user 3.3s, sys 44.6s, output queue size 9
progress 90% @chrX:27000001, elapsed 1.7s, est remaining 0.2s, peak mem 105MB, user 3.9s, sys 48.0s, output queue size 114
progress 95% @chrY:15000001, elapsed 1.9s, est remaining 0.1s, peak mem 123MB, user 4.2s, sys 52.4s, output queue size 276
progress 100% @chr21:41000001, elapsed 2.3s, est remaining 0.0s, peak mem 176MB, user 5.2s, sys 58.9s, 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: 50411650
reads: 1001089
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.014 user 0.028 sys 0.047 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.450 user 12.681 sys 14.286 real
calc: 3219322 calls 0.380 user 8.848 sys 9.873 real
done: 1 calls 0.014 user 0.028 sys 0.047 real
execute: 1 calls 0.003 user 0.005 sys 2.296 real
fetch: 3219322 calls 0.410 user 9.300 sys 9.878 real
idle: 73 calls 0.013 user 0.019 sys 37.133 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 222822400 mem 5.302 user 59.559 sys 3.358 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% @chr1:168000001, elapsed 0.1s, est remaining 2.4s, peak mem 177MB, user 0.3s, sys 3.1s, output queue size 13
progress 10% @chr2:74000001, elapsed 0.2s, est remaining 2.1s, peak mem 186MB, user 0.5s, sys 5.9s, output queue size 11
progress 15% @chr2:228000001, elapsed 0.3s, est remaining 1.8s, peak mem 216MB, user 0.8s, sys 8.7s, output queue size 7
progress 20% @chr3:153000001, elapsed 0.4s, est remaining 1.7s, peak mem 240MB, user 1.0s, sys 11.4s, output queue size 10
progress 25% @chr4:118000001, elapsed 0.5s, est remaining 1.6s, peak mem 246MB, user 1.3s, sys 14.2s, output queue size 8
progress 30% @chr5:88000001, elapsed 0.6s, est remaining 1.4s, peak mem 255MB, user 1.6s, sys 16.9s, output queue size 21
progress 35% @chr6:66000001, elapsed 0.7s, est remaining 1.3s, peak mem 258MB, user 1.8s, sys 19.7s, output queue size 5
progress 40% @chr7:55000001, elapsed 0.8s, est remaining 1.2s, peak mem 264MB, user 2.2s, sys 22.4s, output queue size 16
progress 45% @chr8:58000001, elapsed 0.9s, est remaining 1.1s, peak mem 270MB, user 2.5s, sys 25.0s, output queue size 6
progress 50% @chr9:64000001, elapsed 1.0s, est remaining 1.0s, peak mem 273MB, user 2.8s, sys 27.7s, output queue size 19
progress 55% @chr10:77000001, elapsed 1.1s, est remaining 0.9s, peak mem 273MB, user 3.0s, sys 30.6s, output queue size 18
progress 60% @chr11:117000001, elapsed 1.3s, est remaining 0.9s, peak mem 273MB, user 3.3s, sys 35.6s, output queue size 17
progress 65% @chr13:13000001, elapsed 1.5s, est remaining 0.8s, peak mem 276MB, user 3.7s, sys 40.8s, output queue size 18
progress 70% @chr14:65000001, elapsed 1.7s, est remaining 0.7s, peak mem 276MB, user 4.1s, sys 46.3s, output queue size 11
progress 75% @chr15:98000001, elapsed 1.9s, est remaining 0.6s, peak mem 276MB, user 4.8s, sys 51.8s, output queue size 17
progress 80% @chr18:26000001, elapsed 2.1s, est remaining 0.5s, peak mem 276MB, user 5.2s, sys 57.2s, output queue size 14
progress 85% @chr20:15000001, elapsed 2.3s, est remaining 0.4s, peak mem 279MB, user 5.5s, sys 64.0s, output queue size 25
progress 90% @chr21:37000001, elapsed 2.6s, est remaining 0.3s, peak mem 516MB, user 8.6s, sys 68.2s, output queue size 114
progress 95% @chrY:2000001, elapsed 2.9s, est remaining 0.2s, peak mem 528MB, user 11.7s, sys 74.2s, output queue size 271
progress 100% @chr21:41000001, elapsed 3.9s, est remaining 0.0s, peak mem 543MB, user 15.2s, sys 82.0s, 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 384
algo: Dedup
license: sentieon:Dedup=31
input file size: 50411650
reads: 1001089
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 25531 calls 0.009 user 0.023 sys 0.061 real
MateInfoByVcf::load: 25531 calls 4.210 user 1.076 sys 4.283 real
MateInfoByVcf::parse_events: 25531 calls 4.168 user 0.981 sys 4.017 real
advance: 3219322 calls 1.209 user 9.970 sys 11.952 real
calc: 3219322 calls 5.212 user 30.232 sys 35.225 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 0.004 sys 3.964 real
fetch: 3219322 calls 0.438 user 9.366 sys 10.544 real
find_pairEnds: 25531 calls 0.274 user 0.044 sys 0.382 real
idle: 1010 calls 0.054 user 0.122 sys 53.398 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 25531 calls 0.997 user 0.235 sys 1.561 real
vcfadvance: 25531 calls 0.018 user 0.115 sys 0.085 real
write: 3219322 calls 2.689 user 10.346 sys 12.335 real
overall: 569532416 mem 15.838 user 83.383 sys 4.990 real