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/d3/3949e7b078ae0a376049d2a073b63e/HCC1395_BL.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/500ff411ac93a70f78f4f5a487b4e0/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/500ff411ac93a70f78f4f5a487b4e0/.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/d3/3949e7b078ae0a376049d2a073b63e/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% @chr1:159000001, elapsed 0.1s, est remaining 1.2s, peak mem 78MB, user 0.2s, sys 1.4s, output queue size 2
progress 10% @chr2:74000001, elapsed 0.1s, est remaining 1.1s, peak mem 78MB, user 0.3s, sys 3.1s, output queue size 7
progress 15% @chr2:232000001, elapsed 0.2s, est remaining 1.0s, peak mem 78MB, user 0.4s, sys 4.8s, output queue size 3
progress 20% @chr3:153000001, elapsed 0.2s, est remaining 1.0s, peak mem 78MB, user 0.6s, sys 6.3s, output queue size 1
progress 25% @chr4:114000001, elapsed 0.3s, est remaining 0.9s, peak mem 78MB, user 0.7s, sys 8.1s, output queue size 1
progress 30% @chr5:85000001, elapsed 0.4s, est remaining 0.8s, peak mem 78MB, user 0.9s, sys 9.7s, output queue size 1
progress 35% @chr6:64000001, elapsed 0.4s, est remaining 0.8s, peak mem 78MB, user 1.0s, sys 11.4s, output queue size 1
progress 40% @chr7:57000001, elapsed 0.5s, est remaining 0.7s, peak mem 78MB, user 1.0s, sys 13.1s, output queue size 27
progress 45% @chr8:56000001, elapsed 0.5s, est remaining 0.7s, peak mem 78MB, user 1.2s, sys 14.7s, output queue size 1
progress 50% @chr9:76000001, elapsed 0.6s, est remaining 0.6s, peak mem 78MB, user 1.3s, sys 16.4s, output queue size 24
progress 55% @chr10:96000001, elapsed 0.7s, est remaining 0.5s, peak mem 78MB, user 1.4s, sys 18.1s, output queue size 16
progress 60% @chr11:124000001, elapsed 0.7s, est remaining 0.5s, peak mem 78MB, user 1.5s, sys 19.8s, output queue size 20
progress 65% @chr13:16000001, elapsed 0.8s, est remaining 0.4s, peak mem 78MB, user 1.6s, sys 21.5s, output queue size 14
progress 70% @chr14:64000001, elapsed 0.8s, est remaining 0.4s, peak mem 78MB, user 1.7s, sys 23.2s, output queue size 13
progress 75% @chr16:14000001, elapsed 0.9s, est remaining 0.3s, peak mem 78MB, user 1.8s, sys 24.9s, output queue size 11
progress 80% @chr17:78000001, elapsed 1.0s, est remaining 0.2s, peak mem 78MB, user 1.9s, sys 27.2s, output queue size 7
progress 85% @chr19:48000001, elapsed 1.1s, est remaining 0.2s, peak mem 78MB, user 2.2s, sys 30.9s, output queue size 33
progress 90% @chrX:26000001, elapsed 1.3s, est remaining 0.1s, peak mem 102MB, user 2.8s, sys 34.0s, output queue size 114
progress 95% @chrY:23000001, elapsed 1.4s, est remaining 0.1s, peak mem 132MB, user 3.1s, sys 38.6s, output queue size 271
progress 100% @chr21:41000001, elapsed 1.8s, est remaining 0.0s, peak mem 173MB, user 3.8s, sys 45.1s, 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 384
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 50411658
reads: 1001089
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.029 user 0.010 sys 0.049 real
VcfLineRecordHelper::sort: 28 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.212 user 9.809 sys 11.502 real
calc: 3219322 calls 0.361 user 7.000 sys 7.696 real
done: 1 calls 0.029 user 0.010 sys 0.049 real
execute: 1 calls 0.003 user 0.002 sys 1.772 real
fetch: 3219322 calls 0.398 user 7.065 sys 7.613 real
idle: 81 calls 0.004 user 0.029 sys 35.919 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 229523456 mem 3.931 user 45.808 sys 2.833 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% @chr1:163000001, elapsed 0.1s, est remaining 2.0s, peak mem 177MB, user 0.3s, sys 2.4s, output queue size 12
progress 10% @chr2:76000001, elapsed 0.2s, est remaining 1.7s, peak mem 192MB, user 0.6s, sys 4.6s, output queue size 24
progress 15% @chr2:235000001, elapsed 0.3s, est remaining 1.5s, peak mem 225MB, user 0.9s, sys 6.9s, output queue size 22
progress 20% @chr3:151000001, elapsed 0.3s, est remaining 1.4s, peak mem 246MB, user 1.1s, sys 9.1s, output queue size 9
progress 25% @chr4:116000001, elapsed 0.4s, est remaining 1.3s, peak mem 249MB, user 1.3s, sys 11.3s, output queue size 10
progress 30% @chr5:87000001, elapsed 0.5s, est remaining 1.2s, peak mem 258MB, user 1.5s, sys 13.6s, output queue size 3
progress 35% @chr6:65000001, elapsed 0.6s, est remaining 1.1s, peak mem 258MB, user 1.8s, sys 15.8s, output queue size 14
progress 40% @chr7:35000001, elapsed 0.7s, est remaining 1.0s, peak mem 261MB, user 2.0s, sys 18.1s, output queue size 20
progress 45% @chr8:56000001, elapsed 0.7s, est remaining 0.9s, peak mem 261MB, user 2.1s, sys 20.4s, output queue size 14
progress 50% @chr9:74000001, elapsed 0.8s, est remaining 0.8s, peak mem 267MB, user 2.4s, sys 22.6s, output queue size 18
progress 55% @chr10:95000001, elapsed 0.9s, est remaining 0.7s, peak mem 270MB, user 2.6s, sys 24.8s, output queue size 5
progress 60% @chr11:120000001, elapsed 1.1s, est remaining 0.7s, peak mem 270MB, user 2.9s, sys 28.7s, output queue size 20
progress 65% @chr13:13000001, elapsed 1.2s, est remaining 0.7s, peak mem 270MB, user 3.2s, sys 33.3s, output queue size 23
progress 70% @chr14:56000001, elapsed 1.4s, est remaining 0.6s, peak mem 273MB, user 3.6s, sys 37.9s, output queue size 17
progress 75% @chr16:7000001, elapsed 1.5s, est remaining 0.5s, peak mem 273MB, user 4.0s, sys 42.9s, output queue size 27
progress 80% @chr17:77000001, elapsed 1.8s, est remaining 0.4s, peak mem 273MB, user 4.3s, sys 49.2s, output queue size 20
progress 85% @chr20:20000001, elapsed 2.0s, est remaining 0.3s, peak mem 273MB, user 4.6s, sys 55.5s, output queue size 15
progress 90% @chrX:38000001, elapsed 2.3s, est remaining 0.3s, peak mem 504MB, user 7.5s, sys 59.8s, output queue size 114
progress 95% @chrY:28000001, elapsed 2.5s, est remaining 0.1s, peak mem 516MB, user 11.0s, sys 64.9s, output queue size 271
progress 100% @chr21:41000001, elapsed 3.6s, est remaining 0.0s, peak mem 531MB, user 14.0s, sys 71.7s, 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 384
algo: Dedup
license: sentieon:Dedup=31
input file size: 50411658
reads: 1001089
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 25531 calls 0.000 user 0.000 sys 0.059 real
MateInfoByVcf::load: 25531 calls 3.966 user 1.397 sys 4.298 real
MateInfoByVcf::parse_events: 25531 calls 3.928 user 1.312 sys 4.036 real
advance: 3219322 calls 1.285 user 8.573 sys 10.785 real
calc: 3219322 calls 4.744 user 25.985 sys 31.417 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 3.683 real
fetch: 3219322 calls 0.481 user 8.499 sys 9.214 real
find_pairEnds: 25531 calls 0.262 user 0.039 sys 0.389 real
idle: 1009 calls 0.070 user 0.149 sys 55.555 real
init: 1 calls 0.009 user 0.001 sys 0.006 real
markDup: 25531 calls 0.965 user 0.220 sys 1.592 real
vcfadvance: 25531 calls 0.007 user 0.120 sys 0.103 real
write: 3219322 calls 2.604 user 8.103 sys 11.214 real
overall: 556847104 mem 14.732 user 73.158 sys 4.692 real