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/7d/a67d01832f5abee7768cf1df08fa7d/HCC1395_tumor.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/50dd12f94eeb22331190484c74ad72/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/50dd12f94eeb22331190484c74ad72/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/a67d01832f5abee7768cf1df08fa7d/HCC1395_tumor.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i HCC1395_tumor.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info HCC1395_tumor.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:159000001, elapsed 0.1s, est remaining 1.4s, peak mem 81MB, user 0.2s, sys 1.7s, output queue size 10
progress 10% @chr2:76000001, elapsed 0.1s, est remaining 1.3s, peak mem 81MB, user 0.3s, sys 3.6s, output queue size 28
progress 15% @chr2:236000001, elapsed 0.2s, est remaining 1.2s, peak mem 81MB, user 0.5s, sys 5.4s, output queue size 7
progress 20% @chr3:153000001, elapsed 0.3s, est remaining 1.1s, peak mem 81MB, user 0.6s, sys 7.3s, output queue size 12
progress 25% @chr4:115000001, elapsed 0.3s, est remaining 1.0s, peak mem 81MB, user 0.7s, sys 9.2s, output queue size 10
progress 30% @chr5:87000001, elapsed 0.4s, est remaining 0.9s, peak mem 81MB, user 0.8s, sys 11.1s, output queue size 11
progress 35% @chr6:66000001, elapsed 0.5s, est remaining 0.9s, peak mem 81MB, user 1.0s, sys 13.0s, output queue size 17
progress 40% @chr7:55000001, elapsed 0.5s, est remaining 0.8s, peak mem 81MB, user 1.1s, sys 14.8s, output queue size 12
progress 45% @chr8:58000001, elapsed 0.6s, est remaining 0.7s, peak mem 81MB, user 1.3s, sys 16.8s, output queue size 21
progress 50% @chr9:75000001, elapsed 0.7s, est remaining 0.7s, peak mem 81MB, user 1.4s, sys 18.7s, output queue size 4
progress 55% @chr10:91000001, elapsed 0.7s, est remaining 0.6s, peak mem 81MB, user 1.6s, sys 20.5s, output queue size 21
progress 60% @chr11:123000001, elapsed 0.8s, est remaining 0.5s, peak mem 81MB, user 1.7s, sys 22.4s, output queue size 5
progress 65% @chr13:15000001, elapsed 0.9s, est remaining 0.5s, peak mem 81MB, user 1.8s, sys 24.5s, output queue size 1
progress 70% @chr14:62000001, elapsed 0.9s, est remaining 0.4s, peak mem 81MB, user 1.9s, sys 26.4s, output queue size 3
progress 75% @chr16:15000001, elapsed 1.0s, est remaining 0.3s, peak mem 81MB, user 2.1s, sys 28.5s, output queue size 4
progress 80% @chr18:1000001, elapsed 1.1s, est remaining 0.3s, peak mem 81MB, user 2.2s, sys 30.6s, output queue size 5
progress 85% @chr20:24000001, elapsed 1.1s, est remaining 0.2s, peak mem 81MB, user 2.4s, sys 32.6s, output queue size 3
progress 90% @chrX:33000001, elapsed 1.3s, est remaining 0.1s, peak mem 124MB, user 2.9s, sys 34.5s, output queue size 114
progress 95% @chrY:13000001, elapsed 1.4s, est remaining 0.1s, peak mem 153MB, user 3.3s, sys 37.1s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.6s, est remaining 0.0s, peak mem 190MB, user 4.1s, sys 40.3s, 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: 49787509
reads: 1001320
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.029 user 0.010 sys 0.045 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.398 user 7.979 sys 9.597 real
calc: 3219322 calls 0.533 user 6.698 sys 6.967 real
done: 1 calls 0.029 user 0.010 sys 0.045 real
execute: 1 calls 0.005 user 0.003 sys 1.610 real
fetch: 3219322 calls 0.370 user 6.578 sys 6.979 real
idle: 74 calls 0.008 user 0.019 sys 35.695 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 236003328 mem 4.209 user 40.836 sys 2.668 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i HCC1395_tumor.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info HCC1395_tumor.md.score --metrics HCC1395_tumor.md.metrics HCC1395_tumor.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:165000001, elapsed 0.1s, est remaining 2.1s, peak mem 193MB, user 0.4s, sys 2.6s, output queue size 23
progress 10% @chr2:75000001, elapsed 0.2s, est remaining 1.8s, peak mem 225MB, user 0.5s, sys 5.1s, output queue size 13
progress 15% @chr2:207000001, elapsed 0.3s, est remaining 1.6s, peak mem 240MB, user 0.6s, sys 7.7s, output queue size 28
progress 20% @chr3:153000001, elapsed 0.4s, est remaining 1.5s, peak mem 246MB, user 0.9s, sys 10.1s, output queue size 11
progress 25% @chr4:89000001, elapsed 0.5s, est remaining 1.4s, peak mem 259MB, user 1.1s, sys 12.5s, output queue size 26
progress 30% @chr5:86000001, elapsed 0.5s, est remaining 1.3s, peak mem 259MB, user 1.3s, sys 14.9s, output queue size 16
progress 35% @chr6:65000001, elapsed 0.6s, est remaining 1.2s, peak mem 264MB, user 1.5s, sys 17.3s, output queue size 20
progress 40% @chr7:58000001, elapsed 0.7s, est remaining 1.1s, peak mem 268MB, user 1.7s, sys 19.8s, output queue size 22
progress 45% @chr8:60000001, elapsed 0.8s, est remaining 1.0s, peak mem 270MB, user 1.9s, sys 22.2s, output queue size 22
progress 50% @chr9:51000001, elapsed 0.9s, est remaining 0.9s, peak mem 274MB, user 2.2s, sys 24.7s, output queue size 22
progress 55% @chr10:95000001, elapsed 1.0s, est remaining 0.8s, peak mem 277MB, user 2.5s, sys 27.2s, output queue size 5
progress 60% @chr11:122000001, elapsed 1.1s, est remaining 0.7s, peak mem 277MB, user 2.7s, sys 29.7s, output queue size 19
progress 65% @chr13:15000001, elapsed 1.2s, est remaining 0.6s, peak mem 277MB, user 2.9s, sys 32.3s, output queue size 7
progress 70% @chr14:60000001, elapsed 1.3s, est remaining 0.5s, peak mem 282MB, user 3.1s, sys 35.0s, output queue size 1
progress 75% @chr16:13000001, elapsed 1.3s, est remaining 0.4s, peak mem 283MB, user 3.3s, sys 37.6s, output queue size 2
progress 80% @chr18:1, elapsed 1.4s, est remaining 0.4s, peak mem 285MB, user 3.6s, sys 40.2s, output queue size 4
progress 85% @chr20:22000001, elapsed 1.5s, est remaining 0.3s, peak mem 289MB, user 3.9s, sys 42.7s, output queue size 15
progress 90% @chrX:35000001, elapsed 1.7s, est remaining 0.2s, peak mem 522MB, user 5.7s, sys 44.3s, output queue size 114
progress 95% @chrY:37000001, elapsed 1.8s, est remaining 0.1s, peak mem 544MB, user 7.4s, sys 45.9s, output queue size 276
progress 100% @chr21:41000001, elapsed 2.9s, est remaining 0.0s, peak mem 571MB, user 12.5s, sys 47.8s, output queue size 3664
library HCC1395_tumor:
chimeric_paired 1295
duped 169120
duped_chimeric_paired 30
duped_paired 169118
duped_unpaired 2
optical_dup 5868
paired 999972
reads 1001320
secondary_supplementary 1340
unmapped 4
unpaired 4
optical dup clusters 5659, maxdup 4, total optical dup pairs 5868
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: 49787509
reads: 1001320
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 23378 calls 0.000 user 0.002 sys 0.025 real
MateInfoByVcf::load: 23378 calls 3.756 user 0.768 sys 3.554 real
MateInfoByVcf::parse_events: 23378 calls 3.729 user 0.738 sys 3.436 real
advance: 3219322 calls 1.086 user 5.806 sys 7.512 real
calc: 3219322 calls 4.073 user 17.457 sys 22.056 real
done: 1 calls 0.002 user 0.000 sys 0.003 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.001 user 0.001 sys 2.907 real
fetch: 3219322 calls 0.503 user 5.596 sys 6.486 real
find_pairEnds: 23378 calls 0.209 user 0.003 sys 0.336 real
idle: 2112 calls 0.202 user 0.169 sys 57.262 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 23378 calls 0.843 user 0.079 sys 1.320 real
vcfadvance: 23378 calls 0.008 user 0.058 sys 0.048 real
write: 3219322 calls 2.168 user 5.854 sys 7.968 real
overall: 598917120 mem 13.669 user 48.885 sys 3.928 real