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/8d/8492cf98f0670739fbbe8fa56defc2/HCC1395_tumor.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/62db238db14198336783c99f5aeabe/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/62db238db14198336783c99f5aeabe/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/8492cf98f0670739fbbe8fa56defc2/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% @chr1:162000001, elapsed 0.1s, est remaining 1.2s, peak mem 81MB, user 0.2s, sys 1.5s, output queue size 25
progress 10% @chr2:73000001, elapsed 0.1s, est remaining 1.1s, peak mem 81MB, user 0.3s, sys 3.1s, output queue size 16
progress 15% @chr2:215000001, elapsed 0.2s, est remaining 1.0s, peak mem 81MB, user 0.5s, sys 4.7s, output queue size 20
progress 20% @chr3:133000001, elapsed 0.2s, est remaining 1.0s, peak mem 81MB, user 0.7s, sys 6.4s, output queue size 21
progress 25% @chr4:116000001, elapsed 0.3s, est remaining 0.9s, peak mem 81MB, user 0.8s, sys 8.1s, output queue size 5
progress 30% @chr5:87000001, elapsed 0.4s, est remaining 0.8s, peak mem 81MB, user 0.9s, sys 9.8s, output queue size 20
progress 35% @chr6:64000001, elapsed 0.4s, est remaining 0.8s, peak mem 81MB, user 1.0s, sys 11.5s, output queue size 1
progress 40% @chr7:55000001, elapsed 0.5s, est remaining 0.7s, peak mem 81MB, user 1.1s, sys 13.2s, output queue size 23
progress 45% @chr8:59000001, elapsed 0.5s, est remaining 0.7s, peak mem 81MB, user 1.2s, sys 14.8s, output queue size 6
progress 50% @chr9:74000001, elapsed 0.6s, est remaining 0.6s, peak mem 81MB, user 1.4s, sys 16.5s, output queue size 24
progress 55% @chr10:97000001, elapsed 0.7s, est remaining 0.5s, peak mem 81MB, user 1.5s, sys 18.2s, output queue size 13
progress 60% @chr11:124000001, elapsed 0.7s, est remaining 0.5s, peak mem 81MB, user 1.6s, sys 19.8s, output queue size 27
progress 65% @chr13:17000001, elapsed 0.8s, est remaining 0.4s, peak mem 81MB, user 1.8s, sys 21.5s, output queue size 12
progress 70% @chr14:62000001, elapsed 0.8s, est remaining 0.4s, peak mem 81MB, user 1.9s, sys 23.1s, output queue size 18
progress 75% @chr16:13000001, elapsed 0.9s, est remaining 0.3s, peak mem 81MB, user 2.1s, sys 24.8s, output queue size 15
progress 80% @chr18:1, elapsed 0.9s, est remaining 0.2s, peak mem 81MB, user 2.2s, sys 26.5s, output queue size 15
progress 85% @chr20:23000001, elapsed 1.0s, est remaining 0.2s, peak mem 81MB, user 2.3s, sys 28.3s, output queue size 12
progress 90% @chrX:34000001, elapsed 1.1s, est remaining 0.1s, peak mem 108MB, user 2.6s, sys 29.9s, output queue size 114
progress 95% @chrY:21000001, elapsed 1.2s, est remaining 0.1s, peak mem 144MB, user 3.1s, sys 31.8s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.4s, est remaining 0.0s, peak mem 171MB, user 3.9s, sys 35.8s, 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: 49784680
reads: 1001320
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.026 user 0.009 sys 0.047 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.407 user 7.452 sys 8.446 real
calc: 3219322 calls 0.362 user 5.661 sys 6.388 real
done: 1 calls 0.026 user 0.009 sys 0.047 real
execute: 1 calls 0.001 user 0.001 sys 1.441 real
fetch: 3219322 calls 0.342 user 5.784 sys 6.310 real
idle: 84 calls 0.004 user 0.017 sys 35.385 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 217899008 mem 4.011 user 36.306 sys 2.505 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% @chr1:152000001, elapsed 0.1s, est remaining 2.8s, peak mem 174MB, user 0.4s, sys 3.4s, output queue size 15
progress 10% @chr2:74000001, elapsed 0.3s, est remaining 2.3s, peak mem 189MB, user 0.8s, sys 6.6s, output queue size 45
progress 15% @chr2:219000001, elapsed 0.4s, est remaining 2.1s, peak mem 207MB, user 1.2s, sys 9.8s, output queue size 17
progress 20% @chr3:159000001, elapsed 0.5s, est remaining 2.0s, peak mem 216MB, user 1.5s, sys 13.0s, output queue size 23
progress 25% @chr4:122000001, elapsed 0.6s, est remaining 1.8s, peak mem 228MB, user 1.8s, sys 16.0s, output queue size 15
progress 30% @chr5:72000001, elapsed 0.7s, est remaining 1.6s, peak mem 234MB, user 2.0s, sys 19.1s, output queue size 14
progress 35% @chr6:47000001, elapsed 0.8s, est remaining 1.5s, peak mem 234MB, user 2.3s, sys 21.9s, output queue size 18
progress 40% @chr7:52000001, elapsed 0.9s, est remaining 1.4s, peak mem 237MB, user 2.5s, sys 24.8s, output queue size 3
progress 45% @chr8:57000001, elapsed 1.0s, est remaining 1.2s, peak mem 240MB, user 2.7s, sys 27.7s, output queue size 3
progress 50% @chr9:75000001, elapsed 1.1s, est remaining 1.1s, peak mem 246MB, user 2.9s, sys 30.6s, output queue size 16
progress 55% @chr10:93000001, elapsed 1.2s, est remaining 1.0s, peak mem 246MB, user 3.1s, sys 33.5s, output queue size 11
progress 60% @chr11:103000001, elapsed 1.3s, est remaining 0.9s, peak mem 249MB, user 3.2s, sys 36.9s, output queue size 20
progress 65% @chr13:38000001, elapsed 1.5s, est remaining 0.8s, peak mem 252MB, user 3.5s, sys 42.9s, output queue size 17
progress 70% @chr14:49000001, elapsed 1.8s, est remaining 0.8s, peak mem 258MB, user 3.9s, sys 49.3s, output queue size 18
progress 75% @chr16:4000001, elapsed 2.0s, est remaining 0.7s, peak mem 264MB, user 4.3s, sys 55.9s, output queue size 29
progress 80% @chr17:73000001, elapsed 2.2s, est remaining 0.6s, peak mem 264MB, user 4.7s, sys 62.6s, output queue size 31
progress 85% @chr20:47000001, elapsed 2.4s, est remaining 0.4s, peak mem 264MB, user 5.0s, sys 69.3s, output queue size 49
progress 90% @chrX:39000001, elapsed 2.7s, est remaining 0.3s, peak mem 480MB, user 7.8s, sys 73.5s, output queue size 114
progress 95% @chrY:50000001, elapsed 3.0s, est remaining 0.2s, peak mem 519MB, user 10.6s, sys 78.3s, output queue size 271
progress 100% @chr21:41000001, elapsed 3.9s, est remaining 0.0s, peak mem 531MB, user 14.8s, sys 85.0s, 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 384
algo: Dedup
license: sentieon:Dedup=31
input file size: 49784680
reads: 1001320
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 23378 calls 0.002 user 0.024 sys 0.053 real
MateInfoByVcf::load: 23378 calls 4.092 user 1.186 sys 4.184 real
MateInfoByVcf::parse_events: 23378 calls 4.046 user 1.043 sys 3.941 real
advance: 3219322 calls 1.472 user 10.984 sys 12.582 real
calc: 3219322 calls 4.909 user 31.225 sys 36.694 real
done: 1 calls 0.000 user 0.001 sys 0.003 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.005 user 0.000 sys 3.951 real
fetch: 3219322 calls 0.575 user 10.255 sys 10.614 real
find_pairEnds: 23378 calls 0.203 user 0.019 sys 0.391 real
idle: 892 calls 0.128 user 0.139 sys 48.438 real
init: 1 calls 0.005 user 0.000 sys 0.006 real
markDup: 23378 calls 0.943 user 0.182 sys 1.618 real
vcfadvance: 23378 calls 0.009 user 0.134 sys 0.131 real
write: 3219322 calls 2.659 user 10.414 sys 13.029 real
overall: 556949504 mem 15.496 user 86.477 sys 4.926 real