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/33/c08b4b350456c5a6084efbe15873d2/HCC1395_tumor.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/4595d57f2512c3edbf9d75d6f729ae/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/4595d57f2512c3edbf9d75d6f729ae/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/c08b4b350456c5a6084efbe15873d2/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% @chr1:161000001, elapsed 0.1s, est remaining 1.2s, peak mem 81MB, user 0.3s, sys 1.4s, output queue size 3
progress 10% @chr2:71000001, elapsed 0.1s, est remaining 1.1s, peak mem 81MB, user 0.4s, sys 3.0s, output queue size 2
progress 15% @chr2:234000001, elapsed 0.2s, est remaining 1.1s, peak mem 81MB, user 0.5s, sys 4.8s, output queue size 3
progress 20% @chr3:151000001, elapsed 0.2s, est remaining 1.0s, peak mem 81MB, user 0.6s, sys 6.5s, output queue size 2
progress 25% @chr4:114000001, elapsed 0.3s, est remaining 0.9s, peak mem 81MB, user 0.8s, sys 8.2s, output queue size 21
progress 30% @chr5:87000001, elapsed 0.4s, est remaining 0.9s, peak mem 81MB, user 0.9s, sys 9.9s, output queue size 19
progress 35% @chr6:66000001, elapsed 0.4s, est remaining 0.8s, peak mem 81MB, user 1.0s, sys 11.6s, output queue size 13
progress 40% @chr7:57000001, elapsed 0.5s, est remaining 0.7s, peak mem 81MB, user 1.1s, sys 13.4s, output queue size 26
progress 45% @chr8:58000001, elapsed 0.5s, est remaining 0.7s, peak mem 81MB, user 1.2s, sys 15.2s, output queue size 5
progress 50% @chr9:73000001, elapsed 0.6s, est remaining 0.6s, peak mem 81MB, user 1.3s, sys 17.0s, output queue size 22
progress 55% @chr10:95000001, elapsed 0.7s, est remaining 0.5s, peak mem 81MB, user 1.4s, sys 18.7s, output queue size 20
progress 60% @chr11:123000001, elapsed 0.7s, est remaining 0.5s, peak mem 81MB, user 1.6s, sys 20.4s, output queue size 16
progress 65% @chr13:15000001, elapsed 0.8s, est remaining 0.4s, peak mem 81MB, user 1.6s, sys 22.2s, output queue size 18
progress 70% @chr14:61000001, elapsed 0.8s, est remaining 0.4s, peak mem 81MB, user 1.8s, sys 23.9s, output queue size 13
progress 75% @chr16:13000001, elapsed 0.9s, est remaining 0.3s, peak mem 81MB, user 1.9s, sys 25.7s, output queue size 11
progress 80% @chr17:74000001, elapsed 1.0s, est remaining 0.3s, peak mem 81MB, user 2.1s, sys 29.2s, output queue size 18
progress 85% @chr20:13000001, elapsed 1.2s, est remaining 0.2s, peak mem 81MB, user 2.3s, sys 33.7s, output queue size 12
progress 90% @chrX:19000001, elapsed 1.4s, est remaining 0.2s, peak mem 93MB, user 3.0s, sys 37.5s, output queue size 114
progress 95% @chrY:25000001, elapsed 1.6s, est remaining 0.1s, peak mem 129MB, user 3.3s, sys 42.7s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.9s, est remaining 0.0s, peak mem 171MB, user 4.0s, sys 50.0s, 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 384
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 49784677
reads: 1001320
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.038 user 0.000 sys 0.049 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.280 user 11.974 sys 13.209 real
calc: 3219322 calls 0.434 user 7.612 sys 8.119 real
done: 1 calls 0.038 user 0.000 sys 0.049 real
execute: 1 calls 0.002 user 0.006 sys 1.930 real
fetch: 3219322 calls 0.296 user 7.573 sys 8.027 real
idle: 81 calls 0.007 user 0.022 sys 35.928 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 214921216 mem 4.150 user 50.609 sys 2.994 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% @chr1:158000001, elapsed 0.1s, est remaining 2.0s, peak mem 174MB, user 0.3s, sys 2.5s, output queue size 15
progress 10% @chr2:76000001, elapsed 0.2s, est remaining 1.7s, peak mem 189MB, user 0.5s, sys 4.7s, output queue size 18
progress 15% @chr2:235000001, elapsed 0.3s, est remaining 1.5s, peak mem 210MB, user 0.7s, sys 7.0s, output queue size 19
progress 20% @chr3:153000001, elapsed 0.3s, est remaining 1.4s, peak mem 222MB, user 0.8s, sys 9.3s, output queue size 14
progress 25% @chr4:117000001, elapsed 0.4s, est remaining 1.3s, peak mem 231MB, user 1.0s, sys 11.5s, output queue size 29
progress 30% @chr5:59000001, elapsed 0.5s, est remaining 1.2s, peak mem 237MB, user 1.1s, sys 13.9s, output queue size 27
progress 35% @chr6:65000001, elapsed 0.6s, est remaining 1.1s, peak mem 240MB, user 1.2s, sys 16.3s, output queue size 18
progress 40% @chr7:55000001, elapsed 0.7s, est remaining 1.0s, peak mem 240MB, user 1.4s, sys 18.6s, output queue size 19
progress 45% @chr8:58000001, elapsed 0.7s, est remaining 0.9s, peak mem 246MB, user 1.6s, sys 20.9s, output queue size 3
progress 50% @chr9:65000001, elapsed 0.9s, est remaining 0.9s, peak mem 249MB, user 1.9s, sys 24.8s, output queue size 27
progress 55% @chr10:93000001, elapsed 1.0s, est remaining 0.9s, peak mem 249MB, user 2.3s, sys 29.1s, output queue size 13
progress 60% @chr11:122000001, elapsed 1.1s, est remaining 0.8s, peak mem 249MB, user 2.6s, sys 32.2s, output queue size 13
progress 65% @chr13:17000001, elapsed 1.2s, est remaining 0.7s, peak mem 252MB, user 2.8s, sys 34.6s, output queue size 14
progress 70% @chr14:82000001, elapsed 1.3s, est remaining 0.6s, peak mem 252MB, user 3.0s, sys 37.1s, output queue size 21
progress 75% @chr16:6000001, elapsed 1.5s, est remaining 0.5s, peak mem 255MB, user 3.3s, sys 43.1s, output queue size 36
progress 80% @chr17:76000001, elapsed 1.8s, est remaining 0.4s, peak mem 255MB, user 3.6s, sys 49.8s, output queue size 27
progress 85% @chr20:48000001, elapsed 2.0s, est remaining 0.4s, peak mem 261MB, user 3.8s, sys 56.4s, output queue size 19
progress 90% @chrX:46000001, elapsed 2.3s, est remaining 0.3s, peak mem 489MB, user 6.4s, sys 60.7s, output queue size 114
progress 95% @chrY:50000001, elapsed 2.5s, est remaining 0.1s, peak mem 510MB, user 8.9s, sys 66.1s, output queue size 271
progress 100% @chr21:41000001, elapsed 3.4s, est remaining 0.0s, peak mem 525MB, user 12.9s, sys 71.8s, 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 6.12.88
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: 49784677
reads: 1001320
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 23378 calls 0.009 user 0.013 sys 0.055 real
MateInfoByVcf::load: 23378 calls 3.763 user 1.171 sys 3.877 real
MateInfoByVcf::parse_events: 23378 calls 3.641 user 1.052 sys 3.631 real
advance: 3219322 calls 1.200 user 8.650 sys 10.593 real
calc: 3219322 calls 4.619 user 26.694 sys 31.201 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 0.005 user 0.002 sys 3.519 real
fetch: 3219322 calls 0.357 user 8.741 sys 9.265 real
find_pairEnds: 23378 calls 0.242 user 0.065 sys 0.377 real
idle: 966 calls 0.064 user 0.096 sys 51.451 real
init: 1 calls 0.010 user 0.000 sys 0.007 real
markDup: 23378 calls 0.997 user 0.262 sys 1.511 real
vcfadvance: 23378 calls 0.013 user 0.069 sys 0.065 real
write: 3219322 calls 2.630 user 9.193 sys 11.189 real
overall: 550551552 mem 13.654 user 73.085 sys 4.528 real