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/2b/7d4035cc5722d10d51e12becac59f4/HCC1395_tumor.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/bdb804792874396554f8c9a3111296/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/bdb804792874396554f8c9a3111296/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/7d4035cc5722d10d51e12becac59f4/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 1.3s, output queue size 1
progress 10% @chr2:72000001, elapsed 0.1s, est remaining 1.1s, peak mem 81MB, user 0.5s, sys 2.9s, output queue size 1
progress 15% @chr2:233000001, elapsed 0.2s, est remaining 1.0s, peak mem 81MB, user 0.7s, sys 4.5s, output queue size 2
progress 20% @chr3:153000001, elapsed 0.2s, est remaining 1.0s, peak mem 81MB, user 0.8s, sys 6.2s, output queue size 26
progress 25% @chr4:116000001, elapsed 0.3s, est remaining 0.9s, peak mem 81MB, user 1.0s, sys 7.8s, output queue size 21
progress 30% @chr5:86000001, elapsed 0.4s, est remaining 0.8s, peak mem 81MB, user 1.1s, sys 9.5s, output queue size 11
progress 35% @chr6:66000001, elapsed 0.4s, est remaining 0.8s, peak mem 81MB, user 1.2s, sys 11.1s, output queue size 10
progress 40% @chr7:56000001, elapsed 0.5s, est remaining 0.7s, peak mem 81MB, user 1.5s, sys 12.7s, output queue size 10
progress 45% @chr8:56000001, elapsed 0.5s, est remaining 0.7s, peak mem 81MB, user 1.6s, sys 14.3s, output queue size 15
progress 50% @chr9:72000001, elapsed 0.6s, est remaining 0.6s, peak mem 81MB, user 1.8s, sys 16.0s, output queue size 21
progress 55% @chr10:94000001, elapsed 0.7s, est remaining 0.5s, peak mem 81MB, user 2.0s, sys 17.7s, output queue size 1
progress 60% @chr11:120000001, elapsed 0.7s, est remaining 0.5s, peak mem 81MB, user 2.1s, sys 19.3s, output queue size 3
progress 65% @chr13:14000001, elapsed 0.8s, est remaining 0.4s, peak mem 81MB, user 2.2s, sys 21.1s, output queue size 1
progress 70% @chr14:62000001, elapsed 0.8s, est remaining 0.4s, peak mem 81MB, user 2.3s, sys 22.9s, output queue size 24
progress 75% @chr16:13000001, elapsed 0.9s, est remaining 0.3s, peak mem 81MB, user 2.4s, sys 24.6s, output queue size 13
progress 80% @chr18:1, elapsed 1.0s, est remaining 0.2s, peak mem 81MB, user 2.6s, sys 26.3s, output queue size 13
progress 85% @chr20:23000001, elapsed 1.0s, est remaining 0.2s, peak mem 81MB, user 2.8s, sys 28.0s, output queue size 4
progress 90% @chrX:32000001, elapsed 1.1s, est remaining 0.1s, peak mem 123MB, user 3.2s, sys 29.6s, output queue size 114
progress 95% @chrY:30000001, elapsed 1.2s, est remaining 0.1s, peak mem 154MB, user 3.5s, sys 31.9s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.5s, est remaining 0.0s, peak mem 185MB, user 4.3s, sys 34.7s, 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 192
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 49784679
reads: 1001320
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.013 user 0.024 sys 0.046 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.420 user 6.638 sys 8.724 real
calc: 3219322 calls 0.406 user 5.998 sys 6.167 real
done: 1 calls 0.013 user 0.024 sys 0.046 real
execute: 1 calls 0.004 user 0.003 sys 1.453 real
fetch: 3219322 calls 0.425 user 5.450 sys 6.096 real
idle: 74 calls 0.005 user 0.024 sys 35.919 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 228528128 mem 4.446 user 35.246 sys 2.517 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% @chr1:163000001, elapsed 0.1s, est remaining 2.1s, peak mem 196MB, user 0.3s, sys 2.5s, output queue size 14
progress 10% @chr2:74000001, elapsed 0.2s, est remaining 1.7s, peak mem 230MB, user 0.5s, sys 4.9s, output queue size 16
progress 15% @chr2:235000001, elapsed 0.3s, est remaining 1.6s, peak mem 247MB, user 0.7s, sys 7.2s, output queue size 24
progress 20% @chr3:152000001, elapsed 0.4s, est remaining 1.4s, peak mem 254MB, user 0.9s, sys 9.6s, output queue size 1
progress 25% @chr4:114000001, elapsed 0.4s, est remaining 1.3s, peak mem 257MB, user 1.1s, sys 11.8s, output queue size 26
progress 30% @chr5:85000001, elapsed 0.5s, est remaining 1.2s, peak mem 266MB, user 1.3s, sys 14.2s, output queue size 1
progress 35% @chr6:64000001, elapsed 0.6s, est remaining 1.1s, peak mem 275MB, user 1.5s, sys 16.6s, output queue size 1
progress 40% @chr7:55000001, elapsed 0.7s, est remaining 1.0s, peak mem 281MB, user 1.6s, sys 18.9s, output queue size 5
progress 45% @chr8:57000001, elapsed 0.8s, est remaining 0.9s, peak mem 286MB, user 1.8s, sys 21.3s, output queue size 14
progress 50% @chr9:73000001, elapsed 0.8s, est remaining 0.8s, peak mem 289MB, user 2.0s, sys 23.5s, output queue size 17
progress 55% @chr10:72000001, elapsed 0.9s, est remaining 0.8s, peak mem 289MB, user 2.2s, sys 25.9s, output queue size 23
progress 60% @chr11:121000001, elapsed 1.0s, est remaining 0.7s, peak mem 292MB, user 2.4s, sys 28.2s, output queue size 2
progress 65% @chr13:14000001, elapsed 1.1s, est remaining 0.6s, peak mem 293MB, user 2.7s, sys 30.4s, output queue size 2
progress 70% @chr14:61000001, elapsed 1.2s, est remaining 0.5s, peak mem 298MB, user 3.0s, sys 32.8s, output queue size 7
progress 75% @chr16:15000001, elapsed 1.3s, est remaining 0.4s, peak mem 302MB, user 3.2s, sys 35.4s, output queue size 13
progress 80% @chr18:1000001, elapsed 1.4s, est remaining 0.3s, peak mem 304MB, user 3.4s, sys 38.1s, output queue size 14
progress 85% @chr20:3000001, elapsed 1.5s, est remaining 0.3s, peak mem 307MB, user 3.6s, sys 40.9s, output queue size 19
progress 90% @chrX:35000001, elapsed 1.7s, est remaining 0.2s, peak mem 524MB, user 5.6s, sys 42.6s, output queue size 114
progress 95% @chrY:37000001, elapsed 1.8s, est remaining 0.1s, peak mem 545MB, user 7.5s, sys 44.4s, output queue size 276
progress 100% @chr21:41000001, elapsed 2.8s, est remaining 0.0s, peak mem 571MB, user 12.4s, sys 46.7s, 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 192
algo: Dedup
license: sentieon:Dedup=31
input file size: 49784679
reads: 1001320
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 23378 calls 0.013 user 0.000 sys 0.025 real
MateInfoByVcf::load: 23378 calls 3.859 user 0.696 sys 3.598 real
MateInfoByVcf::parse_events: 23378 calls 3.801 user 0.673 sys 3.479 real
advance: 3219322 calls 1.098 user 5.679 sys 7.428 real
calc: 3219322 calls 4.311 user 16.611 sys 21.725 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 0.001 user 0.003 sys 2.828 real
fetch: 3219322 calls 0.387 user 5.425 sys 6.208 real
find_pairEnds: 23378 calls 0.183 user 0.014 sys 0.338 real
idle: 1802 calls 0.143 user 0.174 sys 55.954 real
init: 1 calls 0.009 user 0.001 sys 0.006 real
markDup: 23378 calls 0.795 user 0.085 sys 1.325 real
vcfadvance: 23378 calls 0.004 user 0.036 sys 0.034 real
write: 3219322 calls 2.361 user 5.383 sys 7.992 real
overall: 599212032 mem 13.372 user 48.088 sys 3.856 real