Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/beta/Homo_sapiens_assembly38.known_indels.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/4595d57f2512c3edbf9d75d6f729ae/HCC1395_tumor.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/af0c565907198621c40991bd318828/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/beta/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/af0c565907198621c40991bd318828/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/4595d57f2512c3edbf9d75d6f729ae/HCC1395_tumor.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/a07cd5c8ddec0b91182b22597ebc21/HCC1395_tumor.table
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz
==> STAGING COMPLETE (13 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -r Homo_sapiens_assembly38.fasta -i HCC1395_tumor.md.bam --read_filter QualCalFilter,table=HCC1395_tumor.table,indel=false --algo QualCal -k dbsnp_146.hg38.vcf.gz -k Mills_and_1000G_gold_standard.indels.hg38.vcf.gz -k Homo_sapiens_assembly38.known_indels.vcf.gz HCC1395_tumor.table.post --algo ReadWriter HCC1395_tumor.recalibrated.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:162000001, elapsed 0.1s, est remaining 2.4s, peak mem 271MB, user 0.3s, sys 3.1s, output queue size 22
progress 10% @chr2:56000001, elapsed 0.2s, est remaining 2.1s, peak mem 442MB, user 0.5s, sys 6.0s, output queue size 33
progress 15% @chr2:231000001, elapsed 0.3s, est remaining 1.9s, peak mem 598MB, user 0.7s, sys 9.0s, output queue size 14
progress 20% @chr3:154000001, elapsed 0.4s, est remaining 1.7s, peak mem 697MB, user 0.9s, sys 11.8s, output queue size 14
progress 25% @chr4:117000001, elapsed 0.5s, est remaining 1.6s, peak mem 799MB, user 1.1s, sys 14.7s, output queue size 20
progress 30% @chr5:58000001, elapsed 0.6s, est remaining 1.5s, peak mem 835MB, user 1.3s, sys 17.4s, output queue size 28
progress 35% @chr6:57000001, elapsed 0.7s, est remaining 1.3s, peak mem 880MB, user 1.5s, sys 20.1s, output queue size 17
progress 40% @chr7:51000001, elapsed 0.9s, est remaining 1.3s, peak mem 919MB, user 1.8s, sys 23.9s, output queue size 13
progress 45% @chr8:50000001, elapsed 1.0s, est remaining 1.3s, peak mem 1036MB, user 2.2s, sys 28.6s, output queue size 8
progress 50% @chr9:55000001, elapsed 1.2s, est remaining 1.2s, peak mem 1147MB, user 2.6s, sys 34.6s, output queue size 34
progress 55% @chr10:91000001, elapsed 1.5s, est remaining 1.2s, peak mem 1201MB, user 3.0s, sys 41.2s, output queue size 44
progress 60% @chr11:108000001, elapsed 1.7s, est remaining 1.1s, peak mem 1243MB, user 3.3s, sys 48.0s, output queue size 15
progress 65% @chr13:36000001, elapsed 1.9s, est remaining 1.0s, peak mem 1315MB, user 3.6s, sys 54.6s, output queue size 13
progress 70% @chr14:80000001, elapsed 2.2s, est remaining 0.9s, peak mem 1372MB, user 4.0s, sys 61.4s, output queue size 26
progress 75% @chr16:11000001, elapsed 2.4s, est remaining 0.8s, peak mem 1411MB, user 4.3s, sys 68.5s, output queue size 10
progress 80% @chr18:15000001, elapsed 2.6s, est remaining 0.7s, peak mem 1453MB, user 4.8s, sys 75.6s, output queue size 12
progress 85% @chr20:14000001, elapsed 2.9s, est remaining 0.5s, peak mem 1564MB, user 5.3s, sys 82.7s, output queue size 11
progress 90% @chrX:37000001, elapsed 3.3s, est remaining 0.4s, peak mem 2764MB, user 8.8s, sys 86.0s, output queue size 114
progress 95% @chrY:38000001, elapsed 3.6s, est remaining 0.2s, peak mem 2788MB, user 13.0s, sys 89.1s, output queue size 276
progress 100% @chr21:41000001, elapsed 6.1s, est remaining 0.0s, peak mem 2812MB, user 26.4s, sys 93.2s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: QualCal ReadWriter
license: sentieon:QualCal=31 sentieon:ReadWriter=31
input file size: 50813906
output file size: 81484554
reads: 1001320
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.004 user 0.004 sys 0.013 real
ReadQualCal::delayed_init: 1 calls 0.001 user 0.001 sys 0.019 real
ReadQualCal::init: 1 calls 0.009 user 0.001 sys 0.006 real
advance: 3219322 calls 1.501 user 12.576 sys 13.666 real
done: 1 calls 0.346 user 0.487 sys 0.838 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.006 user 0.002 sys 6.174 real
fetch: 3219322 calls 0.267 user 11.922 sys 10.607 real
fetch_reads: 3219322 calls 0.303 user 11.445 sys 10.718 real
fetch_ref: 11263 calls 0.026 user 0.046 sys 0.094 real
fetch_vcf: 11263 calls 1.171 user 0.095 sys 1.617 real
idle: 1900 calls 1.163 user 0.312 sys 123.004 real
init: 1 calls 0.001 user 0.001 sys 0.026 real
update: 11451 calls 6.441 user 1.207 sys 8.708 real
write: 3219322 calls 11.172 user 11.770 sys 22.984 real
overall: 2949619712 mem 30.768 user 94.957 sys 8.413 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 --algo QualCal --plot --before HCC1395_tumor.table --after HCC1395_tumor.table.post HCC1395_tumor.csv
This software is licensed to bgold@natera.com by Sentieon Inc.
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: QualCal
license: sentieon:QualCal=31
ReadQualCal::init: 2 calls 0.011 user 0.019 sys 0.025 real
done: 1 calls 0.029 user 0.021 sys 0.053 real
idle: 61 calls 0.002 user 0.000 sys 31.421 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 81944576 mem 0.052 user 0.057 sys 1.057 real