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/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  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/8b/62db238db14198336783c99f5aeabe/HCC1395_tumor.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/02718e86eff8a2d9a131a839cf928e/.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/6c/02718e86eff8a2d9a131a839cf928e/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/62db238db14198336783c99f5aeabe/HCC1395_tumor.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/dd3340e1a6d8f1d6563a2b2e96de7b/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% @chr1:130000001, elapsed 0.2s, est remaining 4.4s, peak mem 268MB, user 1.0s, sys 5.2s, output queue size 31
progress 10% @chr2:71000001, elapsed 0.4s, est remaining 3.8s, peak mem 415MB, user 2.3s, sys 9.9s, output queue size 19
progress 15% @chr3:18000001, elapsed 0.6s, est remaining 3.6s, peak mem 553MB, user 3.9s, sys 14.9s, output queue size 16
progress 20% @chr3:136000001, elapsed 0.8s, est remaining 3.4s, peak mem 619MB, user 4.9s, sys 20.4s, output queue size 17
progress 25% @chr4:100000001, elapsed 1.1s, est remaining 3.2s, peak mem 724MB, user 5.9s, sys 25.8s, output queue size 23
progress 30% @chr5:106000001, elapsed 1.3s, est remaining 3.1s, peak mem 775MB, user 6.9s, sys 33.2s, output queue size 23
progress 35% @chr6:66000001, elapsed 1.6s, est remaining 3.0s, peak mem 811MB, user 7.8s, sys 41.6s, output queue size 27
progress 40% @chr7:33000001, elapsed 1.9s, est remaining 2.9s, peak mem 856MB, user 8.5s, sys 49.8s, output queue size 27
progress 45% @chr8:32000001, elapsed 2.2s, est remaining 2.7s, peak mem 1000MB, user 9.3s, sys 57.8s, output queue size 35
progress 50% @chr9:86000001, elapsed 2.5s, est remaining 2.5s, peak mem 1045MB, user 10.0s, sys 65.4s, output queue size 29
progress 55% @chr10:103000001, elapsed 2.8s, est remaining 2.3s, peak mem 1102MB, user 10.6s, sys 73.3s, output queue size 29
progress 60% @chr11:126000001, elapsed 3.0s, est remaining 2.0s, peak mem 1183MB, user 11.2s, sys 81.2s, output queue size 41
progress 65% @chr12:125000001, elapsed 3.3s, est remaining 1.8s, peak mem 1279MB, user 11.9s, sys 89.0s, output queue size 38
progress 70% @chr14:66000001, elapsed 3.6s, est remaining 1.5s, peak mem 1327MB, user 12.5s, sys 96.8s, output queue size 18
progress 75% @chr16:20000001, elapsed 3.8s, est remaining 1.3s, peak mem 1375MB, user 13.0s, sys 104.5s, output queue size 26
progress 80% @chr18:4000001, elapsed 4.1s, est remaining 1.0s, peak mem 1402MB, user 13.5s, sys 111.9s, output queue size 24
progress 85% @chr20:23000001, elapsed 4.3s, est remaining 0.8s, peak mem 1528MB, user 14.0s, sys 119.3s, output queue size 9
progress 90% @chrX:33000001, elapsed 4.8s, est remaining 0.5s, peak mem 2740MB, user 18.0s, sys 123.4s, output queue size 114
progress 95% @chrY:35000001, elapsed 5.1s, est remaining 0.3s, peak mem 2758MB, user 22.4s, sys 127.2s, output queue size 276
progress 100% @chr21:41000001, elapsed 7.7s, est remaining 0.0s, peak mem 2776MB, user 36.3s, sys 132.4s, 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: QualCal ReadWriter
license: sentieon:QualCal=31 sentieon:ReadWriter=31
input file size: 50813916
output file size: 81484560
reads: 1001320
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.000 user 0.000 sys 0.018 real
ReadQualCal::delayed_init: 1 calls 0.007 user 0.002 sys 0.020 real
ReadQualCal::init: 1 calls 0.009 user 0.001 sys 0.006 real
advance: 3219322 calls 2.353 user 16.492 sys 19.552 real
done: 1 calls 0.315 user 0.357 sys 0.675 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.006 user 0.000 sys 7.745 real
fetch: 3219322 calls 0.662 user 16.094 sys 17.112 real
fetch_reads: 3219322 calls 0.712 user 15.768 sys 17.203 real
fetch_ref: 11263 calls 0.075 user 0.063 sys 0.076 real
fetch_vcf: 11263 calls 1.167 user 0.147 sys 1.510 real
idle: 1870 calls 1.334 user 0.322 sys 95.232 real
init: 1 calls 0.009 user 0.002 sys 0.026 real
update: 11451 calls 6.757 user 1.858 sys 9.468 real
write: 3219322 calls 12.610 user 15.590 sys 28.968 real
overall: 2911862784 mem 40.918 user 133.862 sys 9.063 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 6.12.83
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: QualCal
license: sentieon:QualCal=31
ReadQualCal::init: 2 calls 0.009 user 0.001 sys 0.024 real
done: 1 calls 0.036 user 0.014 sys 0.055 real
idle: 61 calls 0.003 user 0.000 sys 31.366 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 81891328 mem 0.061 user 0.050 sys 1.053 real