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-rnd-pltf-dev-nextflow-scratch-01/work/56/13741b9a5c47905c2325e589b6cf85/HCC1395_BL.md.bam
  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/70/0b29acedfeb470aac125a95a0e0fb7/HCC1395_BL.table
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/2c338fb82705e4e0b4e7a512d35d58/.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/45/2c338fb82705e4e0b4e7a512d35d58/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/13741b9a5c47905c2325e589b6cf85/HCC1395_BL.md.bam.bai
  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_BL.md.bam --read_filter QualCalFilter,table=HCC1395_BL.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_BL.table.post --algo ReadWriter HCC1395_BL.recalibrated.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:161000001, elapsed 0.1s, est remaining 2.7s, peak mem 350MB, user 0.4s, sys 3.0s, output queue size 9
progress 10% @chr2:75000001, elapsed 0.3s, est remaining 2.3s, peak mem 527MB, user 0.6s, sys 6.2s, output queue size 41
progress 15% @chr2:234000001, elapsed 0.4s, est remaining 2.0s, peak mem 612MB, user 0.9s, sys 9.1s, output queue size 6
progress 20% @chr3:154000001, elapsed 0.5s, est remaining 1.8s, peak mem 719MB, user 1.0s, sys 12.0s, output queue size 17
progress 25% @chr4:116000001, elapsed 0.5s, est remaining 1.6s, peak mem 819MB, user 1.2s, sys 14.9s, output queue size 12
progress 30% @chr5:86000001, elapsed 0.6s, est remaining 1.5s, peak mem 864MB, user 1.3s, sys 17.6s, output queue size 6
progress 35% @chr6:66000001, elapsed 0.7s, est remaining 1.4s, peak mem 983MB, user 1.6s, sys 20.4s, output queue size 3
progress 40% @chr7:54000001, elapsed 0.8s, est remaining 1.3s, peak mem 1047MB, user 1.8s, sys 23.2s, output queue size 8
progress 45% @chr8:56000001, elapsed 0.9s, est remaining 1.1s, peak mem 1161MB, user 2.0s, sys 26.0s, output queue size 65
progress 50% @chr9:73000001, elapsed 1.0s, est remaining 1.0s, peak mem 1269MB, user 2.3s, sys 28.8s, output queue size 10
progress 55% @chr10:95000001, elapsed 1.1s, est remaining 0.9s, peak mem 1308MB, user 2.5s, sys 31.5s, output queue size 23
progress 60% @chr11:112000001, elapsed 1.2s, est remaining 0.8s, peak mem 1374MB, user 2.7s, sys 34.3s, output queue size 11
progress 65% @chr13:12000001, elapsed 1.3s, est remaining 0.7s, peak mem 1388MB, user 2.8s, sys 37.0s, output queue size 3
progress 70% @chr14:60000001, elapsed 1.4s, est remaining 0.6s, peak mem 1443MB, user 3.0s, sys 39.9s, output queue size 1
progress 75% @chr16:13000001, elapsed 1.5s, est remaining 0.5s, peak mem 1521MB, user 3.3s, sys 42.6s, output queue size 1
progress 80% @chr17:82000001, elapsed 1.6s, est remaining 0.4s, peak mem 1557MB, user 3.5s, sys 45.4s, output queue size 2
progress 85% @chr20:18000001, elapsed 1.7s, est remaining 0.3s, peak mem 1650MB, user 3.7s, sys 48.3s, output queue size 16
progress 90% @chrX:45000001, elapsed 2.0s, est remaining 0.2s, peak mem 2798MB, user 6.0s, sys 49.7s, output queue size 114
progress 95% @chrY:42000001, elapsed 2.1s, est remaining 0.1s, peak mem 2820MB, user 8.2s, sys 50.6s, output queue size 276
progress 100% @chr21:41000001, elapsed 4.3s, est remaining 0.0s, peak mem 2840MB, user 19.6s, sys 52.0s, 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 192
algo: QualCal ReadWriter
license: sentieon:QualCal=31 sentieon:ReadWriter=31
input file size: 51395363
output file size: 71692773
reads: 1001089
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.009 user 0.009 sys 0.023 real
ReadQualCal::delayed_init: 1 calls 0.006 user 0.002 sys 0.023 real
ReadQualCal::init: 1 calls 0.000 user 0.010 sys 0.006 real
advance: 3219322 calls 1.735 user 6.427 sys 8.169 real
done: 1 calls 0.308 user 0.332 sys 0.642 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.006 user 0.002 sys 4.333 real
fetch: 3219322 calls 0.221 user 6.322 sys 6.545 real
fetch_reads: 3219322 calls 0.366 user 6.470 sys 6.603 real
fetch_ref: 13103 calls 0.076 user 0.021 sys 0.053 real
fetch_vcf: 13103 calls 1.306 user 0.066 sys 1.386 real
idle: 2181 calls 1.069 user 0.316 sys 108.157 real
init: 1 calls 0.006 user 0.002 sys 0.029 real
update: 13298 calls 5.385 user 1.011 sys 7.316 real
write: 3219322 calls 7.185 user 6.826 sys 13.622 real
overall: 2978230272 mem 23.912 user 53.258 sys 6.338 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 --algo QualCal --plot --before HCC1395_BL.table --after HCC1395_BL.table.post HCC1395_BL.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: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 192
algo: QualCal
license: sentieon:QualCal=31
ReadQualCal::init: 2 calls 0.010 user 0.020 sys 0.025 real
done: 1 calls 0.038 user 0.022 sys 0.055 real
idle: 61 calls 0.002 user 0.000 sys 31.269 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 83648512 mem 0.052 user 0.052 sys 1.050 real