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/b3/57a16f0cfbc17f3f3dcbee22c14121/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/63/33a462347e84f707d890a9e2d47601/HCC1395_BL.table
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/3cfabeb790a6f016a7b8ea9337df7f/.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/5d/3cfabeb790a6f016a7b8ea9337df7f/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/57a16f0cfbc17f3f3dcbee22c14121/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% @chr1:164000001, elapsed 0.2s, est remaining 3.1s, peak mem 345MB, user 0.4s, sys 4.0s, output queue size 9
progress 10% @chr2:75000001, elapsed 0.3s, est remaining 2.7s, peak mem 509MB, user 0.9s, sys 7.8s, output queue size 41
progress 15% @chr2:239000001, elapsed 0.4s, est remaining 2.5s, peak mem 639MB, user 1.3s, sys 11.8s, output queue size 8
progress 20% @chr3:156000001, elapsed 0.6s, est remaining 2.3s, peak mem 741MB, user 1.6s, sys 15.8s, output queue size 5
progress 25% @chr4:118000001, elapsed 0.7s, est remaining 2.2s, peak mem 842MB, user 2.0s, sys 19.6s, output queue size 7
progress 30% @chr5:87000001, elapsed 0.9s, est remaining 2.0s, peak mem 870MB, user 2.4s, sys 23.6s, output queue size 20
progress 35% @chr6:71000001, elapsed 1.0s, est remaining 1.9s, peak mem 975MB, user 2.8s, sys 27.5s, output queue size 6
progress 40% @chr7:41000001, elapsed 1.1s, est remaining 1.7s, peak mem 1041MB, user 3.2s, sys 31.4s, output queue size 15
progress 45% @chr8:63000001, elapsed 1.3s, est remaining 1.6s, peak mem 1194MB, user 3.6s, sys 35.2s, output queue size 11
progress 50% @chr9:74000001, elapsed 1.4s, est remaining 1.4s, peak mem 1263MB, user 3.9s, sys 39.1s, output queue size 5
progress 55% @chr10:97000001, elapsed 1.5s, est remaining 1.3s, peak mem 1319MB, user 4.3s, sys 42.7s, output queue size 12
progress 60% @chr11:121000001, elapsed 1.7s, est remaining 1.1s, peak mem 1385MB, user 4.5s, sys 46.4s, output queue size 18
progress 65% @chr13:17000001, elapsed 1.8s, est remaining 1.0s, peak mem 1424MB, user 4.7s, sys 50.1s, output queue size 9
progress 70% @chr14:60000001, elapsed 1.9s, est remaining 0.8s, peak mem 1445MB, user 5.1s, sys 53.5s, output queue size 6
progress 75% @chr16:15000001, elapsed 2.0s, est remaining 0.7s, peak mem 1509MB, user 5.3s, sys 57.0s, output queue size 6
progress 80% @chr17:81000001, elapsed 2.2s, est remaining 0.5s, peak mem 1574MB, user 5.6s, sys 60.4s, output queue size 3
progress 85% @chr20:24000001, elapsed 2.3s, est remaining 0.4s, peak mem 1653MB, user 5.8s, sys 63.9s, output queue size 11
progress 90% @chrX:47000001, elapsed 2.7s, est remaining 0.3s, peak mem 2781MB, user 9.0s, sys 66.1s, output queue size 114
progress 95% @chrY:43000001, elapsed 2.8s, est remaining 0.1s, peak mem 2808MB, user 11.1s, sys 66.8s, output queue size 276
progress 100% @chr21:41000001, elapsed 4.6s, est remaining 0.0s, peak mem 2826MB, user 23.3s, sys 68.4s, 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 192
algo: QualCal ReadWriter
license: sentieon:QualCal=31 sentieon:ReadWriter=31
input file size: 51394915
output file size: 71699821
reads: 1001089
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 0.001 sys 0.021 real
ReadQualCal::init: 1 calls 0.010 user 0.000 sys 0.006 real
advance: 3219322 calls 1.906 user 8.172 sys 10.344 real
done: 1 calls 0.330 user 0.365 sys 0.699 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.006 user 0.000 sys 4.686 real
fetch: 3219322 calls 0.354 user 8.052 sys 8.781 real
fetch_reads: 3219322 calls 0.421 user 7.707 sys 8.940 real
fetch_ref: 13103 calls 0.031 user 0.038 sys 0.093 real
fetch_vcf: 13103 calls 1.205 user 0.115 sys 1.571 real
idle: 2081 calls 1.401 user 0.382 sys 89.584 real
init: 1 calls 0.009 user 0.001 sys 0.028 real
update: 13298 calls 5.791 user 2.072 sys 9.196 real
write: 3219322 calls 8.083 user 8.297 sys 15.848 real
overall: 2964140032 mem 28.128 user 69.659 sys 6.435 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 6.12.83
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 192
algo: QualCal
license: sentieon:QualCal=31
ReadQualCal::init: 2 calls 0.029 user 0.001 sys 0.026 real
done: 1 calls 0.049 user 0.011 sys 0.057 real
idle: 61 calls 0.002 user 0.000 sys 31.282 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 83640320 mem 0.077 user 0.033 sys 1.052 real