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/71/81816b54ab7484624d9fee8b6881d3/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/ee/aee85eec2e1da65108f0fe28adc566/HCC1395_BL.table
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/ceed4bf612d62859d876f95d1d2d6f/.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/53/ceed4bf612d62859d876f95d1d2d6f/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/81816b54ab7484624d9fee8b6881d3/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% @chr1:166000001, elapsed 0.1s, est remaining 2.2s, peak mem 347MB, user 0.3s, sys 2.7s, output queue size 30
progress 10% @chr2:75000001, elapsed 0.2s, est remaining 1.9s, peak mem 506MB, user 0.5s, sys 5.3s, output queue size 41
progress 15% @chr2:235000001, elapsed 0.3s, est remaining 1.7s, peak mem 590MB, user 0.6s, sys 7.8s, output queue size 19
progress 20% @chr3:155000001, elapsed 0.4s, est remaining 1.5s, peak mem 701MB, user 0.8s, sys 10.4s, output queue size 22
progress 25% @chr4:115000001, elapsed 0.5s, est remaining 1.4s, peak mem 788MB, user 1.0s, sys 12.8s, output queue size 24
progress 30% @chr5:87000001, elapsed 0.6s, est remaining 1.3s, peak mem 812MB, user 1.3s, sys 15.1s, output queue size 20
progress 35% @chr6:66000001, elapsed 0.6s, est remaining 1.2s, peak mem 908MB, user 1.5s, sys 17.6s, output queue size 9
progress 40% @chr7:55000001, elapsed 0.7s, est remaining 1.1s, peak mem 989MB, user 1.6s, sys 20.1s, output queue size 20
progress 45% @chr8:56000001, elapsed 0.9s, est remaining 1.1s, peak mem 1121MB, user 1.9s, sys 24.4s, output queue size 65
progress 50% @chr9:44000001, elapsed 1.0s, est remaining 1.0s, peak mem 1229MB, user 2.2s, sys 28.9s, output queue size 29
progress 55% @chr10:89000001, elapsed 1.2s, est remaining 1.0s, peak mem 1250MB, user 2.4s, sys 33.5s, output queue size 9
progress 60% @chr11:116000001, elapsed 1.4s, est remaining 0.9s, peak mem 1331MB, user 2.7s, sys 38.4s, output queue size 36
progress 65% @chr13:7000001, elapsed 1.6s, est remaining 0.9s, peak mem 1358MB, user 3.0s, sys 44.8s, output queue size 8
progress 70% @chr14:59000001, elapsed 1.8s, est remaining 0.8s, peak mem 1439MB, user 3.3s, sys 51.5s, output queue size 2
progress 75% @chr16:9000001, elapsed 2.0s, est remaining 0.7s, peak mem 1478MB, user 3.7s, sys 58.0s, output queue size 4
progress 80% @chr17:82000001, elapsed 2.2s, est remaining 0.6s, peak mem 1532MB, user 4.0s, sys 64.6s, output queue size 2
progress 85% @chr20:20000001, elapsed 2.5s, est remaining 0.4s, peak mem 1589MB, user 4.3s, sys 71.3s, output queue size 2
progress 90% @chrX:42000001, elapsed 2.9s, est remaining 0.3s, peak mem 2729MB, user 7.6s, sys 75.4s, output queue size 114
progress 95% @chrY:40000001, elapsed 3.2s, est remaining 0.2s, peak mem 2750MB, user 11.3s, sys 79.0s, output queue size 276
progress 100% @chr21:41000001, elapsed 5.1s, est remaining 0.0s, peak mem 2759MB, user 21.8s, sys 83.4s, 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: 51395350
output file size: 71692764
reads: 1001089
contig: 3367 intervals 3217346917 bases
ReadQualCal::clearEPSVecOne: 8 calls 0.002 user 0.006 sys 0.013 real
ReadQualCal::delayed_init: 1 calls 0.005 user 0.001 sys 0.026 real
ReadQualCal::init: 1 calls 0.010 user 0.000 sys 0.006 real
advance: 3219322 calls 1.818 user 11.073 sys 12.115 real
done: 1 calls 0.501 user 0.394 sys 0.902 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.006 user 0.001 sys 5.238 real
fetch: 3219322 calls 0.209 user 9.885 sys 9.354 real
fetch_reads: 3219322 calls 0.444 user 10.566 sys 9.466 real
fetch_ref: 13103 calls 0.042 user 0.053 sys 0.070 real
fetch_vcf: 13103 calls 1.190 user 0.130 sys 1.475 real
idle: 1503 calls 0.694 user 0.275 sys 110.449 real
init: 1 calls 0.005 user 0.001 sys 0.032 real
update: 13298 calls 5.724 user 2.365 sys 8.997 real
write: 3219322 calls 8.306 user 10.289 sys 18.795 real
overall: 2896494592 mem 25.210 user 84.979 sys 7.476 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: 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 0.026 user 0.000 sys 0.025 real
done: 1 calls 0.056 user 0.000 sys 0.056 real
idle: 61 calls 0.002 user 0.000 sys 31.356 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 78704640 mem 0.078 user 0.033 sys 1.053 real