Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/0837493c0d08d538b780f1d4f40b73/1029_D5N-N1-BDNA-1_B23KGCJLT4_1.md.bam
  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/85/e0ae35be19831c52cb6eff4752c001/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/0837493c0d08d538b780f1d4f40b73/1029_D5N-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
  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/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed
  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/85/e0ae35be19831c52cb6eff4752c001/.command.run
  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 1029_D5N-N1-BDNA-1_B23KGCJLT4_1.md.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed --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 1029_D5N-N1-BDNA-1_B23KGCJLT4_1.table
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:120048858, elapsed 2.5s, est remaining 47.4s, peak mem 3167MB, user 61.3s, sys 3.5s, output queue size 171
progress 10% @chr2:17515169, elapsed 4.6s, est remaining 41.7s, peak mem 3323MB, user 114.9s, sys 4.3s, output queue size 668
progress 15% @chr2:190469758, elapsed 7.3s, est remaining 41.1s, peak mem 3432MB, user 179.4s, sys 5.0s, output queue size 454
progress 20% @chr3:98592949, elapsed 10.0s, est remaining 39.9s, peak mem 3555MB, user 249.2s, sys 5.9s, output queue size 437
progress 25% @chr4:88439874, elapsed 12.8s, est remaining 38.3s, peak mem 3584MB, user 316.8s, sys 6.9s, output queue size 540
progress 30% @chr5:147509478, elapsed 15.4s, est remaining 35.9s, peak mem 3584MB, user 381.9s, sys 7.6s, output queue size 206
progress 35% @chr6:131949264, elapsed 19.3s, est remaining 35.8s, peak mem 3590MB, user 476.5s, sys 8.7s, output queue size 637
progress 40% @chr7:102248412, elapsed 23.8s, est remaining 35.7s, peak mem 3636MB, user 580.8s, sys 9.7s, output queue size 1415
progress 45% @chr9:2076229, elapsed 28.4s, est remaining 34.7s, peak mem 3670MB, user 698.1s, sys 10.5s, output queue size 106
progress 50% @chr10:33256316, elapsed 32.6s, est remaining 32.6s, peak mem 3702MB, user 803.5s, sys 11.4s, output queue size 107
progress 55% @chr11:48136039, elapsed 36.1s, est remaining 29.6s, peak mem 3713MB, user 891.0s, sys 12.1s, output queue size 26
progress 60% @chr12:11874766, elapsed 40.4s, est remaining 26.9s, peak mem 3713MB, user 997.1s, sys 12.8s, output queue size 749
progress 65% @chr13:49513059, elapsed 43.9s, est remaining 23.7s, peak mem 3713MB, user 1085.2s, sys 13.4s, output queue size 65
progress 70% @chr15:43148755, elapsed 47.1s, est remaining 20.2s, peak mem 3713MB, user 1163.4s, sys 14.0s, output queue size 456
progress 75% @chr16:30964094, elapsed 50.5s, est remaining 16.8s, peak mem 3713MB, user 1250.9s, sys 14.7s, output queue size 78
progress 80% @chr17:42666087, elapsed 53.7s, est remaining 13.4s, peak mem 3720MB, user 1334.3s, sys 15.4s, output queue size 704
progress 85% @chr19:5719704, elapsed 56.4s, est remaining 9.9s, peak mem 3720MB, user 1398.9s, sys 16.0s, output queue size 404
progress 90% @chr19:55486408, elapsed 58.9s, est remaining 6.5s, peak mem 3723MB, user 1462.4s, sys 16.4s, output queue size 104
progress 95% @chr22:36504098, elapsed 61.5s, est remaining 3.2s, peak mem 3809MB, user 1529.2s, sys 17.0s, output queue size 55
progress 100% @chrY:25622443, elapsed 63.1s, est remaining 0.0s, peak mem 3809MB, user 1568.6s, sys 17.4s, output queue size 31
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
input file size: 13575943775
reads: 276873939
contig: 201779 intervals 37922265 bases
advance: 208647 calls 654.510 user 9.658 sys 688.382 real
done: 1 calls 0.297 user 0.782 sys 1.085 real
execute: 1 calls 0.005 user 0.002 sys 63.110 real
fetch_reads: 208647 calls 57.536 user 0.159 sys 61.010 real
fetch_ref: 207169 calls 0.904 user 1.097 sys 1.969 real
fetch_vcf: 207169 calls 92.886 user 2.462 sys 99.011 real
idle: 123 calls 0.165 user 0.000 sys 62.953 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 271518 calls 1020.814 user 3.857 sys 1056.088 real
overall: 3994841088 mem 1900.598 user 19.314 sys 65.575 real
ls: cannot access '*.table.post': No such file or directory
ls: cannot access '*.recalibrated.bam': No such file or directory
ls: cannot access '*.recalibrated.bam.bai': No such file or directory
ls: cannot access '*.csv': No such file or directory
ls: cannot access '*.pdf': No such file or directory