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-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/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
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/0f0237c8c10da2ee07b8c28f184ed4/.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-rnd-pltf-dev-nextflow-scratch-01/work/63/3deb87201b3dbfb093e36f83dee947/1029_T05-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  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-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-rnd-pltf-dev-nextflow-scratch-01/work/2d/0f0237c8c10da2ee07b8c28f184ed4/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/3deb87201b3dbfb093e36f83dee947/1029_T05-T1-TDNA-1_A23MHWWLT4_1.md.bam
  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_T05-T1-TDNA-1_A23MHWWLT4_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_T05-T1-TDNA-1_A23MHWWLT4_1.table
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:119959358, elapsed 8.4s, est remaining 159.0s, peak mem 5304MB, user 223.2s, sys 6.6s, output queue size 172
progress 10% @chr2:23703186, elapsed 17.8s, est remaining 160.3s, peak mem 7198MB, user 481.0s, sys 9.9s, output queue size 1156
progress 15% @chr2:185788643, elapsed 27.3s, est remaining 154.7s, peak mem 8391MB, user 743.2s, sys 13.0s, output queue size 277
progress 20% @chr3:98881540, elapsed 37.4s, est remaining 149.5s, peak mem 8556MB, user 1021.0s, sys 15.3s, output queue size 442
progress 25% @chr4:88487069, elapsed 45.0s, est remaining 134.9s, peak mem 8668MB, user 1226.1s, sys 16.7s, output queue size 89
progress 30% @chr5:147405610, elapsed 51.4s, est remaining 119.9s, peak mem 8689MB, user 1397.5s, sys 18.1s, output queue size 208
progress 35% @chr6:131949264, elapsed 62.0s, est remaining 115.1s, peak mem 9180MB, user 1687.5s, sys 20.1s, output queue size 637
progress 40% @chr7:116769636, elapsed 71.9s, est remaining 107.8s, peak mem 9427MB, user 1954.2s, sys 22.1s, output queue size 1456
progress 45% @chr9:977002, elapsed 81.5s, est remaining 99.6s, peak mem 9598MB, user 2224.3s, sys 24.1s, output queue size 15
progress 50% @chr10:34331117, elapsed 91.8s, est remaining 91.8s, peak mem 9904MB, user 2507.2s, sys 26.2s, output queue size 108
progress 55% @chr11:49058078, elapsed 100.6s, est remaining 82.3s, peak mem 9904MB, user 2745.7s, sys 27.9s, output queue size 14
progress 60% @chr12:26427913, elapsed 110.4s, est remaining 73.6s, peak mem 10217MB, user 3007.2s, sys 29.9s, output queue size 823
progress 65% @chr13:49485630, elapsed 118.9s, est remaining 64.0s, peak mem 10221MB, user 3250.8s, sys 31.5s, output queue size 547
progress 70% @chr15:43151790, elapsed 127.0s, est remaining 54.4s, peak mem 10221MB, user 3470.3s, sys 33.4s, output queue size 455
progress 75% @chr16:30961267, elapsed 136.0s, est remaining 45.3s, peak mem 10221MB, user 3722.9s, sys 35.3s, output queue size 36
progress 80% @chr17:42691806, elapsed 146.9s, est remaining 36.7s, peak mem 10221MB, user 4025.0s, sys 37.4s, output queue size 708
progress 85% @chr19:5754132, elapsed 156.2s, est remaining 27.6s, peak mem 10221MB, user 4285.4s, sys 39.1s, output queue size 406
progress 90% @chr19:55517224, elapsed 166.4s, est remaining 18.5s, peak mem 10221MB, user 4571.4s, sys 41.0s, output queue size 63
progress 95% @chr22:36303995, elapsed 176.8s, est remaining 9.3s, peak mem 10221MB, user 4859.8s, sys 43.0s, output queue size 24
progress 100% @chr6_GL000254v2_alt:3881705, elapsed 186.2s, est remaining 0.0s, peak mem 10221MB, user 5117.7s, sys 45.0s, output queue size 1
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
input file size: 80063761426
reads: 1549027000
contig: 201779 intervals 37922265 bases
advance: 208647 calls 2926.732 user 35.879 sys 3068.114 real
done: 1 calls 0.333 user 0.407 sys 0.741 real
execute: 1 calls 0.000 user 0.009 sys 186.156 real
fetch_reads: 208647 calls 248.314 user 0.486 sys 256.387 real
fetch_ref: 207055 calls 1.116 user 0.951 sys 2.233 real
fetch_vcf: 207055 calls 82.265 user 2.412 sys 86.455 real
idle: 118 calls 0.193 user 0.001 sys 32.939 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 455045 calls 2161.523 user 3.891 sys 2221.729 real
overall: 10717716480 mem 5623.487 user 46.430 sys 187.780 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