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/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/80c7a3c2df156fb3104ea9d1721b43/1029_FZX-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
  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/f2/e6b4191e428c9047c9d238d62bd917/.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-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/b1/80c7a3c2df156fb3104ea9d1721b43/1029_FZX-T1-TDNA-1_A23MHWWLT4_1.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/e6b4191e428c9047c9d238d62bd917/.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_FZX-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_FZX-T1-TDNA-1_A23MHWWLT4_1.table
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:120006167, elapsed 7.6s, est remaining 144.4s, peak mem 5024MB, user 198.3s, sys 6.4s, output queue size 183
progress 10% @chr2:21001730, elapsed 14.4s, est remaining 129.8s, peak mem 5790MB, user 380.7s, sys 8.2s, output queue size 654
progress 15% @chr2:190369103, elapsed 24.4s, est remaining 138.5s, peak mem 7714MB, user 648.9s, sys 11.7s, output queue size 296
progress 20% @chr3:98784945, elapsed 34.3s, est remaining 137.4s, peak mem 7893MB, user 920.6s, sys 13.5s, output queue size 416
progress 25% @chr4:88487069, elapsed 40.9s, est remaining 122.8s, peak mem 8053MB, user 1093.8s, sys 14.9s, output queue size 89
progress 30% @chr5:146514854, elapsed 46.7s, est remaining 108.9s, peak mem 8053MB, user 1241.4s, sys 16.1s, output queue size 210
progress 35% @chr6:131949949, elapsed 56.6s, est remaining 105.1s, peak mem 8220MB, user 1510.5s, sys 18.2s, output queue size 645
progress 40% @chr7:128879522, elapsed 65.8s, est remaining 98.7s, peak mem 8738MB, user 1749.9s, sys 20.3s, output queue size 1431
progress 45% @chr9:990041, elapsed 76.5s, est remaining 93.5s, peak mem 9286MB, user 2045.3s, sys 22.8s, output queue size 68
progress 50% @chr10:33221719, elapsed 87.0s, est remaining 87.0s, peak mem 9778MB, user 2330.9s, sys 24.9s, output queue size 93
progress 55% @chr11:48978872, elapsed 93.8s, est remaining 76.7s, peak mem 9778MB, user 2510.3s, sys 26.2s, output queue size 19
progress 60% @chr12:25519858, elapsed 102.8s, est remaining 68.6s, peak mem 9778MB, user 2752.4s, sys 28.1s, output queue size 794
progress 65% @chr13:49482737, elapsed 112.9s, est remaining 60.8s, peak mem 9778MB, user 3035.5s, sys 29.9s, output queue size 548
progress 70% @chr15:43181181, elapsed 120.2s, est remaining 51.5s, peak mem 9778MB, user 3230.2s, sys 31.2s, output queue size 455
progress 75% @chr16:30766741, elapsed 129.5s, est remaining 43.2s, peak mem 9778MB, user 3487.6s, sys 32.8s, output queue size 31
progress 80% @chr17:42696025, elapsed 140.8s, est remaining 35.2s, peak mem 9778MB, user 3797.8s, sys 34.9s, output queue size 708
progress 85% @chr19:5733856, elapsed 149.0s, est remaining 26.3s, peak mem 9778MB, user 4021.6s, sys 36.4s, output queue size 406
progress 90% @chr19:55738095, elapsed 158.5s, est remaining 17.6s, peak mem 9778MB, user 4284.7s, sys 38.0s, output queue size 92
progress 95% @chr22:36762904, elapsed 169.8s, est remaining 8.9s, peak mem 9778MB, user 4593.8s, sys 40.5s, output queue size 26
progress 100% @chrY:25622443, elapsed 175.6s, est remaining 0.0s, peak mem 9778MB, user 4746.9s, sys 41.5s, output queue size 31
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: 67770633046
reads: 1275212856
contig: 201779 intervals 37922265 bases
advance: 208647 calls 2537.623 user 32.922 sys 2658.642 real
done: 1 calls 0.372 user 0.387 sys 0.760 real
execute: 1 calls 0.004 user 0.010 sys 175.633 real
fetch_reads: 208647 calls 210.849 user 0.542 sys 218.975 real
fetch_ref: 207343 calls 1.003 user 1.018 sys 2.109 real
fetch_vcf: 207343 calls 81.317 user 2.002 sys 85.958 real
idle: 94 calls 0.154 user 0.001 sys 34.008 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 458673 calls 2290.366 user 3.895 sys 2353.531 real
overall: 10253512704 mem 5307.984 user 43.027 sys 177.259 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