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/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/1e/d383e9b9e360f04530b424830aa121/.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/f1/ba12a56257ee3ad2d76071ffc3d404/659_Kh-T1-TDNA-1_A23MHWWLT4_1.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.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/f1/ba12a56257ee3ad2d76071ffc3d404/659_Kh-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/d383e9b9e360f04530b424830aa121/.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 659_Kh-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 659_Kh-T1-TDNA-1_A23MHWWLT4_1.table
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:119918363, elapsed 8.1s, est remaining 153.2s, peak mem 4988MB, user 209.9s, sys 5.2s, output queue size 172
progress 10% @chr2:23639139, elapsed 15.1s, est remaining 136.3s, peak mem 5851MB, user 395.4s, sys 7.1s, output queue size 655
progress 15% @chr2:189877272, elapsed 24.8s, est remaining 140.5s, peak mem 6678MB, user 649.8s, sys 9.8s, output queue size 451
progress 20% @chr3:98390666, elapsed 34.9s, est remaining 139.6s, peak mem 7774MB, user 920.6s, sys 12.7s, output queue size 414
progress 25% @chr4:88472409, elapsed 42.9s, est remaining 128.8s, peak mem 7774MB, user 1130.7s, sys 14.6s, output queue size 98
progress 30% @chr5:147405610, elapsed 49.2s, est remaining 114.9s, peak mem 7774MB, user 1293.7s, sys 15.8s, output queue size 206
progress 35% @chr6:132322679, elapsed 59.5s, est remaining 110.5s, peak mem 7891MB, user 1566.2s, sys 18.2s, output queue size 638
progress 40% @chr7:128840548, elapsed 68.6s, est remaining 102.9s, peak mem 7987MB, user 1792.9s, sys 19.5s, output queue size 540
progress 45% @chr9:1051614, elapsed 79.4s, est remaining 97.1s, peak mem 8270MB, user 2091.9s, sys 21.5s, output queue size 18
progress 50% @chr10:34119613, elapsed 89.8s, est remaining 89.8s, peak mem 8432MB, user 2368.0s, sys 23.3s, output queue size 108
progress 55% @chr11:48978872, elapsed 96.2s, est remaining 78.7s, peak mem 8432MB, user 2533.3s, sys 24.5s, output queue size 16
progress 60% @chr12:25232559, elapsed 106.5s, est remaining 71.0s, peak mem 8432MB, user 2801.2s, sys 26.1s, output queue size 795
progress 65% @chr13:49490822, elapsed 115.3s, est remaining 62.1s, peak mem 8445MB, user 3040.2s, sys 27.7s, output queue size 568
progress 70% @chr15:42695140, elapsed 123.4s, est remaining 52.9s, peak mem 8445MB, user 3252.9s, sys 29.2s, output queue size 455
progress 75% @chr16:30964094, elapsed 133.9s, est remaining 44.6s, peak mem 8445MB, user 3540.6s, sys 30.8s, output queue size 36
progress 80% @chr17:42697274, elapsed 143.1s, est remaining 35.8s, peak mem 8445MB, user 3789.2s, sys 32.3s, output queue size 695
progress 85% @chr19:5745913, elapsed 151.6s, est remaining 26.8s, peak mem 8445MB, user 4015.8s, sys 33.8s, output queue size 408
progress 90% @chr19:55762598, elapsed 161.2s, est remaining 17.9s, peak mem 8445MB, user 4275.1s, sys 35.3s, output queue size 95
progress 95% @chr22:36306414, elapsed 170.2s, est remaining 9.0s, peak mem 8445MB, user 4514.2s, sys 36.8s, output queue size 24
progress 100% @chrX:67685941, elapsed 181.1s, est remaining 0.0s, peak mem 9921MB, user 4687.3s, sys 38.8s, output queue size 4493
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: 62489204264
reads: 1154230309
contig: 201779 intervals 37922265 bases
advance: 208647 calls 2405.485 user 31.234 sys 2506.856 real
done: 1 calls 0.389 user 0.357 sys 0.753 real
execute: 1 calls 0.006 user 0.001 sys 181.173 real
fetch_reads: 208647 calls 191.488 user 0.525 sys 196.921 real
fetch_ref: 207416 calls 1.087 user 0.865 sys 2.039 real
fetch_vcf: 207416 calls 81.567 user 2.055 sys 85.260 real
idle: 656 calls 2.955 user 0.016 sys 149.491 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 444642 calls 2545.460 user 3.151 sys 2599.536 real
overall: 10403000320 mem 5379.397 user 40.179 sys 182.780 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