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/79/cc50b8b93a1a94f047d99135765358/1029_FRC-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-rnd-pltf-dev-nextflow-scratch-01/work/79/cc50b8b93a1a94f047d99135765358/1029_FRC-T1-TDNA-1_A23MHWWLT4_1.md.bam
  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/cf/8560cd3c00a19148102766acbf45f9/.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/cf/8560cd3c00a19148102766acbf45f9/.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_FRC-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_FRC-T1-TDNA-1_A23MHWWLT4_1.table
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:119966338, elapsed 8.6s, est remaining 162.8s, peak mem 5430MB, user 229.9s, sys 5.0s, output queue size 169
progress 10% @chr2:23757418, elapsed 16.5s, est remaining 148.2s, peak mem 6430MB, user 445.3s, sys 8.0s, output queue size 1157
progress 15% @chr2:185788643, elapsed 25.2s, est remaining 142.9s, peak mem 7455MB, user 686.2s, sys 10.7s, output queue size 275
progress 20% @chr3:100297923, elapsed 34.5s, est remaining 137.8s, peak mem 7671MB, user 940.8s, sys 12.8s, output queue size 707
progress 25% @chr4:88462135, elapsed 41.8s, est remaining 125.3s, peak mem 7763MB, user 1139.9s, sys 14.4s, output queue size 87
progress 30% @chr5:147640704, elapsed 48.6s, est remaining 113.3s, peak mem 7883MB, user 1322.6s, sys 15.7s, output queue size 207
progress 35% @chr6:132374631, elapsed 58.0s, est remaining 107.7s, peak mem 7976MB, user 1578.6s, sys 17.6s, output queue size 638
progress 40% @chr7:128890233, elapsed 68.4s, est remaining 102.6s, peak mem 8771MB, user 1859.2s, sys 19.9s, output queue size 1471
progress 45% @chr9:2028988, elapsed 78.0s, est remaining 95.3s, peak mem 9054MB, user 2126.9s, sys 22.1s, output queue size 1475
progress 50% @chr10:33270675, elapsed 88.1s, est remaining 88.1s, peak mem 9291MB, user 2409.0s, sys 24.4s, output queue size 108
progress 55% @chr11:48123613, elapsed 95.9s, est remaining 78.5s, peak mem 9291MB, user 2620.0s, sys 26.0s, output queue size 20
progress 60% @chr12:11800919, elapsed 105.7s, est remaining 70.4s, peak mem 9291MB, user 2886.1s, sys 28.1s, output queue size 792
progress 65% @chr13:49496002, elapsed 114.1s, est remaining 61.4s, peak mem 9291MB, user 3123.5s, sys 30.0s, output queue size 570
progress 70% @chr15:42751974, elapsed 121.8s, est remaining 52.2s, peak mem 9291MB, user 3333.3s, sys 31.7s, output queue size 457
progress 75% @chr16:30930073, elapsed 131.4s, est remaining 43.8s, peak mem 9291MB, user 3603.2s, sys 33.8s, output queue size 32
progress 80% @chr17:42687720, elapsed 142.0s, est remaining 35.5s, peak mem 9291MB, user 3898.4s, sys 35.8s, output queue size 708
progress 85% @chr19:5713134, elapsed 149.8s, est remaining 26.4s, peak mem 9291MB, user 4114.9s, sys 37.2s, output queue size 406
progress 90% @chr19:55870827, elapsed 157.7s, est remaining 17.5s, peak mem 9291MB, user 4336.0s, sys 38.9s, output queue size 89
progress 95% @chr22:36497991, elapsed 167.2s, est remaining 8.8s, peak mem 9291MB, user 4597.3s, sys 41.1s, output queue size 15
progress 100% @chrY:25622443, elapsed 173.2s, est remaining 0.0s, peak mem 9291MB, user 4761.1s, sys 42.3s, output queue size 31
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31 max 192
algo: QualCal
license: sentieon:QualCal=31
input file size: 72638040988
reads: 1429869427
contig: 201779 intervals 37922265 bases
advance: 208647 calls 2677.850 user 35.731 sys 2805.201 real
done: 1 calls 0.360 user 0.367 sys 0.726 real
execute: 1 calls 0.004 user 0.001 sys 173.253 real
fetch_reads: 208647 calls 262.075 user 0.522 sys 270.877 real
fetch_ref: 207319 calls 0.923 user 0.917 sys 1.745 real
fetch_vcf: 207319 calls 79.343 user 1.864 sys 83.249 real
idle: 120 calls 0.204 user 0.006 sys 33.906 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 430557 calls 2015.839 user 2.079 sys 2068.341 real
overall: 9743118336 mem 5226.438 user 43.516 sys 174.917 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