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/6e/8467a0f89a3b28cafdce3f1ccefdce/Sig_18_tissue.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/6e/8467a0f89a3b28cafdce3f1ccefdce/Sig_18_tissue.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/92af4d544673f720dfb76d88fc8d8a/.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/f7/92af4d544673f720dfb76d88fc8d8a/.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 Sig_18_tissue.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 Sig_18_tissue.table
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:119911554, elapsed 0.0s, est remaining 0.8s, peak mem 169MB, user 0.0s, sys 0.0s, output queue size 5251
progress 10% @chr2:19930396, elapsed 0.1s, est remaining 0.7s, peak mem 169MB, user 0.0s, sys 0.0s, output queue size 15282
progress 15% @chr2:189008924, elapsed 0.1s, est remaining 0.8s, peak mem 181MB, user 0.0s, sys 0.0s, output queue size 6842
progress 20% @chr3:97871842, elapsed 0.2s, est remaining 0.7s, peak mem 190MB, user 0.0s, sys 0.0s, output queue size 17319
progress 25% @chr4:88390652, elapsed 0.2s, est remaining 0.7s, peak mem 190MB, user 0.0s, sys 0.0s, output queue size 27572
progress 30% @chr5:147375090, elapsed 0.3s, est remaining 0.7s, peak mem 208MB, user 0.0s, sys 0.0s, output queue size 37612
progress 35% @chr6:127143030, elapsed 0.4s, est remaining 0.7s, peak mem 211MB, user 0.0s, sys 0.0s, output queue size 9209
progress 40% @chr7:128811800, elapsed 0.4s, est remaining 0.6s, peak mem 220MB, user 0.0s, sys 0.1s, output queue size 18695
progress 45% @chr9:1051614, elapsed 0.4s, est remaining 0.5s, peak mem 370MB, user 0.0s, sys 0.1s, output queue size 28060
progress 50% @chr10:32026460, elapsed 0.5s, est remaining 0.5s, peak mem 400MB, user 0.0s, sys 0.1s, output queue size 38001
progress 55% @chr11:48216810, elapsed 0.6s, est remaining 0.5s, peak mem 424MB, user 0.0s, sys 0.1s, output queue size 48466
progress 60% @chr12:22478313, elapsed 0.6s, est remaining 0.4s, peak mem 427MB, user 0.0s, sys 0.1s, output queue size 58047
progress 65% @chr13:49220338, elapsed 0.7s, est remaining 0.4s, peak mem 478MB, user 0.0s, sys 0.2s, output queue size 69065
progress 70% @chr15:42725489, elapsed 0.8s, est remaining 0.4s, peak mem 481MB, user 0.0s, sys 0.2s, output queue size 79101
progress 75% @chr16:30930073, elapsed 0.9s, est remaining 0.3s, peak mem 484MB, user 0.0s, sys 0.2s, output queue size 8767
progress 80% @chr17:42543028, elapsed 1.0s, est remaining 0.3s, peak mem 493MB, user 0.0s, sys 0.2s, output queue size 19457
progress 85% @chr19:5229491, elapsed 1.1s, est remaining 0.2s, peak mem 493MB, user 0.0s, sys 0.2s, output queue size 29867
progress 90% @chr19:55762598, elapsed 1.2s, est remaining 0.1s, peak mem 502MB, user 0.1s, sys 0.2s, output queue size 39375
progress 95% @chr22:36937342, elapsed 1.7s, est remaining 0.1s, peak mem 2482MB, user 7.0s, sys 6.0s, output queue size 3223
progress 100% @chrY:25624455, elapsed 1.8s, est remaining 0.0s, peak mem 2482MB, user 7.1s, sys 6.0s, output queue size 6511
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: QualCal
license: sentieon:QualCal=31
input file size: 50047059
reads: 1001838
contig: 201779 intervals 37922265 bases
advance: 208647 calls 1.496 user 0.320 sys 2.398 real
done: 1 calls 0.336 user 0.128 sys 0.465 real
execute: 1 calls 0.006 user 0.002 sys 1.773 real
fetch_reads: 208647 calls 0.120 user 0.003 sys 0.215 real
fetch_ref: 2079 calls 0.007 user 0.011 sys 0.031 real
fetch_vcf: 2079 calls 0.668 user 0.041 sys 0.936 real
idle: 92 calls 0.001 user 0.003 sys 31.727 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 2294 calls 6.010 user 5.422 sys 11.812 real
overall: 2603032576 mem 11.249 user 34.811 sys 3.168 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