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/2b/fd9523c3e5735afb5e90371124c285/HCC1395_BL.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
  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/56/d03ede8711a564138da25ea6c0cb27/.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/2b/fd9523c3e5735afb5e90371124c285/HCC1395_BL.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/d03ede8711a564138da25ea6c0cb27/.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 HCC1395_BL.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 HCC1395_BL.table
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:119911554, elapsed 0.0s, est remaining 0.9s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 621
progress 10% @chr2:20202766, elapsed 0.1s, est remaining 0.8s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 10664
progress 15% @chr2:189039272, elapsed 0.1s, est remaining 0.8s, peak mem 164MB, user 0.0s, sys 0.0s, output queue size 1327
progress 20% @chr3:97871842, elapsed 0.2s, est remaining 0.7s, peak mem 164MB, user 0.0s, sys 0.0s, output queue size 11794
progress 25% @chr4:88460095, elapsed 0.2s, est remaining 0.7s, peak mem 167MB, user 0.0s, sys 0.0s, output queue size 22061
progress 30% @chr5:147384375, elapsed 0.3s, est remaining 0.6s, peak mem 173MB, user 0.0s, sys 0.0s, output queue size 32101
progress 35% @chr6:127119291, elapsed 0.3s, est remaining 0.6s, peak mem 173MB, user 0.0s, sys 0.0s, output queue size 42063
progress 40% @chr7:128806237, elapsed 0.3s, est remaining 0.5s, peak mem 173MB, user 0.0s, sys 0.0s, output queue size 51533
progress 45% @chr9:418068, elapsed 0.4s, est remaining 0.5s, peak mem 299MB, user 0.0s, sys 0.0s, output queue size 60891
progress 50% @chr10:32055848, elapsed 0.4s, est remaining 0.4s, peak mem 299MB, user 0.0s, sys 0.0s, output queue size 70844
progress 55% @chr11:48324941, elapsed 0.5s, est remaining 0.4s, peak mem 299MB, user 0.0s, sys 0.0s, output queue size 81308
progress 60% @chr12:21862953, elapsed 0.5s, est remaining 0.3s, peak mem 299MB, user 0.0s, sys 0.0s, output queue size 90856
progress 65% @chr13:49207081, elapsed 0.6s, est remaining 0.3s, peak mem 305MB, user 0.0s, sys 0.0s, output queue size 3375
progress 70% @chr15:42684116, elapsed 0.6s, est remaining 0.3s, peak mem 305MB, user 0.0s, sys 0.0s, output queue size 13408
progress 75% @chr16:30781718, elapsed 0.6s, est remaining 0.2s, peak mem 305MB, user 0.0s, sys 0.0s, output queue size 22987
progress 80% @chr17:42554402, elapsed 0.7s, est remaining 0.2s, peak mem 305MB, user 0.0s, sys 0.0s, output queue size 33666
progress 85% @chr19:5641740, elapsed 0.7s, est remaining 0.1s, peak mem 341MB, user 0.0s, sys 0.0s, output queue size 44076
progress 90% @chr19:55660516, elapsed 0.8s, est remaining 0.1s, peak mem 341MB, user 0.0s, sys 0.0s, output queue size 53576
progress 95% @chr22:36937342, elapsed 1.1s, est remaining 0.1s, peak mem 2528MB, user 5.2s, sys 2.7s, output queue size 3224
progress 100% @chr6_GL000254v2_alt:3881705, elapsed 1.1s, est remaining 0.0s, peak mem 2528MB, user 5.4s, sys 2.7s, output queue size 8078
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: 51395359
reads: 1001089
contig: 201779 intervals 37922265 bases
advance: 208647 calls 1.613 user 0.108 sys 2.032 real
done: 1 calls 0.319 user 0.030 sys 0.357 real
execute: 1 calls 0.006 user 0.001 sys 1.150 real
fetch_reads: 208647 calls 0.071 user 0.000 sys 0.143 real
fetch_ref: 2042 calls 0.003 user 0.025 sys 0.022 real
fetch_vcf: 2042 calls 0.710 user 0.064 sys 0.902 real
idle: 92 calls 0.001 user 0.002 sys 31.631 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 2207 calls 3.637 user 2.455 sys 6.441 real
overall: 2651820032 mem 8.780 user 15.672 sys 2.553 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