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/c0/27a7120bbd056aabaf825da99c116d/.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/c0/27a7120bbd056aabaf825da99c116d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/bbd12b88b5b205c4c95cb8bf8866c9/Sig_18_Blood.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/bbd12b88b5b205c4c95cb8bf8866c9/Sig_18_Blood.md.bam.bai
  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_Blood.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_Blood.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 105
progress 10% @chr2:20001955, elapsed 0.1s, est remaining 0.8s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 4867
progress 15% @chr2:189039272, elapsed 0.1s, est remaining 0.7s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 10362
progress 20% @chr3:97871842, elapsed 0.2s, est remaining 0.7s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 1115
progress 25% @chr4:88061906, elapsed 0.2s, est remaining 0.6s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 6212
progress 30% @chr5:146589947, elapsed 0.2s, est remaining 0.6s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 59
progress 35% @chr6:127144950, elapsed 0.3s, est remaining 0.5s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 10005
progress 40% @chr7:128810139, elapsed 0.3s, est remaining 0.5s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 19483
progress 45% @chr9:893912, elapsed 0.3s, est remaining 0.4s, peak mem 280MB, user 0.0s, sys 0.0s, output queue size 28842
progress 50% @chr10:32583034, elapsed 0.4s, est remaining 0.4s, peak mem 292MB, user 0.0s, sys 0.0s, output queue size 4435
progress 55% @chr11:48263861, elapsed 0.4s, est remaining 0.3s, peak mem 301MB, user 0.0s, sys 0.0s, output queue size 14894
progress 60% @chr12:21916937, elapsed 0.5s, est remaining 0.3s, peak mem 301MB, user 0.0s, sys 0.0s, output queue size 24442
progress 65% @chr13:49198362, elapsed 0.5s, est remaining 0.3s, peak mem 301MB, user 0.0s, sys 0.0s, output queue size 35500
progress 70% @chr15:42730925, elapsed 0.5s, est remaining 0.2s, peak mem 301MB, user 0.0s, sys 0.0s, output queue size 45548
progress 75% @chr16:30965601, elapsed 0.6s, est remaining 0.2s, peak mem 301MB, user 0.0s, sys 0.0s, output queue size 55108
progress 80% @chr17:42562612, elapsed 0.6s, est remaining 0.2s, peak mem 301MB, user 0.0s, sys 0.0s, output queue size 65787
progress 85% @chr19:5591748, elapsed 0.7s, est remaining 0.1s, peak mem 331MB, user 0.0s, sys 0.0s, output queue size 8913
progress 90% @chr19:55613619, elapsed 0.7s, est remaining 0.1s, peak mem 331MB, user 0.0s, sys 0.0s, output queue size 18422
progress 95% @chr22:37073532, elapsed 1.1s, est remaining 0.1s, peak mem 2521MB, user 6.3s, sys 2.1s, output queue size 3248
progress 100% @chrY:57189969, elapsed 1.1s, est remaining 0.0s, peak mem 2521MB, user 6.5s, sys 2.1s, output queue size 2119
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: 52290598
reads: 1001133
contig: 201779 intervals 37922265 bases
advance: 208647 calls 1.998 user 0.113 sys 2.290 real
done: 1 calls 0.276 user 0.169 sys 0.445 real
execute: 1 calls 0.012 user 0.001 sys 1.118 real
fetch_reads: 208647 calls 0.100 user 0.001 sys 0.166 real
fetch_ref: 2072 calls 0.005 user 0.005 sys 0.025 real
fetch_vcf: 2072 calls 0.691 user 0.030 sys 0.977 real
idle: 92 calls 0.003 user 0.001 sys 31.632 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 2257 calls 4.587 user 1.977 sys 7.126 real
overall: 2644267008 mem 10.033 user 4.865 sys 2.509 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