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/ba/64a6bea760832d59a43a4ef754f9ac/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/ba/64a6bea760832d59a43a4ef754f9ac/Sig_18_tissue.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/a7d9046b400b3218c8077eb7033aff/.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/d7/a7d9046b400b3218c8077eb7033aff/.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% @chr1:119893964, elapsed 0.0s, est remaining 0.8s, peak mem 172MB, user 0.0s, sys 0.0s, output queue size 4188
progress 10% @chr2:20033205, elapsed 0.1s, est remaining 0.7s, peak mem 172MB, user 0.0s, sys 0.0s, output queue size 3066
progress 15% @chr2:189002955, elapsed 0.1s, est remaining 0.7s, peak mem 181MB, user 0.0s, sys 0.0s, output queue size 13462
progress 20% @chr3:97871842, elapsed 0.2s, est remaining 0.7s, peak mem 190MB, user 0.0s, sys 0.0s, output queue size 23927
progress 25% @chr4:87982492, elapsed 0.2s, est remaining 0.6s, peak mem 190MB, user 0.0s, sys 0.0s, output queue size 3804
progress 30% @chr5:147401540, elapsed 0.2s, est remaining 0.6s, peak mem 208MB, user 0.0s, sys 0.0s, output queue size 13844
progress 35% @chr6:127119291, elapsed 0.3s, est remaining 0.5s, peak mem 208MB, user 0.0s, sys 0.0s, output queue size 23785
progress 40% @chr7:128805359, elapsed 0.3s, est remaining 0.5s, peak mem 217MB, user 0.0s, sys 0.0s, output queue size 33276
progress 45% @chr9:916763, elapsed 0.4s, est remaining 0.4s, peak mem 370MB, user 0.0s, sys 0.1s, output queue size 42635
progress 50% @chr10:32689053, elapsed 0.4s, est remaining 0.4s, peak mem 406MB, user 0.0s, sys 0.1s, output queue size 52587
progress 55% @chr11:48245104, elapsed 0.4s, est remaining 0.4s, peak mem 442MB, user 0.0s, sys 0.1s, output queue size 63044
progress 60% @chr12:22201552, elapsed 0.5s, est remaining 0.3s, peak mem 447MB, user 0.0s, sys 0.1s, output queue size 72634
progress 65% @chr13:49131137, elapsed 0.5s, est remaining 0.3s, peak mem 475MB, user 0.0s, sys 0.1s, output queue size 83654
progress 70% @chr15:42684116, elapsed 0.6s, est remaining 0.2s, peak mem 498MB, user 0.0s, sys 0.1s, output queue size 93721
progress 75% @chr16:30899415, elapsed 0.6s, est remaining 0.2s, peak mem 505MB, user 0.0s, sys 0.1s, output queue size 8215
progress 80% @chr17:42553439, elapsed 0.6s, est remaining 0.2s, peak mem 514MB, user 0.0s, sys 0.1s, output queue size 18902
progress 85% @chr19:5653338, elapsed 0.7s, est remaining 0.1s, peak mem 514MB, user 0.0s, sys 0.1s, output queue size 29312
progress 90% @chr19:55695148, elapsed 0.7s, est remaining 0.1s, peak mem 514MB, user 0.0s, sys 0.1s, output queue size 38813
progress 95% @chr22:37074610, elapsed 1.1s, est remaining 0.1s, peak mem 2523MB, user 7.1s, sys 2.8s, output queue size 3249
progress 100% @chr6_GL000254v2_alt:3877373, elapsed 1.1s, est remaining 0.0s, peak mem 2523MB, user 7.3s, sys 2.8s, output queue size 9180
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 50045074
reads: 1001838
contig: 201779 intervals 37922265 bases
advance: 208647 calls 1.532 user 0.067 sys 2.042 real
done: 1 calls 0.246 user 0.088 sys 0.339 real
execute: 1 calls 0.014 user 0.001 sys 1.146 real
fetch_reads: 208647 calls 0.070 user 0.000 sys 0.161 real
fetch_ref: 2079 calls 0.000 user 0.004 sys 0.015 real
fetch_vcf: 2079 calls 0.787 user 0.019 sys 0.929 real
idle: 92 calls 0.002 user 0.002 sys 31.600 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 2294 calls 5.839 user 2.645 sys 8.780 real
overall: 2645995520 mem 11.193 user 11.916 sys 2.517 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