Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/357f565c741fe7a2742e5321a0f4f9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/4406a1bfb9d83176bb762a0d501666/1029_0DT-T1-TDNA-1_23K7YCLT4_1_vs_1029_0DT-N1-BDNA-1_235YY7LT3_1.filtered.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/POT/aih_tumor_1577_pot_1pct_artifacts_only.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/xgen-exome-hyb-panel-v2-targets-hg38_short.mrg.bed
  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/PON/pon_tnseq_42_curated_v4.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/altera_v3_targets_coding_postQC_hg38.bed
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/tso500/pepe_blacklist_sorted_hg38.bed
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/tso500/TruSight_Oncology_500_Manifest_hg38.st.mrg.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/357f565c741fe7a2742e5321a0f4f9/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/hotspots/hotspot_definitions.tsv
==> STAGING COMPLETE (12 inputs)

Loading hotspot definitions from hotspot_definitions.tsv
Loading PON positions from pon_tnseq_42_curated_v4.vcf.gz
[E::idx_find_and_load] Could not retrieve index file for 'pon_tnseq_42_curated_v4.vcf.gz'
  Loaded 550680 PON positions
Loading POT positions from aih_tumor_1577_pot_1pct_artifacts_only.vcf.gz
[E::idx_find_and_load] Could not retrieve index file for 'aih_tumor_1577_pot_1pct_artifacts_only.vcf.gz'
  Loaded 545 POT positions
Loading BED files
Opening reference FASTA Homo_sapiens_assembly38.fasta
Extracting variants from 1029_0DT-T1-TDNA-1_23K7YCLT4_1_vs_1029_0DT-N1-BDNA-1_235YY7LT3_1.filtered.vcf.gz (mode=test)
[E::idx_find_and_load] Could not retrieve index file for '1029_0DT-T1-TDNA-1_23K7YCLT4_1_vs_1029_0DT-N1-BDNA-1_235YY7LT3_1.filtered.vcf.gz'
  VEP CSQ header found with 26 fields
  Samples: tumor=1029_0DT-T1-TDNA-1_23K7YCLT4_1 (idx=0), normal=1029_0DT-N1-BDNA-1_235YY7LT3_1 (idx=1)
Wrote 27988 variants to 1029_0DT-T1-TDNA-1_23K7YCLT4_1_vs_1029_0DT-N1-BDNA-1_235YY7LT3_1.variants.tsv