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/platform-users/sgreer/pipeline-output/sarek_tools_a77_snv_indel__380c4714--20260524-002943/variant_calling/snv_indel/1029_2LI-T1-TDNA-1_23K7YCLT4_1_vs_1029_2LI-N1-BDNA-1_235YY7LT3_1/1029_2LI-T1-TDNA-1_23K7YCLT4_1_vs_1029_2LI-N1-BDNA-1_235YY7LT3_1.snv_indel.phased.vep.final.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/e5bc4cdb8e231c70befd1bc1c12bbc/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/e5bc4cdb8e231c70befd1bc1c12bbc/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
==> STAGING COMPLETE (5 inputs)

Lines   total/split/joined/realigned/skipped:	29947/0/0/0/0
Lines   total/split/joined/realigned/skipped:	31783/0/0/0/0