Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/a2e58103aa401224b0d28cba63d80b/HCC1395_tumor_R2.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/fb04c289fdf1469361c510ee35891a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/fb04c289fdf1469361c510ee35891a/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/a2e58103aa401224b0d28cba63d80b/HCC1395_tumor_R1.fastq.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.pt
==> STAGING COMPLETE (5 inputs)

pe=1
started reading patternfile
finished reading patternfile
finished building count array
Number of reads in the file : 500000
Scanning fastq file..
finished reading fastq file
finished deleting hash
finished printing count array