Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/864be2d37ff1eb551a3461c6effcf8/HCC1395_BL_R2.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/2f602bf7eeb00217702c36664706c3/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/2f602bf7eeb00217702c36664706c3/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/864be2d37ff1eb551a3461c6effcf8/HCC1395_BL_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