Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/35329fba84c043f2fa3f57b883a6ed/HCC1395_BL_R2.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/411aec6222acd428a359e65b5ab446/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/411aec6222acd428a359e65b5ab446/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/35329fba84c043f2fa3f57b883a6ed/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