Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/60d2b07dc708880856f1aecf58def0/1029_FZX-T1-TDNA-1_A23MHWWLT4_1_R1.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/60d2b07dc708880856f1aecf58def0/1029_FZX-T1-TDNA-1_A23MHWWLT4_1_R2.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/351db29f72d0155421d7e391a788d6/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/351db29f72d0155421d7e391a788d6/.command.run
  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 : 647406165
Scanning fastq file..
finished reading fastq file
finished deleting hash
finished printing count array