Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/3ef5d4fc97d376e3503cd75e3bae38/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/3ef5d4fc97d376e3503cd75e3bae38/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.pt
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/54dcf158e7ff79c64e402b6bb65ec6/1029_T05-T1-TDNA-1_A23MHWWLT4_1_R2.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/54dcf158e7ff79c64e402b6bb65ec6/1029_T05-T1-TDNA-1_A23MHWWLT4_1_R1.fastq.gz
==> STAGING COMPLETE (5 inputs)

pe=1
started reading patternfile
finished reading patternfile
finished building count array
Number of reads in the file : 783010071
Scanning fastq file..
finished reading fastq file
finished deleting hash
finished printing count array