Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/ensembl/Homo_sapiens.GRCh38.102.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/8c417b5095604bdce69409ae38a8ef/22Rv1_FFPE_RNA_0001_B23LG7FLT4_2_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/19d3171d11506d7bad2a7445ded0b7/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/8c417b5095604bdce69409ae38a8ef/22Rv1_FFPE_RNA_0001_B23LG7FLT4_2_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/bb7cc1d07e19f8d2500aee7658ea87/kallisto
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/19d3171d11506d7bad2a7445ded0b7/.command.run
==> STAGING COMPLETE (6 inputs)


[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 194,360
[index] number of k-mers: 112,035,259
[quant] running in paired-end mode
[quant] will process pair 1: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2_1.fastp.fastq.gz
                             22Rv1_FFPE_RNA_0001_B23LG7FLT4_2_2.fastp.fastq.gz
[quant] finding pseudoalignments for the reads ...
[progress] 1M reads processed (85.2% mapped)             
[progress] 2M reads processed (85.3% mapped)             
[progress] 3M reads processed (85.3% mapped)             
[progress] 4M reads processed (85.3% mapped)             
[progress] 5M reads processed (85.3% mapped)             
[progress] 6M reads processed (85.3% mapped)             
[progress] 7M reads processed (85.3% mapped)             
[progress] 8M reads processed (85.3% mapped)             
[progress] 9M reads processed (85.3% mapped)             
[progress] 10M reads processed (85.3% mapped)             
[progress] 11M reads processed (85.3% mapped)             
[progress] 12M reads processed (85.3% mapped)              done
[quant] processed 13,073,429 reads, 11,151,112 reads pseudoaligned
[quant] estimated average fragment length: 103.9
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,639 rounds