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/62/6536c8bb6092baf57c0e0fefb78c08/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/946570d262adb8b2bf6eff1526fd47/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/bb7cc1d07e19f8d2500aee7658ea87/kallisto
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/946570d262adb8b2bf6eff1526fd47/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/6536c8bb6092baf57c0e0fefb78c08/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2_1.fastp.fastq.gz
==> 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: BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2_1.fastp.fastq.gz
                             BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2_2.fastp.fastq.gz
[quant] finding pseudoalignments for the reads ...
[progress] 1M reads processed (89.3% mapped)             
[progress] 2M reads processed (89.3% mapped)             
[progress] 3M reads processed (89.3% mapped)             
[progress] 4M reads processed (89.2% mapped)             
[progress] 5M reads processed (89.2% mapped)             
[progress] 6M reads processed (89.2% mapped)             
[progress] 7M reads processed (89.2% mapped)             
[progress] 8M reads processed (89.2% mapped)              done
[quant] processed 9,022,667 reads, 8,049,284 reads pseudoaligned
[quant] estimated average fragment length: 86.6
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,324 rounds