Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/b2f95d5599bd6d0b260f1635eba37a/A549_FFPE_01_RNA_0001_B23LG7FLT4_3_2.fastp.fastq.gz
  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/91/d086263e71c226a0c552a1ac03465b/.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/91/d086263e71c226a0c552a1ac03465b/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/b2f95d5599bd6d0b260f1635eba37a/A549_FFPE_01_RNA_0001_B23LG7FLT4_3_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: A549_FFPE_01_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz
                             A549_FFPE_01_RNA_0001_B23LG7FLT4_3_2.fastp.fastq.gz
[quant] finding pseudoalignments for the reads ... done
[quant] processed 393,174 reads, 5,736 reads pseudoaligned
[quant] estimated average fragment length: 35.1978
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 646 rounds