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/f1/704d43844a8623c687e6c18ebb3ef0/rna_s1200_S21_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/fc1e08ef1d769fefce475f476bf1c0/kallisto
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/e2a35d244f6f516c575c7f8fc3a360/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/e2a35d244f6f516c575c7f8fc3a360/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/704d43844a8623c687e6c18ebb3ef0/rna_s1200_S21_2.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: rna_s1200_S21_1.fastp.fastq.gz
                             rna_s1200_S21_2.fastp.fastq.gz
[quant] finding pseudoalignments for the reads ...
[progress] 1M reads processed (97.9% mapped)             
[progress] 2M reads processed (97.8% mapped)             
[progress] 3M reads processed (97.8% mapped)             
[progress] 4M reads processed (97.8% mapped)             
[progress] 5M reads processed (97.8% mapped)             
[progress] 6M reads processed (97.8% mapped)             
[progress] 7M reads processed (97.8% mapped)             
[progress] 8M reads processed (97.8% mapped)             
[progress] 9M reads processed (97.8% mapped)              done
[quant] processed 9,937,706 reads, 9,721,684 reads pseudoaligned
[quant] estimated average fragment length: 181.2
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,157 rounds