Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/b6f0e4a893bdda1ab76c19af1707ef/rna_s1221_S42_1.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/2d/dd0e6474e26e1c1890768c5ba4b893/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/7218c4725915c1b9cbe6b6f149e7d4/kallisto
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/dd0e6474e26e1c1890768c5ba4b893/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/b6f0e4a893bdda1ab76c19af1707ef/rna_s1221_S42_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_s1221_S42_1.fastp.fastq.gz
                             rna_s1221_S42_2.fastp.fastq.gz
[quant] finding pseudoalignments for the reads ...
[progress] 1M reads processed (96.3% mapped)             
[progress] 2M reads processed (96.4% mapped)             
[progress] 3M reads processed (96.4% mapped)             
[progress] 4M reads processed (96.4% mapped)             
[progress] 5M reads processed (96.4% mapped)             
[progress] 6M reads processed (96.4% mapped)             
[progress] 7M reads processed (96.4% mapped)             
[progress] 8M reads processed (96.4% mapped)             
[progress] 9M reads processed (96.4% mapped)              done
[quant] processed 9,932,006 reads, 9,571,272 reads pseudoaligned
[quant] estimated average fragment length: 175.9
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,172 rounds