Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/b2ec6a5e8e2c9415df34f192edce33/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/46/d22dce95a9c01db4347147996ba1d6/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/f0987298ca4c0c782ae3ea0235856b/kallisto
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/d22dce95a9c01db4347147996ba1d6/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/b2ec6a5e8e2c9415df34f192edce33/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 (96.4% 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 9,928,008 reads, 9,569,002 reads pseudoaligned
[quant] estimated average fragment length: 175.9
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,197 rounds