Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/ef5d1527101e2289b751125ea98fcf/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/2c/da9bfa44afd9fb82393b460efe6b14/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/d06450a3cbb69cc754f82391f47125/kallisto
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/da9bfa44afd9fb82393b460efe6b14/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/ef5d1527101e2289b751125ea98fcf/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 9,932,006 reads, 9,571,272 reads pseudoaligned
[quant] estimated average fragment length: 175.4
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,263 rounds