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/90/b93eff8afebd4901e384b56c831777/tih_rna_sample_00575_B23MVV7LT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/4166c1963242d52283e61d8f60af86/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/b93eff8afebd4901e384b56c831777/tih_rna_sample_00575_B23MVV7LT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/0a594ab6c0ca65a871c6e125dd857a/kallisto
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/4166c1963242d52283e61d8f60af86/.command.run
==> 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: tih_rna_sample_00575_B23MVV7LT4_1_1.fastp.fastq.gz
                             tih_rna_sample_00575_B23MVV7LT4_1_2.fastp.fastq.gz
[quant] finding pseudoalignments for the reads ...
[progress] 1M reads processed (97.9% mapped)             
[progress] 2M reads processed (97.9% mapped)             
[progress] 3M reads processed (97.9% mapped)             
[progress] 4M reads processed (97.9% mapped)             
[progress] 5M reads processed (97.9% mapped)             
[progress] 6M reads processed (97.9% mapped)             
[progress] 7M reads processed (97.9% mapped)             
[progress] 8M reads processed (97.9% mapped)             
[progress] 9M reads processed (97.9% mapped)             
[progress] 10M reads processed (97.9% mapped)             
[progress] 11M reads processed (97.9% mapped)             
[progress] 12M reads processed (97.9% mapped)             
[progress] 13M reads processed (97.9% mapped)             
[progress] 14M reads processed (97.9% mapped)             
[progress] 15M reads processed (97.9% mapped)             
[progress] 16M reads processed (97.9% mapped)             
[progress] 17M reads processed (97.9% mapped)             
[progress] 18M reads processed (97.9% mapped)             
[progress] 19M reads processed (97.9% mapped)             
[progress] 20M reads processed (97.9% mapped)             
[progress] 21M reads processed (97.9% mapped)             
[progress] 22M reads processed (97.9% mapped)             
[progress] 23M reads processed (97.9% mapped)             
[progress] 24M reads processed (97.9% mapped)             
[progress] 25M reads processed (97.9% mapped)             
[progress] 26M reads processed (97.9% mapped)             
[progress] 27M reads processed (97.9% mapped)             
[progress] 28M reads processed (97.9% mapped)             
[progress] 29M reads processed (97.9% mapped)             
[progress] 30M reads processed (97.9% mapped)             
[progress] 31M reads processed (97.9% mapped)             
[progress] 32M reads processed (97.9% mapped)             
[progress] 33M reads processed (97.9% mapped)             
[progress] 34M reads processed (97.9% mapped)             
[progress] 35M reads processed (97.9% mapped)             
[progress] 36M reads processed (97.9% mapped)             
[progress] 37M reads processed (97.9% mapped)             
[progress] 38M reads processed (97.9% mapped)             
[progress] 39M reads processed (97.9% mapped)             
[progress] 40M reads processed (97.9% mapped)             
[progress] 41M reads processed (97.9% mapped)             
[progress] 42M reads processed (97.9% mapped)             
[progress] 43M reads processed (97.9% mapped)             
[progress] 44M reads processed (97.9% mapped)             
[progress] 45M reads processed (97.9% mapped)             
[progress] 46M reads processed (97.9% mapped)             
[progress] 47M reads processed (97.9% mapped)             
[progress] 48M reads processed (97.9% mapped)             
[progress] 49M reads processed (97.9% mapped)             
[progress] 50M reads processed (97.9% mapped)             
[progress] 51M reads processed (97.9% mapped)             
[progress] 52M reads processed (97.9% mapped)             
[progress] 53M reads processed (97.9% mapped)             
[progress] 54M reads processed (97.9% mapped)             
[progress] 55M reads processed (97.9% mapped)             
[progress] 56M reads processed (97.9% mapped)             
[progress] 57M reads processed (97.9% mapped)             
[progress] 58M reads processed (97.9% mapped)             
[progress] 59M reads processed (97.9% mapped)             
[progress] 60M reads processed (97.9% mapped)             
[progress] 61M reads processed (97.9% mapped)             
[progress] 62M reads processed (97.9% mapped)             
[progress] 63M reads processed (97.9% mapped)             
[progress] 64M reads processed (97.9% mapped)             
[progress] 65M reads processed (97.9% mapped)             
[progress] 66M reads processed (97.9% mapped)             
[progress] 67M reads processed (97.9% mapped)             
[progress] 68M reads processed (97.9% mapped)             
[progress] 69M reads processed (97.9% mapped)             
[progress] 70M reads processed (97.9% mapped)             
[progress] 71M reads processed (97.9% mapped)             
[progress] 72M reads processed (97.9% mapped)             
[progress] 73M reads processed (97.9% mapped)             
[progress] 74M reads processed (97.9% mapped)             
[progress] 75M reads processed (97.9% mapped)             
[progress] 76M reads processed (97.9% mapped)              done
[quant] processed 76,710,456 reads, 75,108,163 reads pseudoaligned
[quant] estimated average fragment length: 112.2
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,398 rounds