Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/9d987c5c8df046f7f4a619e267e157/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1_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/dd/9d987c5c8df046f7f4a619e267e157/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/cbd700059645eea2a3c03d9ece103d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/20e95d6a200022f004e69bf9014134/kallisto
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/cbd700059645eea2a3c03d9ece103d/.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: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz
                             1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz
[quant] finding pseudoalignments for the reads ...
[progress] 1M reads processed (98.1% mapped)             
[progress] 2M reads processed (98.1% mapped)             
[progress] 3M reads processed (98.1% mapped)             
[progress] 4M reads processed (98.1% mapped)             
[progress] 5M reads processed (98.1% mapped)             
[progress] 6M reads processed (98.1% mapped)             
[progress] 7M reads processed (98.1% mapped)             
[progress] 8M reads processed (98.1% mapped)             
[progress] 9M reads processed (98.1% mapped)             
[progress] 10M reads processed (98.1% mapped)             
[progress] 11M reads processed (98.1% mapped)              done
[quant] processed 11,357,275 reads, 11,145,767 reads pseudoaligned
[quant] estimated average fragment length: 111.8
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,289 rounds