Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/847cf9946eb07c11015704a9f80e5a/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_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/55/c4515bbdeed07cfb548c8478389ad2/kallisto
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/d5ffa61273357281ba7fa1af33866e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/d5ffa61273357281ba7fa1af33866e/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/847cf9946eb07c11015704a9f80e5a/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1_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: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz
                             BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz
[quant] finding pseudoalignments for the reads ...
[progress] 1M reads processed (90.6% mapped)             
[progress] 2M reads processed (90.6% mapped)             
[progress] 3M reads processed (90.6% mapped)             
[progress] 4M reads processed (90.6% mapped)             
[progress] 5M reads processed (90.6% mapped)             
[progress] 6M reads processed (90.6% mapped)             
[progress] 7M reads processed (90.6% mapped)             
[progress] 8M reads processed (90.6% mapped)             
[progress] 9M reads processed (90.6% mapped)             
[progress] 10M reads processed (90.6% mapped)             
[progress] 11M reads processed (90.6% mapped)             
[progress] 12M reads processed (90.6% mapped)             
[progress] 13M reads processed (90.5% mapped)             
[progress] 14M reads processed (90.5% mapped)             
[progress] 15M reads processed (90.5% mapped)             
[progress] 16M reads processed (90.5% mapped)             
[progress] 17M reads processed (90.5% mapped)             
[progress] 18M reads processed (90.5% mapped)             
[progress] 19M reads processed (90.5% mapped)             
[progress] 20M reads processed (90.5% mapped)             
[progress] 21M reads processed (90.5% mapped)             
[progress] 22M reads processed (90.5% mapped)             
[progress] 23M reads processed (90.5% mapped)             
[progress] 24M reads processed (90.5% mapped)             
[progress] 25M reads processed (90.5% mapped)             
[progress] 26M reads processed (90.5% mapped)             
[progress] 27M reads processed (90.5% mapped)             
[progress] 28M reads processed (90.5% mapped)             
[progress] 29M reads processed (90.5% mapped)             
[progress] 30M reads processed (90.5% mapped)             
[progress] 31M reads processed (90.5% mapped)             
[progress] 32M reads processed (90.5% mapped)              done
[quant] processed 33,125,823 reads, 29,990,728 reads pseudoaligned
[quant] estimated average fragment length: 94.2
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,708 rounds