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/b8/4b87f7f93258b167e5def5dd8eb664/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/40d166b702ef9e8a80a7d745dd9360/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/bb7cc1d07e19f8d2500aee7658ea87/kallisto Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/4b87f7f93258b167e5def5dd8eb664/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/40d166b702ef9e8a80a7d745dd9360/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1_1.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_L03_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz [quant] finding pseudoalignments for the reads ... [progress] 1M reads processed (91.7% mapped) [progress] 2M reads processed (91.7% mapped) [progress] 3M reads processed (91.8% mapped) [progress] 4M reads processed (91.7% mapped) [progress] 5M reads processed (91.7% mapped) [progress] 6M reads processed (91.8% mapped) [progress] 7M reads processed (91.8% mapped) [progress] 8M reads processed (91.8% mapped) [progress] 9M reads processed (91.8% mapped) [progress] 10M reads processed (91.8% mapped) [progress] 11M reads processed (91.8% mapped) [progress] 12M reads processed (91.8% mapped) [progress] 13M reads processed (91.8% mapped) [progress] 14M reads processed (91.8% mapped) [progress] 15M reads processed (91.8% mapped) [progress] 16M reads processed (91.7% mapped) [progress] 17M reads processed (91.7% mapped) [progress] 18M reads processed (91.7% mapped) [progress] 19M reads processed (91.7% mapped) [progress] 20M reads processed (91.7% mapped) [progress] 21M reads processed (91.7% mapped) [progress] 22M reads processed (91.7% mapped) [progress] 23M reads processed (91.7% mapped) [progress] 24M reads processed (91.7% mapped) [progress] 25M reads processed (91.7% mapped) [progress] 26M reads processed (91.7% mapped) [progress] 27M reads processed (91.7% mapped) [progress] 28M reads processed (91.7% mapped) [progress] 29M reads processed (91.7% mapped) [progress] 30M reads processed (91.7% mapped) [progress] 31M reads processed (91.7% mapped) [progress] 32M reads processed (91.7% mapped) done [quant] processed 33,064,515 reads, 30,332,004 reads pseudoaligned [quant] estimated average fragment length: 91.6 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,322 rounds