Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/84b854aec6755e3297cddd8b6f2696/22Rv1_FFPE_RNA_0001_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/b3/84b854aec6755e3297cddd8b6f2696/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/2955dd0a113dbaaebcdbfe5d20614e/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/c4515bbdeed07cfb548c8478389ad2/kallisto Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/2955dd0a113dbaaebcdbfe5d20614e/.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: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1_2.fastp.fastq.gz [quant] finding pseudoalignments for the reads ... [progress] 1M reads processed (83.3% mapped) [progress] 2M reads processed (83.4% mapped) [progress] 3M reads processed (83.3% mapped) [progress] 4M reads processed (83.4% mapped) [progress] 5M reads processed (83.4% mapped) [progress] 6M reads processed (83.4% mapped) [progress] 7M reads processed (83.3% mapped) [progress] 8M reads processed (83.3% mapped) [progress] 9M reads processed (83.3% mapped) [progress] 10M reads processed (83.3% mapped) [progress] 11M reads processed (83.3% mapped) [progress] 12M reads processed (83.3% mapped) [progress] 13M reads processed (83.3% mapped) [progress] 14M reads processed (83.3% mapped) done [quant] processed 14,388,080 reads, 11,988,865 reads pseudoaligned [quant] estimated average fragment length: 102.0 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,256 rounds