Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/0e8d4d7f3fd87e87f44e1574a9e0dd/659_bCu-T1-TRNA-1_B23WHTKLT4_1_2.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/ce/f57475d263d9dd6ad84a1cc5c0d760/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/0e8d4d7f3fd87e87f44e1574a9e0dd/659_bCu-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/7e3399ff93089af48e91d5b34147b7/kallisto Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/f57475d263d9dd6ad84a1cc5c0d760/.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: 659_bCu-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz 659_bCu-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz [quant] finding pseudoalignments for the reads ... [progress] 1M reads processed (97.3% mapped) [progress] 2M reads processed (97.2% mapped) [progress] 3M reads processed (97.2% mapped) [progress] 4M reads processed (97.2% mapped) [progress] 5M reads processed (97.2% mapped) [progress] 6M reads processed (97.2% mapped) [progress] 7M reads processed (97.2% mapped) [progress] 8M reads processed (97.2% mapped) [progress] 9M reads processed (97.2% mapped) [progress] 10M reads processed (97.2% mapped) [progress] 11M reads processed (97.2% mapped) [progress] 12M reads processed (97.2% mapped) [progress] 13M reads processed (97.2% mapped) [progress] 14M reads processed (97.2% mapped) [progress] 15M reads processed (97.2% mapped) [progress] 16M reads processed (97.2% mapped) [progress] 17M reads processed (97.2% mapped) [progress] 18M reads processed (97.2% mapped) [progress] 19M reads processed (97.2% mapped) [progress] 20M reads processed (97.2% mapped) [progress] 21M reads processed (97.2% mapped) [progress] 22M reads processed (97.2% mapped) [progress] 23M reads processed (97.2% mapped) [progress] 24M reads processed (97.2% mapped) [progress] 25M reads processed (97.2% mapped) [progress] 26M reads processed (97.2% mapped) [progress] 27M reads processed (97.2% mapped) [progress] 28M reads processed (97.2% mapped) [progress] 29M reads processed (97.2% mapped) [progress] 30M reads processed (97.2% mapped) [progress] 31M reads processed (97.2% mapped) [progress] 32M reads processed (97.2% mapped) [progress] 33M reads processed (97.2% mapped) [progress] 34M reads processed (97.2% mapped) [progress] 35M reads processed (97.2% mapped) [progress] 36M reads processed (97.2% mapped) [progress] 37M reads processed (97.2% mapped) [progress] 38M reads processed (97.2% mapped) [progress] 39M reads processed (97.2% mapped) [progress] 40M reads processed (97.2% mapped) [progress] 41M reads processed (97.2% mapped) [progress] 42M reads processed (97.2% mapped) [progress] 43M reads processed (97.2% mapped) [progress] 44M reads processed (97.2% mapped) [progress] 45M reads processed (97.2% mapped) [progress] 46M reads processed (97.2% mapped) [progress] 47M reads processed (97.2% mapped) [progress] 48M reads processed (97.2% mapped) [progress] 49M reads processed (97.2% mapped) [progress] 50M reads processed (97.2% mapped) [progress] 51M reads processed (97.2% mapped) [progress] 52M reads processed (97.2% mapped) [progress] 53M reads processed (97.2% mapped) [progress] 54M reads processed (97.2% mapped) [progress] 55M reads processed (97.2% mapped) [progress] 56M reads processed (97.2% mapped) [progress] 57M reads processed (97.2% mapped) [progress] 58M reads processed (97.2% mapped) [progress] 59M reads processed (97.2% mapped) [progress] 60M reads processed (97.2% mapped) [progress] 61M reads processed (97.2% mapped) [progress] 62M reads processed (97.2% mapped) [progress] 63M reads processed (97.2% mapped) [progress] 64M reads processed (97.2% mapped) [progress] 65M reads processed (97.2% mapped) [progress] 66M reads processed (97.2% mapped) done [quant] processed 67,466,119 reads, 65,601,007 reads pseudoaligned [quant] estimated average fragment length: 121.1 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,567 rounds