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/6b/9aad8d8e54b7b05ea659daa741227d/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/7747672e215b7907a88a16b9aed1e7/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/9aad8d8e54b7b05ea659daa741227d/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/5464a09423970b06d10705502a1736/kallisto Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/7747672e215b7907a88a16b9aed1e7/.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: aih-tih-sc-0ce15f-R1_A23WJ53LT4_1_1.fastp.fastq.gz aih-tih-sc-0ce15f-R1_A23WJ53LT4_1_2.fastp.fastq.gz [quant] finding pseudoalignments for the reads ... [progress] 1M reads processed (97.9% mapped) [progress] 2M reads processed (97.8% mapped) [progress] 3M reads processed (97.8% mapped) [progress] 4M reads processed (97.8% mapped) [progress] 5M reads processed (97.8% mapped) [progress] 6M reads processed (97.8% mapped) [progress] 7M reads processed (97.8% mapped) [progress] 8M reads processed (97.8% mapped) [progress] 9M reads processed (97.8% mapped) [progress] 10M reads processed (97.8% mapped) [progress] 11M reads processed (97.8% mapped) [progress] 12M reads processed (97.8% mapped) [progress] 13M reads processed (97.8% mapped) [progress] 14M reads processed (97.8% mapped) [progress] 15M reads processed (97.9% mapped) [progress] 16M reads processed (97.9% mapped) [progress] 17M reads processed (97.9% mapped) [progress] 18M reads processed (97.9% mapped) [progress] 19M reads processed (97.9% mapped) [progress] 20M reads processed (97.9% mapped) [progress] 21M reads processed (97.9% mapped) [progress] 22M reads processed (97.9% mapped) [progress] 23M reads processed (97.9% mapped) [progress] 24M reads processed (97.9% mapped) [progress] 25M reads processed (97.9% mapped) [progress] 26M reads processed (97.9% mapped) [progress] 27M reads processed (97.9% mapped) [progress] 28M reads processed (97.9% mapped) [progress] 29M reads processed (97.9% mapped) [progress] 30M reads processed (97.9% mapped) [progress] 31M reads processed (97.9% mapped) [progress] 32M reads processed (97.9% mapped) [progress] 33M reads processed (97.9% mapped) [progress] 34M reads processed (97.9% mapped) [progress] 35M reads processed (97.9% mapped) [progress] 36M reads processed (97.9% mapped) [progress] 37M reads processed (97.9% mapped) [progress] 38M reads processed (97.9% mapped) [progress] 39M reads processed (97.9% mapped) [progress] 40M reads processed (97.9% mapped) [progress] 41M reads processed (97.9% mapped) [progress] 42M reads processed (97.9% mapped) [progress] 43M reads processed (97.9% mapped) [progress] 44M reads processed (97.9% mapped) [progress] 45M reads processed (97.9% mapped) [progress] 46M reads processed (97.9% mapped) [progress] 47M reads processed (97.9% mapped) [progress] 48M reads processed (97.9% mapped) [progress] 49M reads processed (97.9% mapped) [progress] 50M reads processed (97.9% mapped) [progress] 51M reads processed (97.9% mapped) [progress] 52M reads processed (97.9% mapped) [progress] 53M reads processed (97.9% mapped) [progress] 54M reads processed (97.9% mapped) [progress] 55M reads processed (97.9% mapped) [progress] 56M reads processed (97.9% mapped) [progress] 57M reads processed (97.9% mapped) [progress] 58M reads processed (97.9% mapped) [progress] 59M reads processed (97.9% mapped) [progress] 60M reads processed (97.9% mapped) [progress] 61M reads processed (97.9% mapped) [progress] 62M reads processed (97.9% mapped) [progress] 63M reads processed (97.9% mapped) [progress] 64M reads processed (97.9% mapped) [progress] 65M reads processed (97.9% mapped) [progress] 66M reads processed (97.9% mapped) [progress] 67M reads processed (97.9% mapped) [progress] 68M reads processed (97.9% mapped) [progress] 69M reads processed (97.9% mapped) [progress] 70M reads processed (97.9% mapped) [progress] 71M reads processed (97.9% mapped) [progress] 72M reads processed (97.9% mapped) [progress] 73M reads processed (97.9% mapped) [progress] 74M reads processed (97.9% mapped) [progress] 75M reads processed (97.9% mapped) [progress] 76M reads processed (97.9% mapped) [progress] 77M reads processed (97.9% mapped) [progress] 78M reads processed (97.9% mapped) [progress] 79M reads processed (97.9% mapped) [progress] 80M reads processed (97.9% mapped) [progress] 81M reads processed (97.9% mapped) [progress] 82M reads processed (97.9% mapped) [progress] 83M reads processed (97.9% mapped) [progress] 84M reads processed (97.9% mapped) [progress] 85M reads processed (97.9% mapped) [progress] 86M reads processed (97.9% mapped) [progress] 87M reads processed (97.9% mapped) [progress] 88M reads processed (97.9% mapped) [progress] 89M reads processed (97.9% mapped) [progress] 90M reads processed (97.9% mapped) [progress] 91M reads processed (97.9% mapped) [progress] 92M reads processed (97.9% mapped) [progress] 93M reads processed (97.9% mapped) [progress] 94M reads processed (97.9% mapped) [progress] 95M reads processed (97.9% mapped) [progress] 96M reads processed (97.9% mapped) [progress] 97M reads processed (97.9% mapped) [progress] 98M reads processed (97.9% mapped) [progress] 99M reads processed (97.9% mapped) [progress] 100M reads processed (97.9% mapped) [progress] 101M reads processed (97.9% mapped) [progress] 102M reads processed (97.9% mapped) [progress] 103M reads processed (97.9% mapped) [progress] 104M reads processed (97.9% mapped) [progress] 105M reads processed (97.9% mapped) [progress] 106M reads processed (97.9% mapped) [progress] 107M reads processed (97.9% mapped) [progress] 108M reads processed (97.9% mapped) [progress] 109M reads processed (97.9% mapped) [progress] 110M reads processed (97.9% mapped) [progress] 111M reads processed (97.9% mapped) [progress] 112M reads processed (97.9% mapped) [progress] 113M reads processed (97.9% mapped) [progress] 114M reads processed (97.9% mapped) [progress] 115M reads processed (97.9% mapped) [progress] 116M reads processed (97.9% mapped) [progress] 117M reads processed (97.9% mapped) [progress] 118M reads processed (97.9% mapped) [progress] 119M reads processed (97.9% mapped) [progress] 120M reads processed (97.9% mapped) [progress] 121M reads processed (97.9% mapped) [progress] 122M reads processed (97.9% mapped) [progress] 123M reads processed (97.9% mapped) [progress] 124M reads processed (97.9% mapped) [progress] 125M reads processed (97.9% mapped) [progress] 126M reads processed (97.9% mapped) [progress] 127M reads processed (97.9% mapped) [progress] 128M reads processed (97.9% mapped) [progress] 129M reads processed (97.9% mapped) [progress] 130M reads processed (97.9% mapped) [progress] 131M reads processed (97.9% mapped) [progress] 132M reads processed (97.9% mapped) [progress] 133M reads processed (97.9% mapped) [progress] 134M reads processed (97.9% mapped) [progress] 135M reads processed (97.9% mapped) [progress] 136M reads processed (97.9% mapped) [progress] 137M reads processed (97.9% mapped) [progress] 138M reads processed (97.9% mapped) [progress] 139M reads processed (97.9% mapped) [progress] 140M reads processed (97.9% mapped) [progress] 141M reads processed (97.9% mapped) [progress] 142M reads processed (97.9% mapped) [progress] 143M reads processed (97.9% mapped) [progress] 144M reads processed (97.9% mapped) [progress] 145M reads processed (97.9% mapped) [progress] 147M reads processed (97.9% mapped) [progress] 148M reads processed (97.9% mapped) [progress] 149M reads processed (97.9% mapped) [progress] 150M reads processed (97.9% mapped) [progress] 151M reads processed (97.9% mapped) [progress] 152M reads processed (97.9% mapped) [progress] 153M reads processed (97.9% mapped) [progress] 154M reads processed (97.9% mapped) [progress] 155M reads processed (97.9% mapped) [progress] 156M reads processed (97.9% mapped) [progress] 157M reads processed (97.9% mapped) [progress] 158M reads processed (97.9% mapped) [progress] 159M reads processed (97.9% mapped) [progress] 160M reads processed (97.9% mapped) [progress] 161M reads processed (97.9% mapped) [progress] 162M reads processed (97.9% mapped) [progress] 163M reads processed (97.9% mapped) [progress] 164M reads processed (97.9% mapped) [progress] 165M reads processed (97.9% mapped) [progress] 166M reads processed (97.9% mapped) [progress] 167M reads processed (97.9% mapped) [progress] 168M reads processed (97.9% mapped) [progress] 169M reads processed (97.9% mapped) [progress] 170M reads processed (97.9% mapped) done [quant] processed 170,457,736 reads, 166,798,365 reads pseudoaligned [quant] estimated average fragment length: 119.1 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,414 rounds