-------------------------------------------------------------------------------- [log] Date: 2020-08-01 [log] Sample: sample_1_fished [log] Input file(s): sample_1_fished.fastq sample_2_fished.fastq [log] Reference: 7ca733b18edab1fc837a34e3764b7d55e8dc93b0 -------------------------------------------------------------------------------- [alignment] Analyzing read length [alignment] Pseudoaligning with Kallisto: kallisto pseudo -i /projects/rwarren_prj2/bin/arcasHLA/scripts/../dat/ref/hla.idx -t 8 -o /tmp/arcas_30bcfc6d-4e40-45bb-be6a-4e71692e1269/ sample_1_fished.fastq sample_2_fished.fastq [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 11,226 [index] number of k-mers: 264,111 [index] number of equivalence classes: 25,101 [quant] running in paired-end mode [quant] will process pair 1: sample_1_fished.fastq sample_2_fished.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 545 reads, 66 reads pseudoaligned [alignment] Processing pseudoalignment [alignment] Processed 1120 reads, 66 pseudoaligned to HLA reference [alignment] 65 reads mapped to a single HLA gene [alignment] Observed HLA genes: gene abundance read count classes HLA-A 26.04% 17 16 HLA-B 46.33% 30 29 HLA-C 18.33% 12 12 HLA-E 9.31% 6 6 -------------------------------------------------------------------------------- [genotype] Genotyping parameters: population: prior minimum count: 75 max iterations: 1000 tolerance: 1e-06 drop iterations: 20 drop threshold: 0.1 zygosity threshold: 0.15 -------------------------------------------------------------------------------- [genotype] Genotyping HLA-A [genotype] Not enough reads aligned to HLA-A to genotype. -------------------------------------------------------------------------------- [genotype] Genotyping HLA-B [genotype] Not enough reads aligned to HLA-B to genotype. -------------------------------------------------------------------------------- [genotype] Genotyping HLA-C [genotype] Not enough reads aligned to HLA-C to genotype. -------------------------------------------------------------------------------- [genotype] Genotyping HLA-DPA1 [genotype] Not enough reads aligned to HLA-DPA1 to genotype. -------------------------------------------------------------------------------- [genotype] Genotyping HLA-DPB1 [genotype] Not enough reads aligned to HLA-DPB1 to genotype. -------------------------------------------------------------------------------- [genotype] Genotyping HLA-DQA1 [genotype] Not enough reads aligned to HLA-DQA1 to genotype. -------------------------------------------------------------------------------- [genotype] Genotyping HLA-DQB1 [genotype] Not enough reads aligned to HLA-DQB1 to genotype. --------------------------------------------------------------------------------