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[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
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[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_dcbe5c67-b36d-4e14-95c0-ea5f721939c7/ 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 1,151 reads, 137 reads pseudoaligned
	
	
[alignment] Processing pseudoalignment
[alignment] Processed 2416 reads, 137 pseudoaligned to HLA reference
[alignment] 137 reads mapped to a single HLA gene
[alignment] Observed HLA genes:
		gene          abundance    read count    classes
		HLA-A            19.60%            27         21
		HLA-B            64.42%            88         79
		HLA-C            13.03%            18         17
		HLA-E             2.94%             4          4
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[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
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[genotype] Genotyping HLA-A
[genotype] Not enough reads aligned to HLA-A to genotype.
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[genotype] Genotyping HLA-B
[genotype] 88 reads aligned to HLA-B in 79 classes
[genotype] Top 10 alleles by undivided read count:
		allele                  read count	
		B*51:01:63                      50	
		B*51:01:01                      49	
		B*51:01:05                      49	
		B*51:01:07                      49	
		B*51:01:55                      49	
		B*51:01:56                      49	
		B*51:01:57                      49	
		B*51:01:60                      49	
		B*51:01:61                      49	
		B*51:01:64                      49	

[genotype] Quantifying allele transcript abundance
[genotype] EM converged after 24 iterations

[genotype] Top alleles by abundance:
		allele                  abundance
		B*51:01:63                 73.21%
		B*51:220                   26.79%

[genotype] Pairs by % explained reads:
		allele pair                     explained	
		B*51:01:63, B*51:220                73.86%	

[genotype] Checking zygosity
[genotype] Likely heterozygous: minor/major nonshared count 0.37

[genotype] Most likely genotype explaining 65 reads:
		B*51:01:63
		B*51:220
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[genotype] Genotyping HLA-C
[genotype] Not enough reads aligned to HLA-C to genotype.
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[genotype] Genotyping HLA-DPA1
[genotype] Not enough reads aligned to HLA-DPA1 to genotype.
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[genotype] Genotyping HLA-DPB1
[genotype] Not enough reads aligned to HLA-DPB1 to genotype.
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[genotype] Genotyping HLA-DQA1
[genotype] Not enough reads aligned to HLA-DQA1 to genotype.
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[genotype] Genotyping HLA-DQB1
[genotype] Not enough reads aligned to HLA-DQB1 to genotype.
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