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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_1a94fa1a-9f83-4a64-8507-6ae6d58b1d80/ 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 832 reads, 74 reads pseudoaligned
	
	
[alignment] Processing pseudoalignment
[alignment] Processed 1675 reads, 74 pseudoaligned to HLA reference
[alignment] 74 reads mapped to a single HLA gene
[alignment] Observed HLA genes:
		gene          abundance    read count    classes
		HLA-A             9.23%             7          7
		HLA-B            54.53%            41         40
		HLA-C            11.84%             9          9
		HLA-E            13.36%            10         10
		HLA-G             4.27%             3          3
		HLA-J             1.32%             1          1
		HLA-K             1.33%             1          1
		HLA-L             1.32%             1          1
		HLA-V             2.80%             1          1
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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] Not enough reads aligned to HLA-B to genotype.
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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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