Issue with hisatgenotype

[Januaryyiyue]

Hello,

I am trying to run hisatgenotype. I installed both hisat2/2.2.1 and hisatgenotype. Here's my exact command:

python3 /cluster/home/user/hisatgenotype/hisatgenotype --base hla --locus-list A -1 file_R1_10000.fastq.gz -2 file-BL_R2_10000.fastq.gz

I then get the following message:

	1: Extracting reads from file_R1_10000.fastq.gz
No /cluster/home/user/hisatgenotype/indicies/hla.graph.1.ht2 file found
No /cluster/home/user/hisatgenotype/indicies/hla.graph.1.ht2 file found
Error: indexing HLA failed! Perhaps, you forgot to build hisat2 executables?

I checked my /indices directory and found the following files:

genome.fa               genotype_genome.coord      hla_backbone.fa
genome.fa.fai           genotype_genome.fa         hla.haplotype
genotype_genome.1.ht2   genotype_genome.fa.fai     hla.index.snp
genotype_genome.2.ht2   genotype_genome.haplotype  hla.link
genotype_genome.3.ht2   genotype_genome.index.snp  hla.locus
genotype_genome.4.ht2   genotype_genome.link       hla.partial
genotype_genome.5.ht2   genotype_genome.locus      hla_sequences.fa
genotype_genome.6.ht2   genotype_genome.partial    hla.snp
genotype_genome.7.ht2   genotype_genome.snp        hla.snp.freq
genotype_genome.8.ht2   grch38                     hla.version
genotype_genome.allele  hisatgenotype_db
genotype_genome.clnsig  hla.allele

Please let me know what I can do to fix this issue. Thank you so much.

[alicebraun]

I'm encountering exactly the same error. Let me know if you have found a solution