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:
Hello,
I am trying to run hisatgenotype. I installed both hisat2/2.2.1 and hisatgenotype. Here's my exact command:
I then get the following message:
I checked my /indices directory and found the following files:
Please let me know what I can do to fix this issue. Thank you so much.