Hisat2-build (5.ht2 and 6.ht2 are missing)

Question

[tokitokito99]

Hi all,

I am trying to index the reference.fasta file using hisat2/stringtie. First I want to index the genome using hisat2. (hisat2-build ref.fa ref)

The manual states that 8 files should be produced after indexing 1.ht2 to 8.h2t. However, I only have six files with this suffix (5.ht2 and 6.ht2 are missing).

Does anyone know why this is? Was there an error with indexing or can I use these files as is?

Please help me

[ATpoint]

Your indexing might have crashed. Check your logs. Which genome are you indexing and how much memory is available?