Hisat2-build index error

Question

[emily449977]

Hi there,

I'm trying to use hisat2-build to index my genome but it keeps coming back errors. I'm not sure how to fix it and I'm stuck on this. Could someone give me any advice please? Thank you so much!!

I used command of below:

hisat2-build -p 7 --ss nasonia_genome.ss --exon nasonia_genome.exon nasonia_genome.fa hisat2_index_nv/nasonia_tran

The error comes back as:

Could not open file for reading a reference graph: "hisat2_index_nv/nasonia_tran.0.rf"
Error:encountered internal HISAT2 exception (#1)
Deleting "hisat2_index_nv/nasonia_tran.1.ht2l" file written during aborted indexing attempt.

.... and so on

[ATpoint]

Does folder hisat2_index_nv exist?

[emily449977]

yes i have made the hisat2_index_nv folder

Answer 1

[lieven.sterck]

do you have enough storage space left on your device (laptop, desktop, server) ?

[emily449977]

That was indeed the problem, once I switched to an interactive node with less restrictions on our server, the command just ran perfectly! Thank you!