my hisat cannot build index fileds normaly

Question

[sxm891114]

hello,

I used this command: hisat2-build -f genome.fa -p 4 genome

then I got 8 index files. Theoretically, there're 8 file named genome.1.ht2 to genome.8.ht2

but my output had .1.ht2 .2.ht2 .3.ht2 .4.ht2 .7.ht2 .8.ht2 and .2.sa .3.sa

lack of genome.5.ht2/.6.ht2 but 2 extra genome.2.sa/.3.sa

could you give me some help about that?

many thanks

Answer 1

[GenoMax]

As long as there was no error and you had 8 files you should be all set (A: How many index files will be generated from hisat2-build ). Move on to the mapping step.

[sxm891114]

thanks. I don't know if I should re-name the two .sa file. I'll try to move on directly

[WouterDeCoster]

You shouldn't rename them. The manual is unclear on the files created but there is nothing to worry about.

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[sxm891114]

Thanks, the problem has solved. I added a memory bank, then it worked normally

T_T