Index building failed
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9 weeks ago
Gaye • 0

For H.sapiens , after downloading the index file via the link and unzip/untar, I ran the .sh file with the bash command. bash make_grch38_tran.sh

Everything was ok until generation 4, when it hits the generation 4 I got the index building failed error as you can see in the output image.

I thought it might a connection error because mine is not stable, so I tried again but it kept giving the same error. Could you please help me with that?

hisat2 • 370 views
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9 weeks ago
ATpoint 68k

If you download a premade index such as this one then it's ready to use. Running the indexing again defeats the purpose of downloading that index and requires extensive memory which you probably don't have, it likely gets killed due to out-of-memory. Just use the included index files for your alignment, no need to build anything.

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Thanks for your reply, I'm new to this stuff and thought I had to run the .sh file first to be able to use the indexes.