This is a test version of Biostars. For the public version, visit https://www.biostars.org.
hisat2-build half done

I was running hisat2-build on wheat genome. It seems to me the job stopped somehow. I got 7 files, it's clear that the job is half done. How do I know what's wrong in the process? Am I supposed to run the whole process from top again?
output file

rna-seq
• 1,742 views • link
updated by michael.ante michael.ante • written by crystalpang • crystalpang

You should get used to save the logs that the tool produces, e.g. with 2> to collect stderr to a file. This will tell you if something went wrong. In this case 7 and 8 seem suspiciously small. I would re-do it and collect the logs.

• 0 views • link
written by ATpoint ATpoint

Thank you. I am redoing it now. It would be perfect if the program can pick up from where it went wrong, the wheat genome is huge and the index building really takes time.

• 0 views • link
written by crystalpang • crystalpang

1 answer

Wheat has a huge genome. With STAR I needed more than 145 GB memory and some tricks as described in several post to reduce the Index size.

I don't know what memory footprint Hisat2 is producing, but I guess you have similar memory requirements.

Cheers,

Michael

• 0 views • link
written by michael.ante michael.ante

Log in to answer this question.

More posts like this