Question: hisat2-build half done
0
gravatar for crystalpang
6 weeks ago by
crystalpang0 wrote:

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 • 156 views
ADD COMMENTlink modified 29 days ago by michael.ante3.3k • written 6 weeks ago by crystalpang0

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.

ADD REPLYlink written 6 weeks ago by ATpoint17k

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.

ADD REPLYlink written 6 weeks ago by crystalpang0
0
gravatar for michael.ante
29 days ago by
michael.ante3.3k
Austria/Vienna
michael.ante3.3k wrote:

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

ADD COMMENTlink written 29 days ago by michael.ante3.3k
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