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shendurelab / MPRAflow

A portable, flexible, parallelized tool for complete processing of massively parallel reporter assay data
Apache License 2.0
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Running MPRAflow without internet #46

Closed xunchen85 closed 3 years ago

xunchen85 commented 3 years ago

Hi,

Our HPC computing nodes do not have the access to the internet. Is there any way to run it without connection?

I am also trying it locally in my personal Ubuntu, although i got the error of "create BWA ref." which was previously reported to be the out of memory issue?

I am wondering what is the memory needed to run your test dataset?

Thanks, Xun

visze commented 3 years ago

Hi Xun,

The issue #45 is not an memory issue. For the test set not much memory is needed. Here it seems that the design file is empty and this causes the error. Mabye it is the same in you case. can you check the design_rmIllegalChars.fa file in your out folder? Also the initial design.fa file if any of them is empty? On my side I cannot reproduce the error.

About your problem with internet connection. We are using conda to dowload the dependencies. So you need at least one node (maybe your login node) that has access to the internet and to you file system. There you can run mpraflow first. It should install the dependencies. Then you cancel it and run it on the cluster again using the --resume in nextflow.

Meanwhiel I will try to find the issue about the create_BWA_ref process..

Best, Max

xunchen85 commented 3 years ago

Hi Max,

I tried it on our login node, although our server set a cap of 8Gb. I was not able to run the association.nf tool with the Out of Memory issue even though MPRAflow may not need so much.

Regarding the create reference issue, sorry that I refer to your previous reply to #45. I have pasted some example lines of design.fa I obtained in #45, and the design_rmIllegalChars.fa is empty.

Thanks, Xun