brie-factor utility causes error about brie HOT 4 CLOSED

Hi Stephanie,

Thanks for using BRIE, and apologize for the delay. I just tested the brie-factor on my machine and it works well, but I can't direct see the problem in your case.

First, I don't think it is the problem with from .utils.gtf_utils import loadgene as the loading annotation file can be finished.

Second, could you try a few things more to diagnose the bug:

• run brie-factor -a AS_events/SE.gold.gtf -r GRCm38.p5.genome.fa -c mm10.60way.phastCons.bw -o mouse_features.csv -p 1 this will use only one CUP so it will avoid the error from multiprocessing.
• run bigWigSummary to see whether you could run it directly.

Could you let me if you try these two things?

Best,
Yuanhua

from brie.

Dear Yuanhua,

Thanks for your reply.

• Running BRIE with the –p option leads to the same error I posted above.
• Running bigWigSummary directly in terminal works, e.g running bigWigSummary hg38.phyloP100way.bw chrX 4000 80000 1 has the output 0.0755242.

Best,
Stephanie

from brie.

Hi Stephanie,

Sorry I haven't figured out this error. I suspect this is because of the incompatibility between the python2.7/multiprocessing/pool.py and the system or some other Python packages. I found quite a few similar errors report by searching your error report. You may get some ideas of the bug.

In addition, it is strange to see the same error when you tried -p 1 option, as this mode won't use multiprocessing any more.

Let me know if you have any idea of the bug.

Best,
Yuanhua

from brie.

Hi Yuanhua,

I think I managed to fix my problem.

First I created a new conda environment just for BRIE because sometimes I have issues with version conflicts. Afterward I was able to run brie-factor with the –p 1 option without using multiprocessing.

However, I run into a new bug concerning subprocessing. Adding shell=True to the subprocessing command in your get_factor function in the fasta_utils.py file (line 130) solved that problem und brie-factor run successfully.

Best,
Stephanie

from brie.