Example run failure about peaks2utr

[haessar]

I wonder, are you using macOS? I've spotted the same issue presenting for another tool GoogleCloudPlatform/gsutil#961. The consensus seems to be that the combination of multiprocessing, python3.8 and macOS can lead to this (with gsutil, anyway).
If you are using macOS, can you try to run the demo again using a conda env with python 3.9 to see if the issue persists?

[haessar]

Another thing to try (either with python 3.8 or 3.9), as you are using a conda env, you might need to run pip install buildtools after activating it, and before running pip install peaks2utr. I believe some of the peaks2utr dependencies (such as MACS2) were failing to install due to the lack of buildtools. If this works for you, I'll add a note in the README.

[jasonleongbio]

Thanks @haessar

Indeed I'm using macOS. Sorry for forgetting to mention this.
May I know if preferably it should be run on a linux-based machine?

I just tried to re-install by following the additional step (pip install buildtools) before installing peaks2utr. I also replaced Python with version 3.9 (3.9.16) this time. (I'm still trying with my macOS device though.)
But sadly I still got the error message (at the same step).

The error messages are exactly the same as the previous ones.

[haessar]

Yes it's only been tested on Linux systems, and not on macOS (perhaps I should add that info to the README). If you need to continue using mac, can you try cloning the source code, and adding
multiprocessing.set_start_method("fork")
near the top of utils.py. Then build and install as described here https://github.com/haessar/peaks2utr#installation.

(from https://stackoverflow.com/a/73902878/6683132)

[jasonleongbio]

Thank you so much @haessar

I tried to run the example code on my local (macOS) device just because my own mapped BAM files have all been transferred from the Linux server to my local harddisks.

I just tried to execute the example run on my Linux server and it worked perfectly fine! So the problem on my side was really because I was using macOS instead of a Linux system.

And thanks so much for your advice on the additional multiprocessing code. I guess it would be useful to specify which line to add to the file instead of simply stating "near the top" of that file.