cdsoria

Hi @simonvh, I was actually waiting for the fix as I have the same issue of memory. Using the ananse network I got to 65% and then it is killed....

Hello @simonvh. No problem at all and happy to help. I tried with n2, n1 and no 'n',, but I get the same error. It seems something about wanting to...

Thanks @simonvh so it goes a bit further but stops at Computing network ananse network -b tests/data/network/binding.tsv.gz -e tests/data/network/heart_expression.txt -o test_network.txt -n 2 2021-06-28 16:27:05 | INFO | Loading expression...

@simonvh Just to say that, when I go back to my previous version of Ananse ("pip install git+https://github.com/vanheeringen-lab/ANANSE.git@9de0982"), your test data runs ok. I am re-running again with the full...

@simonvh Thank you so much again. So this time it goes further to 99% but then it hangs in there, as it stops and re-starts workers. I tested this in...

> Huh, that worker memory is too high, it should no reach more than 4/5GB. Can you double-check something for me, and post the output of this: > > ```...

> You can also try running the command like this > > ``` > OMP_NUM_THREADS=1 ananse network -b fibroblast.binding/binding.tsv -e ANANSE_example_data/RNAseq/fibroblast*TPM.txt -n 4 -o fibroblast.network.txt > ``` Hi again @simonvh...

> So you also get this on an Amazon EC2 instance right? That should make it possible to see if we can reproduce and thereby test this. Do you have...

> Great! Just out of curiosity, what is the total memory size of the computer on which it failed? Sure, this my hardware overview: Model Name: MacBook Pro Model Identifier:...

> Thanks. Mac is indeed a platform that we don't test. If you have some time, can you check if the following works on your Mac? > > ``` >...