Error in rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R about drop HOT 10 CLOSED

Hi @mmartinezj DROP 1.3.4 is available on GitHub now and you can install it using pip:
pip install git+https://github.com/gagneurlab/drop.git

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Hi, this is related to the fix we are now implementing. It will be out very soon, sorry!

from drop.

Hi Vicente,

thanks for letting me know! As it was at the beginning of the workflow I thought it had something to do with the installation or my own files. I will be looking foward for the next release then, thanks for the great job!

Best,

Miriam

from drop.

Hi Ata, thanks for the update. I have installed DROP 1.3.4 with pip, but I'm still facing errors. As my previous installation was with conda, I have installed DROP with pip and the dependencies on my own computer, but now I'm having more errors, both with the pipeline and R. I will leave some screenshots here in case I can have some help on what's going on. I have installed r-base with ubuntu but now it seems some packages/dependencies can't be installed. Thanks for the help in advance!

If you need more information, please let me know.

Best,

Miriam

from drop.

Hi, drop 1.3.4 is now also available in biconda since 2 hours ago. Please create a fresh environment and install it using mamba install -c bioconda drop=1.3.4. This will hopefully solve your issue.

If the issue still persists, please first try to run drop demo:

mkdir ~/drop_demo
cd ~/drop_demo
drop demo
snakemake -c4

Please let me know if the demo runs through or not, then we can investigate the issue in more details.

from drop.

Hi, I have just finished running the demo with the conda install and it run smoothly. Thanks!

from drop.

great to hear Miriam!

from drop.

Hi, after testing the demo run, it went smoothly, but today, when trying to use my data, I'm facing a new problem but at the same point:

I have rerun the demo but changing fraser to fraser2, just in case it was a problem with fraser version, but it all went correctly too. Thus, I guess it's something related to my data, but I don't know where the problem is. Sorry for reopening the issue. I appreciate all the help and feedback! Thanks in advance.

from drop.

Hi, that's usually related to memory. Can you provide more memory to the run or use less cores?

from drop.

Hi, after testing the use of different cores, indeed is a memory issue. Once I used less cores, the pipeline started running. I keep having those memory issues (even with 1 core), but that's a problem of my own resources. Thank you very much for replying so fast and all the feedback!

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