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gagneurlab / drop

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
MIT License
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Error in rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R #541

Closed mmartinezj closed 1 month ago

mmartinezj commented 1 month ago

Hi,

when trying to run the aberrant splicing module, the following error appears:

drop_error_3

(I don't have more info about the error, the only log file I found was the snakemake one and it had the same info that the screenshot).

Also, before this error appears, at some point it states the strand is not specified:

drop_error_4

But as you can see on the next screenshot, I have added a column for strandedness:

strandedness

I don't know if this is relevant for the error itself, but just in case it is related. Thanks in advance!

Best,

Miriam

vyepez88 commented 1 month ago

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

mmartinezj commented 1 month ago

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

AtaJadidAhari commented 1 month ago

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

mmartinezj commented 1 month ago

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!

r_packages

error_1

error_2

If you need more information, please let me know.

Best,

Miriam

AtaJadidAhari commented 1 month ago

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.

mmartinezj commented 1 month ago

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

vyepez88 commented 1 month ago

great to hear Miriam!

mmartinezj commented 1 month ago

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:

error_3

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.

vyepez88 commented 1 month ago

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

mmartinezj commented 1 month ago

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!