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Error in checkForAndCreateDir #558
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Hi, hard to say, the error |
Hi, thanks for the prompt response. I believe I am providing sufficient memory for the run - I'm running DROP on a machine with 256GB memory and 30cores. I re-ran the same set of 10 samples with |
Hi, can you check what the output of |
Hi, |
Also, I should add that when I run the same module on a single sample with external counts from 10 other samples, this AberrantSplicing_pipeline_Counting_03_filter_expression_FraseR_R script runs without error. |
I believe I am running into the same error (DROP version 1.3.3). I have managed to run through the splicing module previously when using external counts. In this run I only have a set of ~100 non-external samples. The AE module went through without external counts. Looking in A bit up in the R script I see that it is symlinking if no external counts are present. Can it be related to this? Seems
The singularity container I am using to run DROP uses Here is my stack trace:
|
Any thoughts on this one? This is the one step blocking us at the moment from evaluating the DROP output in our data. |
Hi @Jakob37, I cannot reproduce this issue and haven't seen it before. My guess is that if you remove the directory (output/processed_data/aberrant_splicing/datasets/savedObjects/raw-fraser) and re-run the pipeline, it will run successfully. |
Hello @AtaJadidAhari and thank you for taking the time to look into this. I digged into this a bit more. I could indeed reproduce the error, and also tried removing the soft-link as you mentioned, which did not solve it. The issue seems to be that the soft link to the
This causes the crash as such:
I tried hard-coding in the absolute path for the work dir into the DROP-script, and then the step successfully went through. Unsure why it sometimes works then, as it works for you. Might be a version issue? (Edit: I see now that the author of the issue has the same issue with the latest version). Or something with running it through SLURM. I am using a container running DROP 1.3.3 (running this through the nextflow pipeline Tomte). |
OK, after some more digging I think I have figured out the issue. It seems the current code will only work if provided an absolute path. If given a relative path, it will crash here. The working dir is calculated as such:
The
I suspect At the moment (as generated by the Nextflow pipeline I am running), it is provided as such, i.e. with a relative path:
I think we could fix this in the Tomte pipeline, such that this isn't an issue. It would be helpful though with an early error for relative paths if not allowed. |
Thanks @Jakob37 for digging out! We'll now see on our side how to prevent this. |
Hi,
I'm running DROP v1.4.0 on a set of 10 samples, with only the AberrantSplicing and AberrantExpression modules. The AberrantExpression module completes successfully, but I get the following error with the AberrantSplicing module:
This is what I have in my config file:
And this is the snakemake command:
snakemake --cores 3 -k
Please let me know if there's something that needs to be updated in the config file. Thanks!
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