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Unable to access jarfile /code/encyclopedia.jar #30
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Hi @animesh 👋 Thanks for giving nf-encyclopedia a try! To fix the error you're seeing here, you'll need to specify
However, I would highly recommend using our provided Docker container! To use the Dockerized version of the workflow, please verify that you first have Docker installed and running. Then you can run the workflow by adding the
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Thanks @wfondrie for tips! I could not make it work though :( first command i didn't really understand? Do i need to download jar file for encyclopedia separately and specify its path with switch --encycopedia.jar? Second command seems to have failed with following message
Any ideas how to proceed over this? Docker is running via WSL2
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This is only needed when running nf-encyclopedia without using Docker. The default value for As for the other error you encountered, I didn't see that you were using our test files in your original post. These files only contain one DIA window from a very short gradient, so there aren't enough detected peptides for Percolator to run successfully with the default parameters. Instead, for our tests we change the following in the pipeline configuration:
You can also specify this from the command line:
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Thanks again @wfondrie 👍🏽 Sorry for this noob q's, I think the command is working fine now but not sure what is the error in the end and where is the final result written?
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No worries @animesh! The "missing output" messages is NextFlow complaining that EncyclopeDIA did not produce the expected output files, in this case, because of an error. It looks like Percolator is failing for some reason while EncyclopeDIA is running:
How much memory does your system have? I'm wondering if this could be the problem. |
How much memory is needed @wfondrie? Currently i have allocated ~64G to WSL
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That should definitely be enough memory to run the pipeline. I didn't run into any issues like this when running on Windows. However, I have seen that Percolator error when a file is not found. What output files are you getting @animesh? |
I see the two directories, reports and work being created @cia23 , following is their tree structure
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Hi @animesh, We're trying to troubleshoot this, but haven't been able to reproduce the problem yet. Can you share the contents of |
Thanks for looking into this @wfondrie 👍🏽 That file seems to be emptpy?
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Hi @animesh, We're still having trouble reproducing this. Can you delete your After deleting these, please try rerunning the pipeline and post any log files, both in the new |
Looks like starting from scratch actually produced some sizeable files @wfondrie 👍🏽 Just to be sure, below is what to expect from this exercise?
because the reports/execution_report_2022-12-03_11-54-51.html says |
@wfondrie | I think I have same issue with different error. First, I used below code to run pipeline: First Trial
My input csv:Nextflow Log:Error:
I guess this error occurred because the 'encyclopedia.quant.proteins.txt' file is empty. Files:encyclopedia.quant.peptides-1.txt Second Trial
I changed the parameters and it increased the number of findings but got a different error. Error
Nextflow Log:Files:encyclopedia.quant.peptides.txt |
Hi @ggokturkk - this appears to be a different issue. From the first trial:
Yes this is exactly right. These are tiny test files, so we don't really expect to find much of anything at all. From the second trial:
The MSstats error here occurs because both of the proteins only have one observed peptide. My recommendation would be to try reanalyzing data from Searle et al. to get a full view of what nf-encyclopedia does. |
I am running the pipeline via WSL2 setup and getting the following error
The inputs are from base repo folder https://github.com/TalusBio/nf-encyclopedia/tree/main/tests/data
Any ideas how to proceed?
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