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Error regarding output directory #21
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Hello! I believe the error happens for two reasons:
With those points in mind, based on the following suggested command line I'd change name of the annotation file, and inputing the full output folder path before running it for the file of interest: Feel free to try it out with said adjustment and to come back to me if there's still issues. Best, |
Hello I got this error, what might be the possible issues in here?
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Hello, I assume you executed At the moment of writing (v1.0.0), the script execution is limited to execution from Right now I/O operations on those files are coded assuming the main script is executed in the original directory, but a reasonable update could be to generalize its use. To answer and hopefully resolve your issue I would execute the script from the Best, |
actually i create a singularity images for this folder seems to be there in that singularity. So I have no idea above how this tools works. |
I guess I'll need a little more info than what you provided then! For instance it could be relevant if you shared what command you used to run A high-level view of how the tool works is included in the manuscript (https://doi.org/10.1016/j.csbj.2022.03.015) and in this Github repository. I'm lacking details regarding Singularity, though, so I'm not really sure how much it matters for your specific problem here. |
Here's are my commands below:
Hope this will sort it out the issues. |
@shibormi I'm not totally familiar with singularity, as I mentioned earlier, nonetheless I'm trying to identify potential issues. Similarly to the main issue that was raised here (by user: timeresistance1996) I assume it could be due to the -O (or --path_output) argument not using an absolute path, whereas it is actually required by I'm not 100% sure that would be possible within the singularity program. Secondly, the way you structured that command line within singularity points to both your Lastly, and connected to your first message in this issue, I'm not entirely sure singularity maintains the If you have suggestions in how to modify kemet source code to help with this issue, feel free to suggest, I'll be receptive! Best, |
Thank you for your code, but I encountered an issue when running it.
This is how I used it. Under the 'eggnog' directory, there is a file named 'emapper.annotations', and under the 'genome' directory, there is a file named 'genome.fna'. The code I used is
python ./kemet.py -I ./eggnog -a eggnog --skip_hmm --skip_gsmm ./genome -q --log --path_output ./output
However, an error occurred: FileNotFoundError: [Errno 2] No such file or directory: './output/ktests/'
Strangely, when I manually created the entire folder, the code seemed to run smoothly, but no output file was generated.
I got the same error even when using your test files.
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