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nanoporetech / modkit

A bioinformatics tool for working with modified bases
https://nanoporetech.com/
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`dmr multi` will not create necessary directories #294

Open Yang990-sys opened 2 weeks ago

Yang990-sys commented 2 weeks ago

After following your guidance in #143 , we have made the following attempts: image

while, all regions failed for the following reason: image

In order to check for file errors, I gave different sample names to four samples, and the results were normal： image

Is there any way to solve my problem？

Yang990-sys commented 2 weeks ago

my modkit version : image

Yang990-sys commented 2 weeks ago

I found the problem. The problem is that the output folder must exist, otherwise an error will occur after creating the folder.

ArtRand commented 2 weeks ago

Hello @Yang990-sys,

Thanks for finding this. I think modkit dmr should make the folder if it doesn't exist to align it's behavior with the rest of the commands. I'll make sure to add this to the next release.

ArtRand commented 2 weeks ago

I'm going to keep this open to track the work. Thanks again for noticing the inconsistency.

Yang990-sys commented 3 days ago

The reason I found seems inaccurate because I encountered this error again. Looking forward to software updates

ArtRand commented 1 day ago

Hello @Yang990-sys,

Could you attach the log file for the command that is failing to this thread? Also could you run

tabix -l ${sample}

for each of the samples you have and attach that as well?

Yang990-sys commented 20 hours ago

Because there is no problem running for a single sample, it should not be an issue with the index itself. When there is a duplicate, the first step of the program is to merge the duplicate samples. So I guess it may be because the merged file cannot use the original index?