nanoporetech
`dmr multi` will not create necessary directories
After following your guidance in #143 , we have made the following attempts:
while, all regions failed for the following reason:
In order to check for file errors, I gave different sample names to four samples, and the results were normal：
Is there any way to solve my problem？
I found the problem. The problem is that the output folder must exist, otherwise an error will occur after creating the folder.
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.
I'm going to keep this open to track the work. Thanks again for noticing the inconsistency.
The reason I found seems inaccurate because I encountered this error again. Looking forward to software updates
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?
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?
Hello @Yang990-sys,
I understand. It would still be helpful for me to debug what's going on if you can provide the logfile dmr_multi.log. Modkit never actually merges the files, it queries the tables for multiple samples and merges the counts. So the data access for each table/index should be the same - that's what's confusing. I'll try and get to the bottom of this problem ASAP.
@Yang990-sys Just to be sure. All of the pileups use the same reference, which in this case is all_transcripts.fa, correct?
I wrote a python script for merging bedmethyl files, and I want to know if it's scientific to merge first and then run modkit dmr
@Yang990-sys would you be willing to share the data that exposes the problem with me? We can do it through email so that it's not publicly accessible. My email is art.rand [at] nanoporetech.com