diff ERROR: bad order:

[IsaacDiaz026]

Hello,

I am trying to use dnmtools diff to calculate methylation differences between two .meth files generated using dnmtools counts. The command I used is dnmtools diff "$RESULTS"/hap1.sort.meth "$RESULTS"/hap2.sort.meth -o "$RESULTS"/2023-06-11_hap1_hap2_DiffMeth.diff -A

I get the following error :
ERROR: bad order:
chrom=chr1 [id=0] pos=0
appears after
chrom=chr1 [id=0] pos=140725478431896

I tried sorting the .meth files even though they are already sorted. One thing that is strange is a the end of the error message is says "pos=140725478431896". There is definitely not a position 140725478431896 in my data, since my genome is only 350 Mb. I also noticed that if I rerun the exact same command it generates the same error but with a different pos=Number at the end.

For example, the same command with the same input files produced the following error
ERROR: bad order:
chrom=chr1 [id=0] pos=0
appears after
chrom=chr1 [id=0] pos=7811889804981395782

[andrewdavidsmith]

Can you confirm that the two files have the same number of lines, and that the position number (all those digits) appears in the .meth file? You can verify the first with wc -l and the second with grep.

[IsaacDiaz026]

The two files both have 115903749 lines. The position number mentioned in the error does not appear in the .meth file.

[andrewdavidsmith]

Thanks. I'll try to look into this soon. In the meantime, any help you can give me reproducing this error would accelerate the process. I do understand your data might be confidential, so that might not be possible.

[IsaacDiaz026]

Can I share the .meth files to you through google drive?

[andrewdavidsmith]

Yes. And feel free to send me an email if you prefer.

[IsaacDiaz026]

Just shared it

[andrewdavidsmith]

I reproduced the error and it was pretty surface-level so I was able to fix it with some minor changes I think. It's fixed with 3266dde

If you are not able to build by cloning the repo, and want me to make a release, let me know. That might take a day or so.

[IsaacDiaz026]

If you could make a release that would be great. I am having trouble cloning the repo

[andrewdavidsmith]

@IsaacDiaz026 The new release is available. It should fix the problem you had. If it has more problems, please create another issue -- thanks for your input!

[xies4]

Can you confirm that the two files have the same number of lines, and that the position number (all those digits) appears in the .meth file? You can verify the first with wc -l and the second with grep.
Hi @andrewdavidsmith, I encountered the same error:

bad order:
chrom=chrUn_KI270315v1 [id=73] pos=89
appears after
chrom=chrUn_KI270315v1 [id=73] pos=829 

But I have different numbers of lines in the two input files. Is this required? I didn't read anything saying that the two input files have to have the same positions. Thanks.

[andrewdavidsmith]

@xies4 Please open a new issue.