Comments (11)
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
.
from dnmtools.
The two files both have 115903749 lines. The position number mentioned in the error does not appear in the .meth file.
from dnmtools.
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.
from dnmtools.
Can I share the .meth files to you through google drive?
from dnmtools.
Yes. And feel free to send me an email if you prefer.
from dnmtools.
Just shared it
from dnmtools.
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.
from dnmtools.
If you could make a release that would be great. I am having trouble cloning the repo
from dnmtools.
@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!
from dnmtools.
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 withwc -l
and the second withgrep
.
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.
from dnmtools.
@xies4 Please open a new issue.
from dnmtools.
Related Issues (20)
- Error executing dnmtools pmd (core dumped) probably related to GSL HOT 4
- selectsites failing with poor message on unsorted sites processed on disk
- dnmtools diff Error HOT 4
- Calling HMRs on the DNA Methylation Atlas Data HOT 4
- roi "cannot sort data unless all data is loaded" HOT 3
- mlml "error: chrom or pos mismatch in both files" HOT 3
- Keep non-CpG sites after sym command
- Broken progress bar
- roi -M return different values for "number of CpGs in the region" for different count files HOT 3
- roi should check for input files before reporting any problems with arguments
- pmd crash if insufficient data unless verbose mode used HOT 1
- -v flag opposite in guessprotocol
- A question for 'dnmtools allelic' HOT 2
- format: max distance when merging mates seems ignored
- merge -t header seems to be not properly formatted HOT 3
- HMR crash when nothing identified
- bad count line HOT 1
- resolved.
- unknown vectorizer cost model ‘very-cheap’ HOT 6
- summary hmr_count is non-zero but hmr output file is empty HOT 5
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from dnmtools.