Comments (11)
Colud you attach or send the .ds on which it breaks? I will look into it...
from p2rank.
HEADER: prediction protein
dir_test/1a52.pdb
dir_test/2a52.pdb
This is how my .ds file looks like. I used only 2 files for testing. I also tried including their whole path but it doesn't work like that.
from p2rank.
In your case the header should be
HEADER: protein
because you have only one data column in the file. You can compare it with other *.ds files in test_data directory. Let me know if it helped.
I will add more halpful error message for this case. Thank you for reporting this.
from p2rank.
I tried it with HEADER: protein and it still gives me the error
"""P2Rank 2.0
ERROR: dataset contains invalid files"""
It doesn't read the files whereas when I try it with one of the .ds from test_data it works. I still don't understand why.
from p2rank.
Do all the pdb files exist? The paths should be relative to the location of *.ds file.
If so, you could try removing the heather altogether.
If it doesn't help, could you attach the zip file with your working directory including ds file and pdb files?
from p2rank.
Yes all the pdb files exist. I used the paths relative to the .ds file only. I transferred my .ds file and the directory with pdb files to test_data folder in p2rank_2.0 and it works now. I still do not understand why. I can use this but would really like to know the reason behind it.
Thanks !
from p2rank.
It's probably a bug. Could you help me to reproduce it? I will need some more information.
What is your operating system and shell (bash/cmd/...)?
What was the exact full command that produced the error and in what directory it was executed?
What was the directory structure (location of p2rank, ds file and pdb files)?
from p2rank.
Yes I thought so too that it was a bug.
Sure.
I am using bash terminal on Kubuntu16.04. I executed the command "./prank predict test.ds -o test_output" in the p2rank_2.0 directory and my .ds file and the directory containing the pdb files were in the same folder (p2rank_2.0).
Hope it helps you to solve the bug. Let me know if you need more information.
from p2rank.
Fixed in version 2.0.1 (https://github.com/rdk/p2rank/releases/tag/2.0.1).
@purvi24, thank you for the bug report and provided details!
from p2rank.
@rdk I'm also experiencing the issue, even in 2.0.1 and 2.1.
Running:
/opt/p2rank_2.1-dev.1/prank predict -f file.pdb works
while
/opt/p2rank_2.1-dev.1/prank predict dataset.ds doesn't
dataset.ds:
file.pdb
from p2rank.
I was not able to reproduce the problem with version 2.0.1. Could you provide more details? What is your operating system and what was the output the run? Could you also include <p2ank_dir>/log/prank.log?
Version 2.1-dev.1 indeed has that problem but this is to be expected since it has been released before the bugfix. I will create new 2.1-dev.2 release with the bugfix, but first let's figure out what is the problem with the version 2.0.1 so I can include fix for that as well.
from p2rank.
Related Issues (20)
- Does p2rank require git ? HOT 1
- Add README section about running dockerized version
- Any idea why there is a difference?
- Java options unrecognized by OpenJDK 15 HOT 1
- Make p2rank behave more like a standard unix program by default (wrt output location and working directory) HOT 2
- Add probability to output *_predictions.csv file HOT 1
- Add README section abut P2Rank framework
- Extend and reorganize documentation
- Bug in -conservation_dirs argument parsing HOT 2
- Output directory parameter `-o` is sometimes ignored. HOT 1
- Building on WSL failing HOT 2
- easy way to get features HOT 2
- Issue with loading mmCIF files created in PyMOL HOT 3
- Out of memory error HOT 1
- installation not clear? HOT 12
- dataset-joined pdb_residues file doesn`t match with fasta sequence
- File path in *.ds file HOT 3
- [SUGGESTION] Release Binary Should Log To STDERR instead of to install directory HOT 1
- Dataset contains invalid files HOT 2
- No SLF4J providers were found! 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 p2rank.