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asl / BandageNG

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
GNU General Public License v3.0
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Error loading .gfa file in BandageNG - "Malformed path string for path 'EU305676.1'" #164

Open florenmartino opened 1 day ago

florenmartino commented 1 day ago

Hi, I'm encountering an error when attempting to open a .gfa file in BandageNG. The following message appears:

There was an error when attempting to load /home/florenmartino/Documents/Code/Dylans_results/AS5/AS5_24mo.all_contigs.minimus.multi_assembly.norm.gfa: malformed path string for path 'EU305676.1', cannot reconstruct path through the graph

I've verified with others gfa files, and I could open the same file in another computer using BandageNG. I'm using BandageNG in a computer under

Linux system76-pc 6.9.3-76060903-generic #202405300957~1726766035~22.04~4092a0e~dev-Ubuntu SMP PREEMPT_DY x86_64 x86_64 x86_64 GNU/Linux

The Bandage that Im using is BandageNG-9eb84c2-x86_64.AppImage from

https://github.com/asl/BandageNG/releases/tag/continuous

Could you please confirm if this file format is supported or if there might be an issue with specific path strings in the .gfa file?

Thanks for your help!

asl commented 19 hours ago

Will you please attach the graph in question?

florenmartino commented 14 hours ago

I try in a Mac, and same issue with the file. I was able to open it using the standard Bandage software (Ryan Wick, the older version), and it worked.

AS5_24mo.all_contigs.minimus.clean.multi_assembly.norm.txt

I uploaded as .txt but of course im openning with .gfa

Thanks in advance!