Paths not found in bandageNG

[Ecoulembier]

I have a .gfa file with added P-lines, but once uploaded in BandageNG the path Length is considered '0'. I checked the input file and there are actually complete paths in the file for all the input assemblies. Is there another way to add the Paths to BandageNG?

[asl]

Likely your GFA has wrong format. We do not have good ways to diagnose this currently (though this is planned). Please attach the corresponding GFA, so I can take a look

[Ecoulembier]

Hi,

Here is the GFA I used: https://we.tl/t-nvdDay8FR0

Thanks in advance!

From: Anton Korobeynikov @.> Sent: Tuesday, 3 September 2024 17:19 To: asl/BandageNG @.> Cc: Ecoulembier @.>; Author @.> Subject: Re: [asl/BandageNG] Paths not found in bandageNG (Issue #159)

Likely your GFA has wrong format. We do not have good ways to diagnose this currently (though this is planned). Please attach the corresponding GFA, so I can take a look

— Reply to this email directly, view it on GitHub https://github.com/asl/BandageNG/issues/159#issuecomment-2326797028 , or unsubscribe https://github.com/notifications/unsubscribe-auth/BGPVHE726JN4RBZ57D2QEYTZUXHP3AVCNFSM6AAAAABNSIERX2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMRWG44TOMBSHA . You are receiving this because you authored the thread. https://github.com/notifications/beacon/BGPVHE26NNVEC2H6OSP5NJLZUXHP3A5CNFSM6AAAAABNSIERX2WGG33NNVSW45C7OR4XAZNMJFZXG5LFINXW23LFNZ2KUY3PNVWWK3TUL5UWJTUKWANOI.gif Message ID: @. @.> >

[asl]

The current version of Bandage-NG shows the following error message:

malformed path string for path 'SLF', cannot reconstruct the path through the graph

I went ahead and improved the error reporting further, so it now also shows: "no path between nodes s778+ => s780+".

And indeed, s778 is a deadend: