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RolandFaure / Hairsplitter

Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.
GNU General Public License v3.0
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Fasta assembly not recognized #1

Closed alexvasilikop closed 1 year ago

alexvasilikop commented 1 year ago

Hello,

Thanks for developing such useful tools.

For some reason my assembly file is not recognized:

python3 hairsplitter.py -i $assembly -f $reads -x ont -t 12 -o $outdir

    ******************
    *                *
    *  Hairsplitter  *
    *    Welcome!    *
    *                *
    ******************

ERROR: Assembly file must be in GFA or FASTA format. File extension not recognized.

I have tried with both .fasta and .fa extensions. Any idea what the issue is? I am using 

HairSplitter v1.3.0 (RolandFaure/HairSplitter). Last update: 2023-07-20

Thanks Alex

alexvasilikop commented 1 year ago

Ok apparently the issue was that it most likely expects a .gfa file. When I renamed the fasta file to have a .gfa extension then it worked. Perhaps something to improve in the future.

cheers

RolandFaure commented 1 year ago

Hi Alex, This was a bug occuring when handling the fasta files. Thank you very much for bringing it up, the bug has been corrected in the new version 1.3.1. If you ever need to convert fasta to gfa, do not simply change the name of the file, this will confuse HairSplitter. Actually transform the fasta into GFA (with 'S' lines only).

Do not hesitate if you have other issues :smiley: