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Dear Prof. Poland,
Thanks for giving AnchorWave a try and sharing this problem.
I will discuss fasta file parsing with my colleagues in the Buckler Lab. We may update the code to make it work or update the document to let users avoid this type of inputs.
Some types of fasta headers are not being read correctly if they are using an identifier syntax.
>gi|1
is not read to match the gff file
it runs correct when I renamed to just
>1
assembly files that created this issue are found here
https://genomevolution.org/CoGe/GenomeInfo.pl?gid=51527
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