Closed esraagithub closed 1 year ago
Vini2
commented
2 years ago Hello @esraagithub,
There is no need to run fastg2gfa for metaspades assemblies. Metaspades already provides the assembly graph in .gfa format and that should be used in MetaCoAG.
Let me know how it goes. Please feel free to let me know if you have any further questions.
Best regards, Vijini
esraagithub
commented
2 years ago Yes i have a memory issue in running metaspades at my labtop so i have to do so at Galaxy and it is a default to give fastg file. It isn't available to make Galaxy give gfa.
Also the error message is about the path file Thank you for your concern
في الخميس، ٢٤ مارس ٢٠٢٢ ٦:٤٧ ص Vijini Mallawaarachchi < @.***> كتب:
Hello @esraagithub https://github.com/esraagithub,
There is no need to run fastg2gfa for metaspades assemblies. Metaspades already provides the assembly graph in .gfa format and that should be used in MetaCoAG.
Let me know how it goes. Please feel free to let me know if you have any further questions.
Best regards, Vijini
— Reply to this email directly, view it on GitHub https://github.com/Vini2/MetaCoAG/issues/17#issuecomment-1077093145, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMY4XZTN4NHTD2GENZUBURTVBPXV3ANCNFSM5RNZNFJA . You are receiving this because you were mentioned.Message ID: @.***>
Vini2
commented
2 years ago If it is okay with you, can you share with me the contigs.fasta, contigs.paths and assembly graph file? I can take a look and see what the issue.
Vini2
commented
1 year ago Closing issue due to inactivity.
Hello
Could you help me, please? i got an error after running metacoag
i am sure that the path to my path file is correct
i used metaspades for metagenome assembly and then converted .fastg graph file to .gfa file using fastg2fga tool in this link :https://github.com/lh3/gfa1/tree/master/misc
what is the reason behind that error? can fastg2fga be used to with metaspades or only megahit?
thank you so much