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Published 20 hours ago • verified publisher icon nanoporetech

fasta file upload error

Open AnunayS opened this issue 3 years ago • 5 comments

I tried several commands after the reference file path in the resquiggle command but every time it is showing the following error. Untitled

However the minimap2 is working fine. I tried running basic command given on the minimap2 github page, they are working fine.

Please let me know if any one can help me with the issue.

Thankyou.

AnunayS avatar Jun 05 '21 12:06 AnunayS

Hi AnunayS. Are you totally sure that your FASTA filepath is correct?

SycamoreLeaf avatar Jun 08 '21 14:06 SycamoreLeaf

Yes the fasta file path is correct. I am just not sure whether the command I am writing is correct or not because I am finding several different commands for the same.

AnunayS avatar Jun 10 '21 05:06 AnunayS

@AnunayS Have you tried removing the leading slashes from the filepaths?

SycamoreLeaf avatar Jun 10 '21 21:06 SycamoreLeaf

I tried that too but still the same error. It will be kind of you if you can give me a command that has actually worked for you so that I can try it out. That way I will be sure that the command is correct but there can be some installation problem with tombo or minimap2.

AnunayS avatar Jun 11 '21 05:06 AnunayS

You could run python -c 'import mappy; aligner = mappy.Aligner("/tombotest/fast5/msmeg.fasta")' to help diagnose the underlying issue here.

marcus1487 avatar Jun 15 '21 13:06 marcus1487