BUSCO - issue reading the fasta file
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4.7 years ago
BioBing ▴ 130

Hoping that some of you experienced BUSCO users can help me:

What I did:

  • Using the virtualbox (ubuntu) for BUSCO on MacOS (BUSCO v2 using Ubuntu virtual machine, with all dependencies included from the BUSCO webpage)
  • Downloaded my fasta file trinity.fa (with wget) from dropbox to the virtual machine and saved it in the "busco2" under a folder called "MyProject1" (created by mdir). I have opened the file, and it seems fine.
  • Downloaded the eukaryota_odb9 lineage and extracted it in the lineage folder under BUSCOVM
  • wrote in the ubuntu terminal: python BUSCO.py -i trinity.fa -o transcriptome -l eukaryota_odb9 -m trans

What happened: ERROR Impossible to read trinity.fa

Does anyone know how to overcome this error?

Thank you!

BUSCO RNA-Seq Assembly software error • 2.2k views
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While this is strictly not a bioinformatics question .. here goes. Have you tried to provide directory path: python BUSCO.py -i /path_to/MyProject1/trinity.fa -o transcriptome -l eukaryota_odb9 -m trans?

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Thank you :-) I solved it, I had forgotten to define the paired end reads!

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