BUSCO - issue reading the fasta file
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!
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
EggNOG-mapper problem
written by Salma •
-
Imputation from plink
written by michael.flower.14 •
-
Tutorial: Getting the lineage of an organism from NCBI taxonomy data
written by vimalkvn
-
Unable to install bwa-0.7.17 on ubuntu 10.06 virtualbox machine.
written by ricfoz •
-
kover installation problem: include could not find load file: GatbCore
written by hfan22 •
-
Can Pymsxml Run Under Activepython V2.5.5?
written by Neilfws
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?Thank you :-) I solved it, I had forgotten to define the paired end reads!