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TKSjp / HaplotypeExplorer

HaplotypeExplorer is an interactive haplotype network viewer for spatiotemporal dissection of multimodal epidemic spectra.
GNU General Public License v3.0
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Error when running createHTML.py script #1

Closed AndreaAguadoM closed 2 years ago

AndreaAguadoM commented 2 years ago

Hello, my name is Andrea. I am trying to use the HaplotypeExplorer tool in order to study some quasispecies sequences that proceed from the same sample. Specifically, I am trying to run this script with a multifasta file containing these quasispecies' sequences as input, as it follows: python createHTML.py, within a directory where the input.fasta is contained. At the same time, within the Source directory, I have placed the reference.fasta file that I want to use, but I do obtain the following errors:

ERROR: Alignment not loaded: "input.mafft.fasta" Check the file's content.

and then later:

Fatal Error: Failed to open the database file Program halted !!

I've been checking the different files this tool creates, and for example, input2.fasta remains empty after the program gets killed. I think I am trying to run Haplotype Explorer in the wrong way. Could someone help me?

Thanks in advance!

TKSjp commented 2 years ago

Hi

ERROR: Alignment not loaded: "input.mafft.fasta" Check the file's content.

This indicates trimal could not load the alignment data generated by mafft (input.mafft.fasta), which is from input2.fasta. The input2.fasta is multi-fasta file automatically generated by the seqkit and sed. So there may be problem in running sed or seqkit.

Would you check whether sed and seqkit correctly executed?

Thanks