search

gamcil / clinker

Gene cluster comparison figure generator
MIT License
507 stars 66 forks source link

Error in clinker HTML plotting function #99

Open Nitin123-4 opened 1 year ago

Nitin123-4 commented 1 year ago

Hi, I am trying to generate a synteny/orthology figure for a family of genes among 4 species of interest. The genes within each of these species code for proteins belonging to the same protein family. Using the gff and corresponding genome pasta files, I ran clinker using the following command:

clinker ~/OUR_DATA/ -p Res.html -o Res.txt

The output of clinker is pasted below:

[17:11:47] INFO - Starting cluster alignments [17:11:48] INFO - krait_3ftx_genes vs Greenmamba_3FTx_genes [17:11:48] INFO - krait_3ftx_genes vs Colletts_3FTx_genes [17:11:48] INFO - krait_3ftx_genes vs Nigricollis_3FTx_genes [17:11:48] INFO - Greenmamba_3FTx_genes vs Colletts_3FTx_genes [17:11:48] INFO - Greenmamba_3FTx_genes vs Nigricollis_3FTx_genes [17:11:48] INFO - Colletts_3FTx_genes vs Nigricollis_3FTx_genes [17:12:03] INFO - Generating results summary... [17:12:03] INFO - Writing alignments to: Res [17:12:04] INFO - Building clustermap.js visualisation [17:12:04] INFO - Writing to: Res.html [17:12:04] INFO - Done!

I redirected the alignment output to Res.txt where I do see pairwise alignment identity/similarity rates >0.75 for several query and target pairs. See attached the complete Res.txt file.

However the resulting HTML file does not render any genes or links between genes. See screenshot below for your reference.

image

Can you please help resolve this bug/issue as soon as possible?

Appreciate your help!

Thanks, Nitin Res.txt