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gamcil / clinker

Gene cluster comparison figure generator
MIT License
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Error in plot Visualization #64

Open uneeb-bot opened 3 years ago

uneeb-bot commented 3 years ago

Having issues in visualization of plot on internet explorer after the run is completed. I am using the gene bank files generated by RAST server and using four plasmid sequence for comparison. In the start of run warning signs (shown below) appears and then cluster alignment started once the run is finished internet explorer page appears on the screen showing only clinker instructions but no plots. Please help me to solve this issue @gamcil not find parent gene of . Using coding sequence coordinates instead. [12:21:45] WARNING - Could not find parent gene of . Using coding sequence coordinates instead. [12:21:45] WARNING - Could not find parent gene of . Using coding sequence coordinates instead. [12:21:45] WARNING - Could not find parent gene of . Using coding sequence coordinates instead. [12:21:45] WARNING - Could not find parent gene of . Using coding sequence coordinates instead. [12:21:45] WARNING - Could not find parent gene of . Using coding sequence coordinates instead. [12:21:45] WARNING - Could not find parent gene of . Using coding sequence coordinates instead. [12:21:45] WARNING - Could not find parent gene of . Using coding sequence coordinates instead

gamcil commented 3 years ago

Hi, is it possible for you to upload the files?

You can ignore those warnings, all they mean is that coding sequences could not find a parent gene sequence, so they will use the start/end positions of the coding sequences instead.

uneeb-bot commented 3 years ago

I am attaching two sequences: pAPEC_E956.zip pAPEC_16_1068.zip

gamcil commented 3 years ago

Sorry for taking a while to get back to this. I can't confirm this issue, running clinker on my end with those two files produces: image

The WARNING - Could not find parent gene of . Using coding sequence coordinates instead messages can be ignored - your files only have CDS features in them, so there are no genes to use at all.

All I can really suggest is re-running, or maybe opening in a different browser? Also, are you on clinker v0.0.20?

gabyga16 commented 3 years ago

Hello! Iam having a similar issue. im trying to compare two gene clusters from the same genome, for which im using two gbk files generated by RAST with only the genes in each cluster. While running I get the same warning :"WARNING - Could not find parent gene of . Using coding sequence coordinates instead." and although I get a plot, it doesn't show any genes (screenshot attached). Is something I can do to solve this? hope you can help :) @gamcil

Captura de Pantalla 2021-06-25 a la(s) 22 45 25

agavriilidou commented 7 months ago

You can try to unclick the "show genes to scale". I had the same problem and I had to correct the genbank file. It was because of the gene coordinates that the plot was so skewed.