5. Troubleshooting

Common Problems Encountered

While installing GViz on my Mac, I run into some errors surrounding RMySQL...

Simply run conda install -c bioconda mysqlclient in your terminal before you retry installing Gviz.

I get an error saying the fst_reference.fasta cannot be found!? It just made it!

I haven't got around to solving this one, but if you just rerun the pipeline with the exact same snippet, the genome generation stage should continue as per usual.

ERROR: Column assignment failure. Are you sure you selected the correct columns, are they in the right format?

This occurs when the incorrect information is presented to the Clinker tool, i.e. you've assigned the wrong columns via
the -col argument OR the information in those columns is in a format that the tool does not understand.

Imagine if you will... two formats of data from a fusion caller.

Output 1 sample name Chromosome 1 Name Breakpoint 1 Chromosome 2 Name Breakpoint 2
Biology_rulz chr1 21321543 chr2 423143123
Biology_rulz chr13 21321543 chr21 423143123

The -col argument for the above format should be
-col 2 3 4 5

Output 2
sample name Breakpoint 1 Breakpoint 2
Biology_rulz chr1:21321543 chr2:423143123
Biology_rulz chr13:21321543 chr21:423143123

The -col argument for the above format should be
-col 2 3

If there is another format, you can simply just do some data manipulation to form a two or four column file for input
into Clinker. You can do it, I believe in you. If not, just contact me!

I get a segmentation fault on the Linux for Windows Subsystem?

Known issue, trying to figure it out!

The too many stacks error

This occurs when there is simply too much trying to be printed on the defined PDF sizes. Increase the PDF height OR
reduce the information in protein_domains.bed file (usually the culprit).