C stack usage error

[kieft1bp]

I am trying to run the following command in an R prompt within my shell terminal (not RStudio) in Ubuntu 20:

> algnEnv = cognac(fastaDir = "./all_genome_assemblies/",featureDir = "./all_genome_gffs/")

There are about 40 genomes in the assemblies and gff folders. If I try to run cognac on 20 of them it works fine, but I get the following error when I try to run them all:

Error: C stack usage 503376930900 is too close to the limit

Here is the output of > Cstack_info()

      size    current  direction eval_depth 
   7969177      22928          1          2 

Since I know that cognac can run on at least hundreds of genomes, why am I getting this error? I can't find a simple way to "increase" my C Stack limit.

[rdcrawford]

Sorry you're having trouble. Cognac should definitely be able to handle this dataset. Can you send me the full output so I know at which point it crashes?

[kieft1bp]

This is all I get, actually.

I get the same error (and the same brevity) in RStudio.

[kieft1bp]

The genomes are bacterial, about 4Mbp each.

I can iteratively remove genome/gff files until there are like 18-20 and then it works, but any larger number of inputs gives me the error.

[kieft1bp]

For anyone that finds this thread, I found the issue: one of my genomes had non-canonical nucleotides (Y, R, W, etc.). This is what broke the software.