Error: C stack usage 11957956 is too close to the limit

[mzwaig]

Hi Gavin,

I'm trying to run the moleculeCoverage snakemake file and I keep getting the error
Error: C stack usage 11957956 is too close to the limit. The main suggestion to deal with this seems to be by increasing the stack size with ulimit but I'm working on a cluster can't adjust that.

I also can't seem to load the wig file although I think this is unrelated.
wigToGRanges: WIG file '' not found.

Any suggestions are appreciated.

Thank you,
Melissa

tumor_HSJ-75.molCov.log

[gavinha]

Hi @mzwaig

This sounds like a potential memory issue. See if you can increase the memory limits on your job (e.g. mem_free and h_vmem).

Best,
Gavin

[mzwaig]

Hi Gavin,

I increased the memory a bit and it's now telling me there's a recursion error at the same point. I'm guessing this is why it's running out of memory.

Error: evaluation nested too deeply: infinite recursion / options(expressions=)?

Best,
Melissa

normal_1_HSJ-75.molCov.log