cactus_coverage takes a lot of memory

glennhickey / progressiveCactus

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules

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cactus_coverage takes a lot of memory #38

Open tsackton opened 9 years ago

tsackton commented 9 years ago

Hi folks,

We are finding that the cactus_coverage step often takes a lot of memory, such that it typically fails to run with the default (littleMemory) amount of memory requested. Is there any way to have this step run with mediumMemory or bigMemory? I cannot find anything in the config file that looks like it controls the memory for this step, but maybe I'm missing something.

Thanks.

cooketho commented 8 years ago

I'm experiencing the same problem. I'm using the grid engine batch system. As you say, it would be nice if there were a way to bump up the requested memory, either by getting a better estimate of what it needs before the first attempt, or by incrementing the memory request on the retry attempt after each failure. If I find anything out I'll let you know.

cmhill-zz commented 8 years ago

Do you have a suggestion of what to increase the memory to? I am encountering the same issue. Unfortunately, I am unable to re-run my command with increased memory, so I have to re-run everything from scratch: Error: Existing project ./results_final2/progressiveAlignment not compatible with current input. Please erase the working directory or rerun with the --overwrite option to start from scratch.