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ComparativeGenomicsToolkit / hal

Hierarchical Alignment Format
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hal2mafMP.py Cannot allocate memory #298

Closed bright-hu closed 8 months ago

bright-hu commented 8 months ago

Hello， When I use hal2mafMP.py, I get an error, “OSError: [Errno 12] Cannot allocate memory”. However, the memory is enough. The command is “hal2mafMP.py --noDupes --refGenome Scleropages_formosus --refSequence NC_041814.1 --numProc 10 --sliceSize 10 --hdf5InMemory test.hal test.maf” and "hal2mafMP.py --noDupes --refGenome Scleropages_formosus --refSequence NC_041814.1 --numProc 10 --sliceSize 10 test.hal test.maf"

Do you know any solutions to solve this error? I would appreciate it if you can help me.

glennhickey commented 8 months ago

Please see the documentation and examples about MAF exporting here:

https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/progressive.md#maf-export