problem with repeatscout allocation memory

Question

[Chironex]

hello everybody, I'm using RepeatScout for the first time. I have my genome, that I call mygenome.fa . I have to follow some steps, first of all I need to build the lmer table using this scrpt ./build_lmer_table -l 14 -sequence mygenome.fasta -freq mygenome.freq but it returns to me this message:

Unable to allocate -1909681335 bytes for the sequence

Can anyone help me? thank you

Answer 1

[lieven.sterck]

looks you're running out of memory for that process.

Either add more memory to your job if you run it on a compute cluster or switch to a machine with more memory

[Chironex]

No because my cp has 15 Gb of memory, it is a problem of the software I think...

[GenoMax]

1909681335 bytes should be just about 2G. If your computer indeed has 15G then things should have worked. Are you running something else while trying to run this program?

[lieven.sterck]

we of course have no notion of the amount of memory it was already using when spitting out this message. The allocate usually points to 'extra' memory it's requesting to that specific moment, not the total amount of memory (that at least how I also interpret it)