Genmap map genome/chromsome size limit

[o-william-white]

Hello,

Is there a genome or chromosome size limit with Genmap map?

I am trying to run genmap map for a 48GBp krill genome and I am getting an error. Note that I had no issues with genmap index.

I get the following error message:

terminate called after throwing an instance of 'std::out_of_range'
  what():  stoi
/var/spool/slurm/job23547968/slurm_script: line 17:  3767 Aborted                 (core dumped) genmap map -K 36 -E 0 -I genmap_index/${BASENAME} -O genmap_map/${BASENAME} -t -w -bg --threads 16

I have increased the memory to 2T and I still get the same message.

Alternatively, if it is a memory issue, is there anything I can do to reduce disk usage?

Cheer
Ollie

[colindaven]

I'm not the dev, and this repo is not maintained.

I use this tool on wheat 15-17GB and it works well but consumes a lot of resources.

I can well imagine most tools will fail on a massive genome like krill though. How long are the chromosomes ? Maybe you need to check the integers / longs etc used in the tool for storing chromosome length.

Have you tried a low-resource repeat masker like Red or ncbi's windowmasker?

[o-william-white]

Hi @colindaven,

Thanks for the reply and heads up that this is no longer maintained. I too have used this on the wheat genome and it worked well.

The longest chromosmome is 4,374,437,920 and I suspect this could be the cause.

If it was a simple case of changing the bit sizes for the storage of integers, that could be an easy fix. Unfortunalty I don't have much experience in C. I will have a read and see if I can figure out a workaround.

The easiest option may be to split up the genome and run it using this.

Thanks again

All the best

Cheers
Ollie