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