Errors when chromosome length is >2G

[xiekunwhy]

Hi,

I am trying to use hisat2 to map RNA-seq data to a genome with chromosome length larger than 2G, hisat2 always die out with errors,

Time loading forward index: 00:01:11
Time loading reference: 00:00:00
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
(ERR): hisat2-align died with signal 6 (ABRT) 

Are these error caused by large chromosome ? And how to solve this problem?

Best,
Kun

[eead-csic-compbio]

Hi @xiekunwhy , in case it helps, I had the same problem until I split my long > 2Gbp chrosomes in 1Gbp chunks and now is mapping fine