Hi, 

I am trying to create a HISAT2 index with annotation for Rattus_norvegicus (RAT) genome I downloaded from the Ensembl  release 94. 

I am currently using 220GB memory with 16 cores. My assumption is the memory which I am providing is adequate enough. But I can not create the HISAT2 index, and it gives the error of 

    Reserving space for joined string
    Joining reference sequences
      Time to join reference sequences: 00:00:16
      Time to read SNPs and splice sites: 00:00:04
            is not reverse-deterministic, so reverse-determinize...
      Ran out of memory; automatically trying more memory-economical parameters.
            is not reverse-deterministic, so reverse-determinize...

and eventually fail with 

    Could not find approrpiate bmax/dcv settings for building this index.
    Switching to a packed string representation.
    Total time for call to driver() for forward index: 08:45:56

HISAT2 website does have rat index but they do not have the annotation. 

Iam using the command 

    hisat2-build -p 16 --exon ${EXON} --ss ${SPLICE} ${FASTA_File} ${BASE_NAME}

to create the index.

Any ideas is greatly appreciated.

Thanks

  


I think the answer is to provide more memory for the run. Thank you ATpoint.