bwa-index cannot allocate memory

[silgarco]

Dear all,

I was running the command bwa index fungi, in a folder where I have:
fungi (54GB)
fungi.1 (11bb)
fungi.2 (10gb)
fungi.3 (10gb)
fungi.4 (10gb)
fungi.5 (10gb)
fungi.6 (2.6gb)
And after more than 24h I got the following error:

[bwa_index] Update BWT... [bwt_bwtupdate_core] Failed to allocate 53136247452 bytes at bwtindex.c line 158: Cannot allocate memory

I was running the same command with other file (for bacteria) and I have a total of 4TB of memory.

I searched for solutions in several forums but any answer was clear to me, if allocating more memory is necessary I don't know how to do it.
Please could you tell me any commands I should use to solve this?

Thanks !

[GenoMax]

Does 4TB refer to disk space? bwa is looking for more RAM so my guess is you don't have 53G of free RAM available or you are not the only user on this server.

[silgarco]

Oh, I did not think it was RAM memory. The work station has 64GB of RAM, 4TB of hard disk yes and 512GB SSD.
I run the same command with a file of 49 GB (for bacteria) and it worked, actually they were run at the same time....could this be the problem? Shall I run it again without any other job or do I have to allocate more memory? and if so, how can I do it?

Thanks!

[GenoMax]

You can try running the job again while nothing else is running on the machine. You may be able to just get away with it.