RA stopped after preconstruction stage

Open vmurigneu opened this issue 6 years ago • 3 comments

Hi Robert,

I have installed RA following instructions without errors. But when I tried to run the following command: python /sw/ra/build/bin/ra -t 16 -x ont ont.fastq.gz > ra.fa

I get an empty assembly fasta file and the following message: [Ra::run] preconstruction overlap stage [M::mm_idx_gen::185.227*2.22] collected minimizers [Ra::exit] warning: unable to clean work directory!

Any idea?

Thanks in advance. Valentine

Feb 27 '19 06:02 vmurigneu

Hello Valentine, looking at the log I suspect that minimap crashed due to insufficient memory. How much RAM do you have? How large are your reads?

Best regards, Robert

Feb 27 '19 06:02 rvaser

Yes it is very likely to have insufficient memory. I have 31G and around 43G of compressed of human data. I am trying to run Ra on a larger memory node (120G).

Thanks.

Feb 27 '19 07:02 vmurigneu

Hmmm, not sure what minimap requirement is, but it seems to me that 120GB should be enough.

Feb 27 '19 07:02 rvaser