Entering edit mode
2.9 years ago
Ric
▴
440
Hi, I ran diamond on a 128GB ram computer with a 2.8Gb genome. However, it appears it ran out of memory. Would there be a way to reduce the amount of memory?
$ diamond makedb --in GenbankAA.fasta --db diamond -p 8
$ diamond blastx --threads 1 -q genome.softmasked.fasta --db diamond -o diamond.matches.tab -e 1e-10 -k 0 --more-sensitive -f 6 sseqid slen sstart send qseqid qlen qstart qend pident length evalue score qcovhsp qframe
...
Searching alignments... [0.602s]
Deallocating buffers... [0s]
Clearing query masking... [0.247s]
Computing alignments... Error: std::bad_alloc
Thank you in advance
-F 15
worked. What does frameshift mode mean and why 15 has been chosen?You will need to predict genes and then extract the sequences.
Thank you.
I created for each of the 19 chromosomes a FASTA file. Each of the 19 FASTA files is around 150Mb. Is frameshift mode (option
-F 15
) a good value?I have not tested it on this kind of data but you can surely try.