diamond seems to run out of memory
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9 months ago
Ric ▴ 400

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

alignment gene • 1.1k views
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9 months ago
buchfink ▴ 240

Diamond is limited in processing that long of a query sequence in blastx mode. One thing you can try is to use the frameshift mode (option -F 15). Otherwise, you probably should extract ORFs from the genome and search those.

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  1. Thank you, -F 15 worked. What does frameshift mode mean and why 15 has been chosen?
  2. How would you extract ORFs from the genome?
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You will need to predict genes and then extract the sequences.

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Thank you.

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  1. This mode is able to compute alignments that contain a change in the reading frame. 15 is the penalty and only a recommended value. The mode was also designed to handle longer sequences.
  2. There are tools for doing this, I'm sure google can help.
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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?

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I have not tested it on this kind of data but you can surely try.

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