Do you know what the limitations are in blastn ? I wanted to look up my 15 longest contigs by length via a fasta file and get 5-10 results per contig , but I keep getting the error CPU limit was reached from the server . This is using $ blastn -db nt -remote -query $Input.fasta -out result.txt -outfmt 6 . It even crashes about 50% of the time with a single sequence in the fatsa file .
@@briansalkas349 My server is a good cluster off Dell Power Edges and i do have a few standalone Dell power edge 550's but in my mind the blastn backend(online) is doing the work here and I am just sending the fasta data and pulling back the results , yes nt is huge , but i'm not sure what building a nt database would look like size wise if I was to capture accurate results , but I probably don't have enough space to download the nt database , but I am new to command line so I might be misunderstanding how this works . Great vids btw !
@@briansalkas349 maybe i should rephrase the question to you , if you had a contig fill , ive stripped out the 20 longest , these are between 3k and 30k , how would you do a search for these via CLI , at the minute I am stuck with manual searches , some are human , bacterial , viral and some have no matches at all . I can see that others are producing these results/tables in a few hours , but with manual searches its 1-2 days and the risk of mistakes while copying/pasting . I can only think that I would need to download the entire nt database ?
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Do you know what the limitations are in blastn ? I wanted to look up my 15 longest contigs by length via a fasta file and get 5-10 results per contig , but I keep getting the error CPU limit was reached from the server . This is using $ blastn -db nt -remote -query $Input.fasta -out result.txt -outfmt 6 . It even crashes about 50% of the time with a single sequence in the fatsa file .
First off nt is huge. If you could narrow things down to a smaller database that might help. Also what is your server.
@@briansalkas349 My server is a good cluster off Dell Power Edges and i do have a few standalone Dell power edge 550's but in my mind the blastn backend(online) is doing the work here and I am just sending the fasta data and pulling back the results , yes nt is huge , but i'm not sure what building a nt database would look like size wise if I was to capture accurate results , but I probably don't have enough space to download the nt database , but I am new to command line so I might be misunderstanding how this works . Great vids btw !
@@briansalkas349 maybe i should rephrase the question to you , if you had a contig fill , ive stripped out the 20 longest , these are between 3k and 30k , how would you do a search for these via CLI , at the minute I am stuck with manual searches , some are human , bacterial , viral and some have no matches at all . I can see that others are producing these results/tables in a few hours , but with manual searches its 1-2 days and the risk of mistakes while copying/pasting . I can only think that I would need to download the entire nt database ?