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using blast+ for remote blasting

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  • using blast+ for remote blasting

    Hi I'm trying to run a remote blastn search from linux command line.
    Here's my working syntax for doing this with blastcl3, which is now deprecated:

    blastcl3 -p blastn -i seqs.fasta -p blastn -d nr -o blast.out -T -K 1

    I'm trying to translate this to the new blast+ syntax.
    This is what I thought should work:

    blastn -task blastn -remote -db nr -query suspected.seqs.fasta -evalue 0.00001 -dust no -max_target_seqs 1 -html -out output.blastn.html

    but what happens is that the computer hangs for about 20 min and then spews the following error about 100 times:

    Error: Error: internal_error: (Severe Error) Blast search error: Details: search failed. # Informational Message: [blastsrv4.REAL]: Error: CPU usage limit was exceeded, resulting in SIGXCPU (24).

    any suggestions?

    Thanks
    Roey

  • #2
    How many query sequences do you have? If lots, that explains the NCBI CPU limit. You might be better off running it locally.

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    • #3
      The query file contains about a 100 sequences, which doesn't sound a lot to me.
      the old blastcl3 doesn't seem to have any problem with that.
      In any case I tried running blastn with 1 sequence and I get the right restult, but if the new function isn't working as well as the old one why are the people at NCBI deprecating it?!

      Is my syntax wrong maybe? is there a way to optimise it?

      thanks again
      Roey

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