Hi Stefano No it looks like the script is not getting the database name for some reason or is loosing it.
The line above the error you have should be: seq1-out using database swissprot i.e. should provide the name of the database you are using. Attached is a run_blastx script that works for me. As you know you need to define BLATMAT, BLASTDB and the path to blast. Regards Tim On 30/1/07 17:35, "Stefano Ghignone" <[EMAIL PROTECTED]> wrote: > Hi Tim, > thanks for your ready reply. > I tried your suggestion, but it doesn't work...(I think I also tried > before...) > Well, runnning the old run_ script from terminal I get (same as v.8): > > [EMAIL PROTECTED]:~/artemis$ run_blastx -onefile seq1.txt seq1-out.txt > swissprot > about to start blastall with input from seq1.txt and output to > seq1-out.txt using database > [blastall] ERROR: No argument given for Database > > so I think the problem is that the script doesn't find the database > swissprot! > ...even if I create a DATABASE environment variable with the same value > as BLASTDB... > > Any other idea? > Stefano > > > Tim Carver wrote: >> Hi Stefano >> >> I think you can probably just copy 'etc/run_blastp' from version 7 to >> version 8 then. >> >> Regards >> Tim >> >> >> On 30/1/07 16:16, "Stefano Ghignone" <[EMAIL PROTECTED]> wrote: >> >> >>> Dear all, >>> ....ok...I need an help! >>> >>> I have an artemis v.7 working on a FedoraCore3 machine, perfectly >>> integrated with the blast-2.2.15, so that the blast programs listed in >>> the run menu are working fine using swissprot, nr, nt, and so on... >>> >>> Now, I'm trying to work with artemis v.8 on a Ubuntu machine, but I >>> didn't succed with its integration with blast-2.2.15 (note that the >>> stand alone blast and the artemis itself are working!) >>> On this machine I have copied the same configuration (blast, artemis, >>> artemis/etc in my PATH and BLASTDB environment variable) but the run_ >>> commands from the run menu are still not working.... >>> >>> Usually, for e.g., I get this error: >>> >>> ERROR running blastx: >>> >>> ================= >>> [blastall] ERROR: No argument given for database >>> >>> I get the same error even if I run the run_ script from the terminal. >>> >>> I also tried to specify the database location in the artemis/etc/option : >>> >>> feature_dna_programs = \ >>> tblastx /usr/BioSW/blast-2.2.15/db \ >>> blastn /usr/BioSW/blast-2.2.15/db \ >>> blastx /usr/BioSW/blast-2.2.15/db \ >>> fastx %uniprot \ >>> clustalx DNA >>> >>> but with no success again... >>> >>> It's days I'm working on it......What's wrong? >>> Cheers >>> Stefano >>> >>> >> >> >>
run_blastx
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