Hi John As discussed with you off list but for other users... you can use the output from blast+ (using outfmt 6) as the comparison file. So you do not actually need to use the script to generate that.
Regards Tim On 10/10/12 2:39 PM, "John Legato" <lega...@nhlbi.nih.gov> wrote: > Hello, > > We are attempting to use big_blast.pl and running into errors generating > MSPcrunch output for import into ACT. > > We're running big_blast.pl version: > > "# $Header: /nfs/disk222/yeastpub/Repository/zoo/general/big_blast.pl,v > 1.23 2000/11/27 09:44:12 kmr Exp $" > > > We're running blast+ as follows: > > /v/apps/ncbi-blast-2.2.26+/bin/blastn -query > ../../human_screen/nohost_2.fa -db > ../../../../Ichthyosporea/Ichthyosporea_874 -out > Ichthyosporea_874.2.blast6.txt -outfmt 6 -dust yes > > We've installed the Pathogen Sequencing Unit's internal Perl > module, which the script appears to find. > When we run big_blast.pl we get the following error and 0 length output:" > pened Ichthyosporea_874.1.blast6.txt.crunch for writing > Couldn't read any blast results from Ichthyosporea_874.1.blast6.txt > wrote Ichthyosporea_874.1.blast6.txt.crunch and > Ichthyosporea_874.1.blast6.txt.tab" > > > We've checked the manual which suggests outfmt 6 with blast+. > The mailing list archives didn't have much coverage of blast+. Is there an > updated option we need to pass to > big_blast.pl or blast+? We've attached a sample of the output we are > working with. We've also tried uncommenting the other blast parse from file > line 326 to no avail, Perl can't find the blast parsing module used. > We would appreciate any insight into how to generate blast+ output suitable > for input into ACT. > > Thanks > > John > > > > _______________________________________________ > Artemis-users mailing list > Artemis-users@sanger.ac.uk > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
