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.
On 10/10/12 2:39 PM, "John Legato" <lega...@nhlbi.nih.gov> wrote:
> 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
> 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.
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