Re: maker problem with running blast

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Re: maker problem with running blast

Carson Hinton Holt
Your blast_type parameter in maker_bopts.ctl is set to 'wublast' but the
executables for wublast are blank in maker_exe.ctl.

See, they’re blank —>
xdformat=#location of WUBLAST xdformat executable
blasta=#location of WUBLAST blasta executable



You either need to provide executables or set your blast_type parameter to
something else. For example, you could set it to 'NCBI+', but you will nee
to fix the location of makeblastdb.

makeblastdb is set incorrectly here—>
makeblastdb=/home/AAFC-AAC/borhanh/bin/ncbi-blast-2.2.29+ #location of
NCBI+ makeblastdb executable



Alternativley you can set blast_type to 'NCBI', but you will need to
uncomment the executables.

Here—>
formatdb=#/usr/local/bin/formatdb #location of NCBI formatdb executable
blastall=#/usr/local/bin/blastall #location of NCBI blastall executable



—Carson


On 3/6/14, 3:51 PM, "Borhan, Hossein" <[hidden email]> wrote:

>Hi
>
>I have installed latest version of blast+ and provided the excitable path
>to the maker_exec.ctl  as follow
>
>#-----Location of Executables Used by MAKER/EVALUATOR
>makeblastdb=/home/AAFC-AAC/borhanh/bin/ncbi-blast-2.2.29+ #location of
>NCBI+ makeblastdb executable
>blastn=/home/AAFC-AAC/borhanh/bin/ncbi-blast-2.2.29+/bin/blastn #location
>of NCBI+ blastn executable
>blastx=/home/AAFC-AAC/borhanh/bin/ncbi-blast-2.2.29+/bin/blastx #location
>of NCBI+ blastx executable
>tblastx=/home/AAFC-AAC/borhanh/bin/ncbi-blast-2.2.29+/bin/tblastx
>#location of NCBI+ tblastx executable
>formatdb=#/usr/local/bin/formatdb #location of NCBI formatdb executable
>blastall=#/usr/local/bin/blastall #location of NCBI blastall executable
>xdformat=#location of WUBLAST xdformat executable
>blasta=#location of WUBLAST blasta executable
>RepeatMasker=/usr/local/RepeatMasker/RepeatMasker #location of
>RepeatMasker executable
>exonerate=/home/AAFC-AAC/borhanh/bin/exonerate-2.2.0-x86_64/bin/exonerate
>#location of exonerate executable
>
>#-----Ab-initio Gene Prediction Algorithms
>snap=/home/AAFC-AAC/borhanh/bin/snap/snap #location of snap executable
>gmhmme3=/home/AAFC-AAC/borhanh/bin/gm_es_bp_linux64_v2.3e/gmes/gmhmme3
>#location of eukaryotic genemark executable
>gmhmmp= #location of prokaryotic genemark executable
>augustus=/usr/local/augustus.2.5.5/bin/augustus #location of augustus
>executable
>fgenesh=/usr/local/FGENESH/fgenesh #location of fgenesh executable
>
>#-----Other Algorithms
>fathom=/home/AAFC-AAC/borhanh/bin/snap/fathom #location of fathom
>executable (experimental)
>probuild=/home/AAFC-AAC/borhanh/bin/gm_es_bp_linux64_v2.3e/gmes/probuild
>#location of probuild executable (required for genemark)
>
>
>
>
>
>But when running maker I get this error
>
>
>STATUS: Parsing control files...
>WARNING: blast_type is set to 'wublast' but executables cannot be located
>ERROR: Please provide a valid locaction for a BLAST algorithm in the
>control files.
>
>
>
>
>
>
>

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