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magarveylab / prism-releases

PRISM source code public releases
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Run error #13

Open APengs494 opened 2 years ago

APengs494 commented 2 years ago

Hi: I have downloaded prism.jar file in my centos. When I input an amino acid sequence, I make an error. java -jar prism.jar -a -p -f HGUT-02250.fna -tt -sug -res -rib -w 10000 -o ./

Error: couldn't locate script blastp.sh at filepath /mnt/data1/bgc_qhp/PRISM4_tool_bgc/blast/blastp.sh ca.mcmaster.magarveylab.prism.util.exception.DependencyException: Error: couldn't locate script blastp.sh at filepath /mnt/data1/bgc_qhp/PRISM4_tool_bgc/blast/blastp.sh at ca.mcmaster.magarveylab.prism.PrismDependencyCheck.checkScriptFile(PrismDependencyCheck.java:168) at ca.mcmaster.magarveylab.prism.PrismDependencyCheck.checkScripts(PrismDependencyCheck.java:130) at ca.mcmaster.magarveylab.prism.PrismDependencyCheck.run(PrismDependencyCheck.java:56) at ca.mcmaster.magarveylab.prism.Prism.checkDependencies(Prism.java:119) at ca.mcmaster.magarveylab.prism.Prism.run(Prism.java:71) at ca.mcmaster.magarveylab.prism.PrismDesktop.main(PrismDesktop.java:98)

EXCEPTION: ca.mcmaster.magarveylab.prism.util.exception.DependencyException: Error: couldn't locate script blastp.sh at filepath /mnt/data1/bgc_qhp/PRISM4_tool_bgc/blast/blastp.sh

ca.mcmaster.magarveylab.prism.util.exception.DependencyException: Error: couldn't locate script blastp.sh at filepath /mnt/data1/QinHaiPeng/bgc_qhp/PRISM4_tool_bgc/WebContentDirectory/blast/blastp.sh at ca.mcmaster.magarveylab.prism.PrismDependencyCheck.checkScriptFile(PrismDependencyCheck.java:168) at ca.mcmaster.magarveylab.prism.PrismDependencyCheck.checkScripts(PrismDependencyCheck.java:130) at ca.mcmaster.magarveylab.prism.PrismDependencyCheck.run(PrismDependencyCheck.java:56) at ca.mcmaster.magarveylab.prism.Prism.checkDependencies(Prism.java:119) at ca.mcmaster.magarveylab.prism.Prism.run(Prism.java:71) at ca.mcmaster.magarveylab.prism.PrismDesktop.main(PrismDesktop.java:98) Analysis complete! [Prism] Terminated.

Besides downloading prism.jar, do I need to install BLAST? or How to install with source code (gz.tar file)

nishanthmerwin commented 2 years ago

Yes, BLAST is a required installation. See the README for all required dependencies:

Core dependencies include HMMER (3.1) and BLAST (2.2.25+). Optional but highly recommended dependencies include BioPerl (1.006924) for GenBank file input, Prodigal (2.6.3) for prokaryotic open reading frame prediction, and FIMO (for ribosomally produced and post-translationally modified peptide precursor cleavage).