keshavd
commented
3 years ago I don't think there is an issue with your file input format. You can use a properly formatted FASTA with a genomic (nucleotide) sequence. This looks like an error related to your copy of blastp. I would verify that the dependency has been correctly met.
The build of PRISM available here is quite old. If you are using this for academic purposes I highly recommend using the new web client found here: https://prism.adapsyn.com/
yangziyi1990
Hi: Thank you for your reply. I have received prism.jar file, and can run the prism-releases. However, I ran into another problem. When I input an amino acid sequence, I make an error. So what is the format of the input file for prism-release?
The input file like this:
The problem is this:
Identifying C-11 O-methyltransferase (1) domains... Identifying C-11 O-methyltransferase (2) domains... Identifying Amidotransferase domains... Identifying Phenylalanine ammonia lyase domains... Identifying Type II polyketide priming acyltransferase domains... Identifying Ketosynthase III domains... Analyzing condensation and ketosynthase domains... 2月 08, 2021 3:24:15 下午 ca.mcmaster.magarveylab.wasp.exception.ExceptionHandler throwException 严重: Index 1 out of bounds for length 1 java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1 at ca.mcmaster.magarveylab.prism.blast.BlastSearchReader.read(BlastSearchReader.java:63) at ca.mcmaster.magarveylab.prism.blast.BlastpSearch.run(BlastpSearch.java:64) at ca.mcmaster.magarveylab.prism.blast.DomainBlastpSearch.run(DomainBlastpSearch.java:53) at ca.mcmaster.magarveylab.prism.genome.GenomeSearch.executeBlastpAnalysis(GenomeSearch.java:186) at ca.mcmaster.magarveylab.prism.genome.GenomeSearch.run(GenomeSearch.java:80) at ca.mcmaster.magarveylab.prism.Prism.analyzeOrfs(Prism.java:159) at ca.mcmaster.magarveylab.prism.Prism.run(Prism.java:73) at ca.mcmaster.magarveylab.prism.PrismDesktop.main(PrismDesktop.java:98)
EXCEPTION: java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1
java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1 at ca.mcmaster.magarveylab.prism.blast.BlastSearchReader.read(BlastSearchReader.java:63) at ca.mcmaster.magarveylab.prism.blast.BlastpSearch.run(BlastpSearch.java:64) at ca.mcmaster.magarveylab.prism.blast.DomainBlastpSearch.run(DomainBlastpSearch.java:53) at ca.mcmaster.magarveylab.prism.genome.GenomeSearch.executeBlastpAnalysis(GenomeSearch.java:186) at ca.mcmaster.magarveylab.prism.genome.GenomeSearch.run(GenomeSearch.java:80) at ca.mcmaster.magarveylab.prism.Prism.analyzeOrfs(Prism.java:159) at ca.mcmaster.magarveylab.prism.Prism.run(Prism.java:73) at ca.mcmaster.magarveylab.prism.PrismDesktop.main(PrismDesktop.java:98) Analysis complete! [Prism] Terminated.
Looking forward to your reply!