The problem for inputfile #12
Comments
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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/ |
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Thank you very much! I download the fasta file from the NCBI dataset, and load this file to the prism. Is it because of my blastp version? I use Protein-Protein BLAST 2.11.0+. |
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Sometimes I use a subset of the FASTA sequence and the program runs fine, but sometimes it with the same error. |
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Can you send along the fasta file and Ill try to replicate the issue on my end? |
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OK, the linkage of the fasta file: |
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This genome file runs fine on my end. I'm using Protein-Protein BLAST 2.2.31+. |
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Yes, When I use Protein-Protein BLAST 2.4.0+, it works! Thanks you a lot! But at the end of the program, it has another error. Could it be because I'm using Mac OS? |
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!
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