Uploaded image for project: 'JABAWS'
  1. JABAWS
  2. JWS-27

Jronn fails when there are >3 sequences in the input Fasta file

    XMLWordPrintable

    Details

    • Type: Bug
    • Status: Resolved
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.0
    • Fix Version/s: 2.0.1
    • Component/s: packaging&distribution
    • Labels:
    • Environment:
      Running on the compbio file system either on nanna or ningal.

      Description

      Jronn falls over if a fasta file with >3 sequences in it is used:

      ningal: ~/projects/1433predictor/disorder/Jronn> java -jar ~/bin/min-jaba-client-2.0.jar -h=http://www.compbio.dundee.ac.uk/jabaws -s=Jronnws -i=new.fasta
      Connecting to JABAWS version 2 service
      19-Mar-2012 11:17:57 compbio.ws.client.Jws2Client connect
      INFO: Connected successfully!


      calling analise.........
      Exception while waiting for results. Exception details are below:
      compbio.metadata.ResultNotAvailableException: compbio.data.sequence.UnknownFileFormatException: Jronn file must be in the following format:
      >sequence_name
       M V S
      0.43 0.22 0.65
      Where first line is the sequence name,
      second line is the tab delimited sequence,
      third line contains tab delimited disorder prediction values.
      No lines are allowed between these three. Additionally, the number of sequence residues must be equal to the number of the disorder values.
      at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
      at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
      at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
      at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
      at com.sun.xml.internal.ws.fault.SOAPFaultBuilder.createUserDefinedException(SOAPFaultBuilder.java:294)
      at com.sun.xml.internal.ws.fault.SOAPFaultBuilder.createException(SOAPFaultBuilder.java:124)
      at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(SyncMethodHandler.java:108)
      at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(SyncMethodHandler.java:78)
      at com.sun.xml.internal.ws.client.sei.SEIStub.invoke(SEIStub.java:107)
      at $Proxy24.getAnnotation(Unknown Source)
      at compbio.ws.client.Jws2Client.analize(Unknown Source)
      at compbio.ws.client.Jws2Client.analize(Unknown Source)
      at compbio.ws.client.Jws2Client.<init>(Unknown Source)
      at compbio.ws.client.Jws2Client.main(Unknown Source)

        Attachments

        1. disorderTest.fa
          45 kB
          James Procter
        2. tst.txt
          211 kB
          James Procter

          Activity

            People

            Assignee:
            jprocter James Procter
            Reporter:
            chriscole Chris Cole
            Votes:
            0 Vote for this issue
            Watchers:
            0 Start watching this issue

              Dates

              Created:
              Updated:
              Resolved: