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Problem with my own database #23

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
> What steps will reproduce the problem?
1. I uploaded the .omx and .t.xml from SearchGUI
2. I used the target_decoy DB which was generated in SearchGUI
3. Finally, I clicked on Create.

> What is the expected output? What do you see instead?
*Normal uploading and showing the results.
*I see the following: "Import Cancelled"

> What version of the product are you using? On what operating system?
PeptideShaker-0.19.0, in Mac OS X version 10.7.5

> Please provide any additional information below.
Theres is an attached file...

> If the reported issue resulted in the tool crashing, please
> also upload the file called PeptideShaker.log (found in the
> PeptideShaker-X.Y.Z\conf folder).

Original issue reported on code.google.com by iapa...@gmail.com on 6 Mar 2013 at 3:52

Attachments:

GoogleCodeExporter commented 9 years ago 
Here it is more info about the bug...

Thanks for the help...

Original comment by iapa...@gmail.com on 10 Mar 2013 at 10:44

Attachments:

GoogleCodeExporter commented 9 years ago 
[deleted comment]
GoogleCodeExporter commented 9 years ago 
Those are the files...

Original comment by iapa...@gmail.com on 11 Mar 2013 at 12:37

Attachments:

GoogleCodeExporter commented 9 years ago 
The problem seems to be with the database. Would it be possible for you to make 
the database and search results available to me so that I can try to reproduce 
the problem myself?

Original comment by harald.b...@gmail.com on 11 Mar 2013 at 10:24

GoogleCodeExporter commented 9 years ago 
Hi there,
I loaded a fasta file of Mmulatta annotated protein sequences, created decoy 
sequences using PeptideShaker and then tried loading along with the spectrum 
files and the identified proteins files. I get a sequence file loading error 
almost immediately which seems similar to this one. I am running this on a Mac 
OS X Mountain Lion. Here is the error log (Sorry, unable to attach it):

Thu Feb 06 20:48:43 EST 2014: PeptideShaker version 0.25.0.
Memory given to the Java virtual machine: 1908932608.
Total amount of memory in the Java virtual machine: 129499136.
Free memory: 114164512.
Java version: 1.7.0_51.
1714 script command tokens
(C) 2009 Jmol Development
Jmol Version: 12.0.43  2011-05-03 14:21
java.vendor: Oracle Corporation
java.version: 1.7.0_51
os.name: Mac OS X
memory: 43.2/129.5
processors available: 8
useCommandThread: false
Reindexing: Mmul_Annotated_concatenated_target_decoy.fasta. (changes in the 
file detected)
Reindexing: Mmul_Annotated_concatenated_target_decoy.fasta.
An error occured while loading 
/Users/vishaln/Desktop/Mmul_Annotated_concatenated_target_decoy.fasta.
java.lang.NullPointerException
    at com.compomics.util.db.ObjectsDB.correctKey(ObjectsDB.java:1048)
    at com.compomics.util.db.ObjectsDB.insertObjects(ObjectsDB.java:270)
    at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory.saveProteinLengths(ProteinTreeComponentsFactory.java:264)
    at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.indexProteins(ProteinTree.java:615)
    at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.loadTags(ProteinTree.java:531)
    at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.importDb(ProteinTree.java:423)
    at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.initiateTree(ProteinTree.java:253)
    at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.initiateTree(ProteinTree.java:189)
    at com.compomics.util.experiment.identification.SequenceFactory.getDefaultProteinTree(SequenceFactory.java:1189)
    at com.compomics.util.experiment.identification.SequenceFactory.getDefaultProteinTree(SequenceFactory.java:1156)
    at eu.isas.peptideshaker.fileimport.FileImporter.importSequences(FileImporter.java:194)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:393)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:382)
    at javax.swing.SwingWorker$1.call(SwingWorker.java:296)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at javax.swing.SwingWorker.run(SwingWorker.java:335)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:744)

Original comment by vishal.n...@gmail.com on 7 Feb 2014 at 2:07

GoogleCodeExporter commented 9 years ago 
Seems like there is a problem with the formatting of your database. Could you 
make the database available to us so that we can try to reproduce the problem 
ourselves?

Original comment by harald.b...@gmail.com on 7 Feb 2014 at 9:09

GoogleCodeExporter commented 9 years ago 
Thanks for getting back to me so promptly. Yes, I would be happy to share the 
database. However, it is a fairly large file. How do I send it to you? Thanks!

Original comment by vishal.n...@gmail.com on 7 Feb 2014 at 12:40

GoogleCodeExporter commented 9 years ago 
The easiest way would be to zip it first. And depending on how big it is you 
can either send it by e-mail (just take my name and add gmail.com at the end), 
or you can use something like DropBox. How big is the file after zipping?

Original comment by harald.b...@gmail.com on 7 Feb 2014 at 3:22

GoogleCodeExporter commented 9 years ago

Original comment by harald.b...@gmail.com on 11 Feb 2014 at 7:07