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Error with Validating Results #39

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
> What steps will reproduce the problem?
I created a PTM for the analysis of cross-linking data. The mass I used was 
156.0834 (BS3 + water). This works fine and I can view the results in Peptide 
Shaker. I then changed the PTM mass by +1da to identify false positives, this 
again worked fine. When I change the mass by -1da it does not seem to work. 

> What is the expected output? What do you see instead?
Error occurs during data import. I get an error stating "An error occurred 
while validating the results."

> What version of the product are you using? On what operating system?
Version: 0.25.2
OS Mac OSx

> Please provide any additional information below.
I cannot attach files, it states "Issue attachment storage exceeded", so I will 
paste the log and error below.

> If the reported issue resulted in the tool crashing, please
> also upload the file called PeptideShaker.log (found in the
> PeptideShaker-X.Y.Z\resources folder).
====== Error Start ======
Wed Feb 26 12:36:54 GMT 2014        Import process for Casfasf (Sample: 
asfasfdasf, Replicate: 0)

Wed Feb 26 12:36:54 GMT 2014        Importing sequences from 
cbpa_linear_concatenated_target_decoy.fasta.
Wed Feb 26 12:36:55 GMT 2014        Expected import time: 596523 hours. (See 
Protein Inference.)
Wed Feb 26 12:37:04 GMT 2014        FASTA file import completed.
Wed Feb 26 12:37:04 GMT 2014        Establishing local database connection.
Wed Feb 26 12:37:04 GMT 2014        Reading identification files.
Wed Feb 26 12:37:04 GMT 2014        Parsing 270114_CBPA_D15_1.t.xml.
Wed Feb 26 12:37:05 GMT 2014        Importing 270114_CBPA_D15_1.mgf
Wed Feb 26 12:37:05 GMT 2014        270114_CBPA_D15_1.mgf imported.
Wed Feb 26 12:37:05 GMT 2014        Importing PSMs from 270114_CBPA_D15_1.t.xml
Wed Feb 26 12:37:08 GMT 2014        File import completed. 342 first hits 
imported (1 secondary) from 1730 spectra.
Wed Feb 26 12:37:08 GMT 2014        [199 first hits passed the initial 
filtering]
Wed Feb 26 12:37:08 GMT 2014        Computing assumptions probabilities.
Wed Feb 26 12:37:08 GMT 2014        Saving assumptions probabilities.
Wed Feb 26 12:37:08 GMT 2014        Selecting best peptide per spectrum.
Wed Feb 26 12:37:08 GMT 2014        Computing PSM probabilities.
Wed Feb 26 12:37:08 GMT 2014        Scoring PTMs in PSMs (D-score and A-score)
Wed Feb 26 12:37:09 GMT 2014        Thresholding PTM localizations.
Wed Feb 26 12:37:09 GMT 2014        Resolving peptide inference issues.
Wed Feb 26 12:37:09 GMT 2014        Saving probabilities, building peptides and 
proteins.
Wed Feb 26 12:37:10 GMT 2014        Simplifying protein groups.
Wed Feb 26 12:37:10 GMT 2014        Generating peptide map.
Wed Feb 26 12:37:10 GMT 2014        Computing peptide probabilities.
Wed Feb 26 12:37:10 GMT 2014        Saving peptide probabilities.
Wed Feb 26 12:37:10 GMT 2014        Generating protein map.
Wed Feb 26 12:37:10 GMT 2014        Resolving protein inference issues, 
inferring peptide and protein PI status.
Wed Feb 26 12:37:11 GMT 2014        52 conflicts resolved. 43 protein groups 
remaining (0 suspicious).
Wed Feb 26 12:37:11 GMT 2014        Correcting protein probabilities.
Wed Feb 26 12:37:11 GMT 2014        Saving protein probabilities.
Wed Feb 26 12:37:11 GMT 2014        Validating identifications at 1% FDR.
Wed Feb 26 12:37:11 GMT 2014        An error occurred while validating the 
results.

Wed Feb 26 12:37:11 GMT 2014        Importing Data Canceled!

===== Error end =====

===== Log Start =====
Wed Feb 26 12:36:27 GMT 2014: PeptideShaker version 0.25.2.
Memory given to the Java virtual machine: 3817865216.
Total amount of memory in the Java virtual machine: 129499136.
Free memory: 114118176.
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: 24.6/129.5
processors available: 8
useCommandThread: false
java.lang.IllegalArgumentException: Attempting to estimate the percentile of an 
empty list.
    at com.compomics.util.math.BasicMathFunctions.percentile(BasicMathFunctions.java:121)
    at com.compomics.util.math.BasicMathFunctions.median(BasicMathFunctions.java:69)
    at com.compomics.util.math.statistics.ditributions.NonSymmetricalNormalDistribution.getRobustNonSymmetricalNormalDistribution(NonSymmetricalNormalDistribution.java:60)
    at eu.isas.peptideshaker.PeptideShaker.validateIdentifications(PeptideShaker.java:720)
    at eu.isas.peptideshaker.PeptideShaker.fdrValidation(PeptideShaker.java:601)
    at eu.isas.peptideshaker.PeptideShaker.processIdentifications(PeptideShaker.java:406)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:482)
    at eu.isas.peptideshaker.fileimport.FileImporter$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)

===== Log End =====

Original issue reported on code.google.com by harpal28...@gmail.com on 26 Feb 2014 at 12:50

GoogleCodeExporter commented 9 years ago 
We just detected the same bug ourselves yesterday and a fix has already been 
made. A new version will be released as soon as possible.

The reason for the error being thrown in the first place is exactly as the 
message states "Attempting to estimate the percentile of an empty list", and 
this only happens when you have a spectrum file, i.e. an mgf file, contains has 
no validated peptide to spectrum matches (PSMs). Which explains why it works 
fine with your first two modifications (as these produce validated PSMs) while 
your final modification option does not.

I'll let you know as soon as the new version is available.

Original comment by harald.b...@gmail.com on 26 Feb 2014 at 2:18

GoogleCodeExporter commented 9 years ago 
PeptideShaker v0.26.0 has just been released and the bug should now be fixed.

Original comment by harald.b...@gmail.com on 3 Mar 2014 at 10:57