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Interpretation of proteomics identification results

Home Page: http://compomics.github.io/projects/peptide-shaker.html

Java 95.34% HTML 4.66%

proteomics protein-identification bioinformatics java

peptide-shaker's Introduction

PeptideShaker

PeptideShaker Publication:

Vaudel et al. Nature Biotechnol. 2015 Jan;33(1):22–24.
If you use PeptideShaker as part of a publication please include this reference.


	v3.0.8 - All platforms	ReleaseNotes

(Click on an image to see the full size version)

Introduction

PeptideShaker is a search engine independent platform for interpretation of proteomics identification results from multiple search and de novo engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda, MetaMorpheus, Sage, Novor, DirecTag and mzIdentML.

PeptideShaker aggregates the results in a single identification set, annotates spectra, computes a consensus score, maps sequences and performs protein inference, scores post-translational modification localization, runs statistical validation, quality control, and annotates the results using multiple sources of information like Gene Ontology, UniProt and Ensembl annotation, and protein structures.

PeptideShaker can be used in command line and comes with rich visualization capabilities to navigate the results. It can be used on local data as well as on data sets deposited to the ProteomeXchange PRIDE repository.

PeptideShaker currently supports nine different analysis tasks:

Overview: get a simple yet detailed overview of all the proteins, peptides and PSMs in your dataset.
Spectrum IDs: compare the search engine performance and see how the search engine results are combined.
Fractions: inspect from which fractions proteins and peptides are likely to come from.
Modifications: get a detailed view of the post-translational modifications in the dataset.
3D Structure: map the detected peptides and modifications onto corresponding PDB structures.
GO Enrichment: perform GO enrichment and find enriched GO terms in your dataset.
Validation: inspect and fine tune the validation process.
QC Plots: examine the quality of the results with Quality Control plots.
Reshake PRIDE: re-analyze public datasets in PRIDE as if they were your own.

All data can also easily be exported for follow up analysis in other tools.

For further help see the Bioinformatics for Proteomics Tutorial.

If you have any questions, suggestions or remarks, feel free to contact us via the PeptideShaker Google Group. For specific bug reports or issues please use the issues tracker.

To start using PeptideShaker, unzip the downloaded file, and double-click the PeptideShaker-X.Y.Z.jar file. No additional installation required!

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Minimum Requirements

It should be possible to run PeptideShaker on almost any computer where Java 1.8 or newer is installed. We recommend always using the latest version of Java.

However to get the best out of PeptideShaker a newer machine with at least 4 GB of memory is recommended. If parsing big datasets even more memory is required: the bigger the dataset the more memory you need.

Note that in order to use more than 1500 MB of memory you need to install the 64 bit version of Java. See our Java Troubleshooting for help.

The minimum screen resolution for PeptideShaker is 1280 x 800, but it is highly recommended to use at least 1680 x 1050. Again, the bigger the better.

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From the Command Line

The main purpose of PeptideShaker is to make it simpler to process and display the results of multiple search engines. A graphical user interface is the best choice for smaller projects. PeptideShaker can also be used via the command line, and be incorporated in different analysis pipelines.

For details about the command line see: PeptideShakerCLI.

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Bioconda

PeptideShaker is available as a Miniconda package in the bioconda channel here.

You can install PeptideShaker with:

conda install -c conda-forge -c bioconda peptide-shaker

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Docker

A Docker container is available via the biocontainers project. You can make use of the container via:

docker run quay.io/biocontainers/peptide-shaker:X.Y.Z--1 peptide-shaker eu.isas.peptideshaker.cmd.PeptideShakerCLI

Replace X.Y.Z with the wanted PeptideShaker version number.

In case you need to use your own files, you will need to map (using -v Docker parameter) your local folders containing them into the Docker internal file system, like

docker run -v /home/my_user/resources:/myresources 
quay.io/biocontainers/peptide-shaker:X.Y.Z--1 
peptide-shaker eu.isas.peptideshaker.cmd.PeptideShakerCLI 
...

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SearchGUI

PeptideShaker has a strong connection to the SearchGUI project.

SearchGUI is a user-friendly, lightweight and open-source graphical user interface for configuring and running proteomics identification search engines, namely X! Tandem, MyriMatch, MS Amanda, MS-GF+, OMSSA, Comet, Tide, Andromeda, MetaMorpheus, Sage, Novor and DirecTag.

Importing output from SearchGUI is especially simple in PeptideShaker as the parameters and files used for the search is easily available.

For more information on SearchGUI see http://compomics.github.io/projects/searchgui.html.

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User Defined Modifications

To add user defined modifications see User Defined Modifications in SearchGUI.

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Database Help

For help on obtaining a valid sequence database see the Database Help.

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Mascot Support

PeptideShaker supports the import of data from Mascot dat files. Make sure that the spectra are available in the mgf format where every spectrum should have a unique title.

Mascot's randomised protein sequences decoy option is not compatible with PeptideShaker. The reason being that this is a random decoy approach and not a reverse decoy approach. When combining results from different search engines it is important that the database and decoys used are identical, something that cannot be guaranteed when using the random approach.

To combine Mascot results with your results from SearchGUI you therefore have to use the same target-decoy database as the one used in the SearchGUI search and not select the decoy option when performing the Mascot search. It may also be possible to use the reversed protein sequences decoy option in Mascot, but then there is no guarantee that the generated decoys are identical and the comparison against the other search engines may be less straightforward.

To get target-decoy databases that are fully compatible with PeptideShaker see the Decoy Databases section below.

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mzIdentML Support

PeptideShaker can load results from virtually any identification algorithm in the mzIdentML format as long as the minimal peptide to spectrum match information is present in the file.

The following is required:

Spectrum file format has to be mgf.
Each PSM has a score or e-value as a PSM score CV term.

If you have mzIdentML files that fulfill these criteria but do not load in PeptideShaker, please let us know.

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Decoy Databases

In order for PeptideShaker to be able validate your identifications you need to provide the sequence database (i.e., the FASTA file) as a concatenated target-decoy database.

This is achieved by adding non-existing protein sequences (so-called decoy sequences) to the original protein database. There are various ways of creating the artificial sequences. In the context of PeptideShaker, it is recommended to use reversed versions of the actual sequences. When working with multiple search engines, make sure that they use the exact same database.

This means that whenever a mistake is made when searching in the combined database, it is as likely to happen in the real database (called the target database) as it is in the artificial database (called the decoy database).

Note that we only guarantee the performance of PeptideShaker when using concatenated forward and reversed sequences. If you use other types of databases it is at your own risks!

Target-decoy database compatible with PeptideShaker can be created using SearchGUI.

Note that PeptideShaker will load search results from searches not using decoy databases, but this is not recommended as this makes it impossible to statistically validate the identifications!

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Converting Spectrum Data

PeptideShaker supports mgf and mzML files as the input format for the spectra. To convert your raw data we recommend using ThermoRawFileParser for Thermo raw files and msconvert from ProteoWizard for other raw file formats.

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Troubleshooting

Mascot Issues - See Mascot Support and Database Help.
mzIdentML Issues - See mzIdentML Support.
Database Help - For help on how to set up a proper FASTA database, please see Database Help. For Mascot databases see Mascot Support. Also see Databases Decoy Databases.
Does Not Start I - Do you have Java installed? Download the latest version of Java here and try again. (You only need the JRE version (and not the JDK version) to run PeptideShaker.)
Does Not Start II - Have you unzipped the zip file? You need to unzip the file before double clicking the jar file. If you get the message "A Java Exception has occurred", you are most likely trying to run PeptideShaker from within the zip file. Unzip the file and try again.
Does Not Start III - Is PeptideShaker installed in a path containing special characters, i.e. [, %, æ, ø, å, etc? If so, move the whole folder to a different location or rename the folder(s) causing the problem and try again. (Note that on Linux PeptideShaker has to be run from a path not containing spaces).
Does Not Start IV - If PeptideShaker fails during start-up a file called startup.log will be created in the PeptideShaker resources\conf folder. Here you can find detailed information about why the program was not able to start.
Unidentified Developer - If you run PeptideShaker on a Mac you can get the warning "PeptideShaker" can't be opened because it is from an unidentified developer. To escape this warning control-click on the file icon and then select "Open." This will give you the option of opening it regardless of its unidentified source. This only has to be done once for each PeptideShaker version.
Memory Issues I - Big datasets can require a lot of memory. If the software unexpectedly fails on a big project, and the software mentions that it ran out of memory, you should try to give the program more memory. This can be done by selecting Java Options on the Edit menu in PeptideShaker. Set the memory limit in MB, e.g., 2500 for a maximum of appr. 2.5GB of memory. Please note that on a 32-bit operating system you cannot increase this value beyond 2000M (and usually the maximum limit is lower than this).
Memory Issues II - Using more than 2GB of memory requires the installation of 64 bit Java. 64 bit Java is downloaded from the same place as the 32 bit version: Java. Note that 64 bit Java can only be used on 64 bit operating systems!
Java 32 bit vs 64 bit - If you have both 32 and 64 bit versions of Java installed the operating system can sometimes get confused about which version to use to run PeptideShaker. For Windows platform PeptideShaker tries to default to the 64 bit version of Java if it is installed. You can however override this option by setting your own Java Home. This is done by creating a file called JavaHome.txt in the resources\conf folder of PeptideShaker, with the path to the bin folder of the Java version to use, e.g., C:\Program Files\Java\jdk1.6.0_29\bin\. If the folder does not exist (or it does not contain the required files), the default Java version will be used.
Xlib/X11 errorrs - When running the command lines on systems without a grahpical user interface you may get errors related to X11. If that happens try adding -Djava.awt.headless=true to the command line.
Protein Not Found - In order to provide the most comprehensive results, PeptideShaker needs to link the protein accession retrieved by the various search engines to the FASTA file. Various errors can result in PeptideShaker not being able to find your protein. First, verify that the accession number is indeed in your FASTA file. Then, set up an issue describing the problem and provide the accession not found together with its header and sequence in the FASTA file. Please, also mention the database type and version. See also Database Help, Mascot Support and Databases Decoy Databases. Example for P60323 in UniProt:

            >sw|P60323|NANO3_HUMAN Nanos homolog 3 OS=Homo sapiens GN=NANOS3 PE=2 SV=1
            MGTFDLWTDYLGLAHLVRALSGKEGPETRLSPQPEPEPMLEPDQKRSLESSPAPERLCSFCKHNGESRAIYQSHV
            LKDEAGRVLCPILRDYVCPQCGATRERAHTRRFCPLTGQGYTSVYSHTTRNSAGKKLVRPDKAKTQDTGHRRGGG
            GGAGFRGAGKSEPSPSCSPSMST

Proxy Server - Are you using a proxy server to access the Internet? Then you need to add your proxy settings to the JavaOptions.txt file located in the resources\conf folder of PeptideShaker. Add the following lines (replacing the values between the brackets and skipping the last two lines if username and password is not required):

            -Dhttp.proxyHost=<myproxyserver.com>
            -Dhttp.proxyPort=<proxy port>
            -Dhttp.proxyUser=<user>
            -Dhttp.proxyPassword=<password>

General Error Diagnosis - If you go to Help and then Bug Report, you will find a log of the PeptideShaker activity. This includes transcripts of any errors that the application has encountered, and can be very useful in diagnosing issues.
Problem Not Solved? Or Problem Not In List? Contact the developers of PeptideShaker by setting up an issue describing the problem.

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peptide-shaker's People

Contributors

Stargazers

Watchers

Forkers

twojenski uhaifabioinfo vladie0 bgruening genomicsnx alison-horne max-l alenzhao pariswu1988 jj-umn trishorts hemed myjajarm pride-toolsuite carloshorro anuragraj jxwangxl stephanholgerd oscar-gr

peptide-shaker's Issues

Loading of search results fails

> What steps will reproduce the problem?

Import a search-GUI result (the issue happens for both omx and t.xml result 
files). Hard to attach, since they are at least 100 MB.

> What is the expected output? What do you see instead?

While importing, the error message "No amino acid found for letter >."
pops up. Log below.

> What version of the product are you using? On what operating system?

PeptideShaker-0.26.2 (Win64)

> Please provide any additional information 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).

Tue Mar 18 11:33:40 CET 2014: PeptideShaker version 0.26.2.
Memory given to the Java virtual machine: 7546077184.
Total amount of memory in the Java virtual machine: 129499136.
Free memory: 116025976.
Java version: 1.7.0_45.
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_45
os.name: Windows 7
memory: 34.5/129.5
processors available: 16
useCommandThread: false
<CompomicsError>PeptideShaker processing failed. See the PeptideShaker log for 
details.</CompomicsError>
java.lang.IllegalArgumentException: No amino acid found for letter >.
    at com.compomics.util.experiment.biology.AminoAcid.getAminoAcid(AminoAcid.java:200)
    at com.compomics.util.experiment.biology.Protein.computeMolecularWeight(Protein.java:207)
    at com.compomics.util.experiment.identification.SequenceFactory.computeMolecularWeight(SequenceFactory.java:1027)
    at eu.isas.peptideshaker.PeptideShaker.retainBestScoringGroups(PeptideShaker.java:3393)
    at eu.isas.peptideshaker.PeptideShaker.processIdentifications(PeptideShaker.java:384)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:488)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:388)
    at javax.swing.SwingWorker$1.call(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at javax.swing.SwingWorker.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
Free memory: 902156200

Original issue reported on code.google.com by [email protected] on 18 Mar 2014 at 10:57

no identifications retained - import cancelled

> What steps will reproduce the problem?
data import

> What is the expected output? What do you see instead?
identified proteins/PTMs

> What version of the product are you using? On what operating system?
0.16.2, mac os x

> Please provide any additional information below.

mgf of deconvoluted ETD spectra of intact proteins

> 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 [email protected] on 27 Apr 2012 at 1:12

Peptide shaker failed to start

> What steps will reproduce the problem?
I downloaded PeptideShaker-0.17.1, unzip and run.
It simply returned start up error. I can't successful run
the program.

> What is the expected output? What do you see instead?
I expect to see the program fire up without problem, just like I am using 
SearchGUI. Now I can't start up the program.


> What version of the product are you using? On what operating system?
I using using PeptideShaker-0.17.1, win 7 ultimate (fully updated).
I have java jre 7 installed, but I uninstalled it and download from oracle 
again, install it. Still I can't start up the program.
I can still run SearchGUI, nothing wrong. But I just can't startup
peptide shaker.


> Please provide any additional information below.
I attached my windows information, and the start-up log error
of the program. I checked the path of java in the log file, it's correct. I 
hopes these informaiton can help.

Thanks! Wish I can sort this out soon.

> 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 [email protected] on 3 Jun 2012 at 8:24

An error occurred when importing the sequences

Hi
I download the last version of the peptide shaker 0.19.3 and when I use it I 
get this error 
(An error occurred when importing the sequences. Please check the Search 
Parameters. See the log file for details. If the error persists please let us 
know at http://peptide-shaker.googlecode.com.)

the serchGui is working fine without any problem.

you will see attached the log file and screen shot image. 


regards

Marwan

Original issue reported on code.google.com by [email protected] on 5 Apr 2013 at 10:03

Attachments:

PeptideShaker.log
[screen image.jpg](https://storage.googleapis.com/google-code-attachments/peptide-shaker/issue-26/comment-0/screen image.jpg)

how can I include bacetial species(Bacillus subtulis) in the species panel

> What steps will reproduce the problem?


> What is the expected output? What do you see instead?


> What version of the product are you using? On what operating system?


> Please provide any additional information 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).

Original issue reported on code.google.com by [email protected] on 17 Dec 2013 at 11:16

Error while loading spectrum IDs from Xtandem results file

source files:
http://genesis.ugent.be/public_data/xtandem_peptideshaker_issue_120227.zip

> What steps will reproduce the problem?
Load the project and open the SpectrumID tab

> What is the expected output? What do you see instead?
See screenshot.

> What version of the product are you using? On what operating system?
0.13.0


> PeptideShaker.log stacktrace


java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
    at java.util.ArrayList.rangeCheck(Unknown Source)
    at java.util.ArrayList.get(Unknown Source)
    at eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel.fileSelectionChanged(SpectrumIdentificationPanel.java:2659)
    at eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel.access$5700(SpectrumIdentificationPanel.java:64)
    at eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel$55.run(SpectrumIdentificationPanel.java:2504)

Original issue reported on code.google.com by [email protected] on 27 Feb 2012 at 2:47

String index or t of range

Dear Colleague,

For the first time I am using peptide shaker and wondered if you can help me 
with the problems that can be found in the files attached.

Many thanks!

> What steps will reproduce the problem?
I've generated MGF files out of the Thermo RAW data (.raw) using Mascot Daemon. 
MGF (.mgf) and Mascot Distiller (.rov) files were generated. The Distiller 
files (.rov) were used to Mascot database search in Mascot Distiller to 
generate mascot search results (.dat). 
Then I loaded in PeptideShaker these .mgf and .dat files plus the fasta file I 
used in Distiller. 

> What is the expected output? What do you see instead?
There was an error to all files loaded as specified in the attached figure.

> What version of the product are you using? On what operating system?
Latest version of distiller, 2.2.2 of Daemon, and PeptideShaker-0.22.5.

> Please provide any additional information below.
Please, check the .log attached.

> 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).
It is here attached.

Thanks a lot!

Original issue reported on code.google.com by [email protected] on 23 Jul 2013 at 2:35

Attachments:

Failure loading MASCOT and X! Tandem files

> What steps will reproduce the problem?
Loading X!Tandem XML, or Mascot DAT files. I can only load OMSSA files 
successfully. I thought the number of mods searched influenced this, but I 
don't think that is an issue now. These files have only MSO and deamination 
(N,Q).

> What is the expected output? What do you see instead?
Loading of files. Files fail to load, with the error that spectrum XXX cannot 
be found in the MGF. I can confirm the scan is in fact in the MGF! I'm happy to 
provide any and all files as required.

> What version of the product are you using? On what operating system?
0.17.3, Win 7 32-bit

> Please provide any additional information below.
All dialogues and excerpts from the log file follow;

Loading DAT files dialogue...

Tue Aug 14 10:11:46 EST 2012        Import process for fdgfxdf (Sample: sdfdf, 
Replicate: 1)

Tue Aug 14 10:11:46 EST 2012        Importing sequences from 
LM_rodentia_concatenated_target_decoy.fasta.
Tue Aug 14 10:11:47 EST 2012        FASTA file import completed.
Tue Aug 14 10:11:47 EST 2012        Reading identification files.
Tue Aug 14 10:11:47 EST 2012        Parsing MEF4_10_FT_03_F022745.dat.
Tue Aug 14 10:11:49 EST 2012        Importing MEF4_10_FT_03.mgf
Tue Aug 14 10:11:49 EST 2012        MEF4_10_FT_03.mgf imported.
Tue Aug 14 10:11:49 EST 2012        Importing PSMs from 
MEF4_10_FT_03_F022745.dat
Tue Aug 14 10:11:49 EST 2012        Spectrum 1885: Sum of 2 scans in range 
100661 (rt=54.7566, p=0, c=6291, e=4) to 100662 (rt=54.7583, p=0, c=6291, e=5) 
[\cmri-nas\massspecdata2\Data\5600\PGH\260612\MEF4_10_FT_03.wiff] number 2035 
not found in file MEF4_10_FT_03.mgf.

Tue Aug 14 10:11:49 EST 2012        Import canceled.
Tue Aug 14 10:11:49 EST 2012        Parsing MEF4_2_FT_03_F022743.dat.
Tue Aug 14 10:11:50 EST 2012        Importing MEF4_2_FT_03.mgf
Tue Aug 14 10:11:50 EST 2012        MEF4_2_FT_03.mgf imported.
Tue Aug 14 10:11:50 EST 2012        Importing PSMs from MEF4_2_FT_03_F022743.dat
Tue Aug 14 10:11:50 EST 2012        Parsing MEF4_5_FT_03_F022744.dat.
Tue Aug 14 10:11:52 EST 2012        Importing MEF4_5_FT_03.mgf
Tue Aug 14 10:11:52 EST 2012        MEF4_5_FT_03.mgf imported.
Tue Aug 14 10:11:52 EST 2012        Importing PSMs from MEF4_5_FT_03_F022744.dat
Tue Aug 14 10:11:52 EST 2012        No identifications retained.

Tue Aug 14 10:11:52 EST 2012        Import canceled.


Tue Aug 14 10:11:21 EST 2012: PeptideShaker version 0.17.3.

1714 script command tokens
(C) 2009 Jmol Development
Jmol Version: 12.0.43  2011-05-03 14:21
java.vendor: Sun Microsystems Inc.
java.version: 1.6.0_21
os.name: Windows 7
memory: 19.8/129.9
processors available: 2
useCommandThread: false
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!

Loading Tandem files dialogue...


Tue Aug 14 10:13:47 EST 2012        Import process for sfdgsdfg (Sample: nmbnm, 
Replicate: 1)

Tue Aug 14 10:13:47 EST 2012        Importing sequences from 
LM_rodentia_concatenated_target_decoy.fasta.
Tue Aug 14 10:13:49 EST 2012        The database is too large to be parsed into 
peptides. Note that X!Tandem peptides might present protein inference issues.
Tue Aug 14 10:13:49 EST 2012        FASTA file import completed.
Tue Aug 14 10:13:49 EST 2012        Reading identification files.
Tue Aug 14 10:13:49 EST 2012        Parsing 
MEF4_10_FT_03.2012_08_09_17_32_02.t.xml.
Tue Aug 14 10:13:51 EST 2012        Importing MEF4_10_FT_03.mgf
Tue Aug 14 10:13:51 EST 2012        MEF4_10_FT_03.mgf imported.
Tue Aug 14 10:13:51 EST 2012        Importing PSMs from 
MEF4_10_FT_03.2012_08_09_17_32_02.t.xml
Tue Aug 14 10:13:51 EST 2012        Spectrum 1195: Scan 98984 (rt=50.8955, p=0, 
c=6186, e=7) [\cmri-nas\massspecdata2\Data\5600\PGH\260612\MEF4_10_FT_03.wiff] 
number 1195 not found in file MEF4_10_FT_03.mgf.

Tue Aug 14 10:13:51 EST 2012        Import canceled.
Tue Aug 14 10:13:51 EST 2012        Parsing 
MEF4_2_FT_03.2012_08_09_18_06_34.t.xml.
Tue Aug 14 10:13:53 EST 2012        Importing MEF4_2_FT_03.mgf
Tue Aug 14 10:13:53 EST 2012        MEF4_2_FT_03.mgf imported.
Tue Aug 14 10:13:53 EST 2012        Importing PSMs from 
MEF4_2_FT_03.2012_08_09_18_06_34.t.xml
Tue Aug 14 10:13:53 EST 2012        Parsing 
MEF4_5_FT_03.2012_08_09_18_43_20.t.xml.
Tue Aug 14 10:13:55 EST 2012        Importing MEF4_5_FT_03.mgf
Tue Aug 14 10:13:55 EST 2012        MEF4_5_FT_03.mgf imported.
Tue Aug 14 10:13:55 EST 2012        Importing PSMs from 
MEF4_5_FT_03.2012_08_09_18_43_20.t.xml
Tue Aug 14 10:13:55 EST 2012        An error occured while loading the 
identification files:
Tue Aug 14 10:13:55 EST 2012        Spectrum '18: Sum of 2 scans in range 71762 
(rt=25.7244, p=0, c=4485, e=1) to 71778 (rt=25.7591, p=0, c=4486, e=1) 
[\cmri-nas\massspecdata2\Data\5600\PGH\260612\MEF4_5_FT_03.wiff]' in mgf file 
'MEF4_5_FT_03.mgf' not found!

Tue Aug 14 10:13:55 EST 2012        Import canceled.


Tue Aug 14 10:13:23 EST 2012: PeptideShaker version 0.17.3.

1714 script command tokens
(C) 2009 Jmol Development
Jmol Version: 12.0.43  2011-05-03 14:21
java.vendor: Sun Microsystems Inc.
java.version: 1.6.0_21
os.name: Windows 7
memory: 19.7/129.9
processors available: 2
useCommandThread: false
java.io.IOException: Spectrum '18: Sum of 2 scans in range 71762 (rt=25.7244, 
p=0, c=4485, e=1) to 71778 (rt=25.7591, p=0, c=4486, e=1) 
[\cmri-nas\massspecdata2\Data\5600\PGH\260612\MEF4_5_FT_03.wiff]' in mgf file 
'MEF4_5_FT_03.mgf' not found!
    at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getPrecursor(SpectrumFactory.java:413)
    at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getPrecursor(SpectrumFactory.java:350)
    at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getPrecursor(SpectrumFactory.java:212)
    at eu.isas.peptideshaker.fileimport.IdFilter.validateId(IdFilter.java:150)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:720)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:565)
    at javax.swing.SwingWorker$1.call(Unknown Source)
    at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at javax.swing.SwingWorker.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)


> 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 [email protected] on 14 Aug 2012 at 12:53

Protein accession containing ' ' are not supported.

> What steps will reproduce the problem?

An error occured while loading the identification files:

Data file import is broken during parsing X!Tandem result, because of not 
supported protein accession,although the database Metagenomic and Environmental 
Sequences (UniMES) from Uniprot was downloaded.


> What version of the product are you using? On what operating system?
Peptide Shaker 0.18.3/ Win 7 /i7-2600 3,4 GHz/ 16 GB RAM

> Please provide any additional information below.
 following is the output on the screen

Fri Dec 14 17:18:16 CET 2012        Import process for a (Sample: c, Replicate: 
0)

Fri Dec 14 17:18:16 CET 2012        Establishing database connection.
Fri Dec 14 17:18:18 CET 2012        Importing sequences from 
unimes_concatenated_target_decoy.fasta.
Fri Dec 14 17:21:36 CET 2012        The database is too large to be parsed into 
peptides. Note that X!Tandem peptides might present protein inference issues.
Fri Dec 14 17:21:36 CET 2012        FASTA file import completed.
Fri Dec 14 17:21:36 CET 2012        Reading identification files.
Fri Dec 14 17:21:36 CET 2012        Parsing Pool1_wdh.2012_12_12_07_54_47.t.xml.
Fri Dec 14 17:21:39 CET 2012        An error occured while loading the 
identification files:
Fri Dec 14 17:21:39 CET 2012        Protein accession containing ' ' are not 
supported. Conflicting accession: MES00000601547 Putative uncharacterized 
protein GOS_5872725 (Fragment) OS=marine...

Fri Dec 14 17:21:39 CET 2012        Importing Data Canceled!

Original issue reported on code.google.com by [email protected] on 14 Dec 2012 at 4:38

Custom database error

> What steps will reproduce the problem?
Using a custom database

> What is the expected output? What do you see instead?
Importing Data Cancelled!

> What version of the product are you using? On what operating system?
0.25.0, Windows 7 or Server 2012, 64-bit

> Please provide any additional information below.
I was able to use this database successfully with older versions of 
PeptideShaker. I thought perhaps the issue was related to the header line, so I 
altered the database to exactly follow your guidelines. I searched again with 
SearchGUI 1.16.0 (and Mascot), using the same database and settings. SearchGUI 
has no problems with the database. PeptideShaker fails when it tries to load 
the database.

> 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).

The output follows, along with the log file and the first few entries in the 
database.

OUTPUT***
Wed Feb 05 15:09:30 EST 2014        Import process for test (Sample: 
test, Replicate: 0)  Wed Feb 05 15:09:30 EST 2014        Importing 
sequences from ICKP_140_seq_concatenated_target_decoy.fasta. Wed Feb 05 
15:09:34 EST 2014        Expected import time: 0 seconds. (See Protein 
Inference.)  Wed Feb 05 15:09:34 EST 2014        Importing Data 
Canceled! Wed Feb 05 15:09:34 EST 2014        An error occurred when 
importing the sequences. Please check the Search Parameters. See the log file 
for details. If the error persists please let us know using our issue tracker. 

LOG FILE***
LOG FILE

Tue Feb 04 18:57:03 CET 2014: PeptideShaker version 0.25.0.
Memory given to the Java virtual machine: 5592449024.
Total amount of memory in the Java virtual machine: 128647168.
Free memory: 115702824.
Java version: 1.7.0_21.
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_21
os.name: Windows 7
memory: 36.5/128.6
processors available: 2
useCommandThread: false


Wed Feb 05 15:08:29 EST 2014: PeptideShaker version 0.25.0.
Memory given to the Java virtual machine: 61084270592.
Total amount of memory in the Java virtual machine: 129499136.
Free memory: 114106352.
Java version: 1.7.0_45.
jshortcut.dll loaded via tmp generated pathname: 
C:\Users\phains\AppData\Local\Temp\3\jshortcut-3262724105231552420.dll
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_45
os.name: Windows Server 2012
memory: 20.2/129.5
processors available: 16
useCommandThread: false
An error occured while loading I:\MassspecCoreGroup\Search 
Engine\DB\SearchGUI\ICKP_140_seq_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:444)
    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$1.call(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at javax.swing.SwingWorker.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)


DATABASE***
>SYK(1-635)|AAH01645.1|SYK
MASSGMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRNYLGGFALSVAHGRKAHHYTIERELNGTYAIAGGR
THASPADLCHYHSQESDGLVCLLKKPFNRPQGVQPKTGPFEDLKENLIREYVKQTWNLQGQALEQAIISQKPQLEKLIAT
TAHEKMPWFHGKISREESEQIVLIGSKTNGKFLIRARDNNGSYALCLLHEGKVLHYRIDKDKTGKLSIPEGKKFDTLWQL
VEHYSYKADGLLRVLTVPCQKIGTQGNVNFGGRPQLPGSHPATWSAGGIISRIKSYSFPKPGHRKSSPAQGNRQESTVSF
NPYEPELAPWAADKGPQREALPMDTEVYESPYADPEEIRPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVA
VKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSM
GMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGV
LMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVN
>AAH01645.1_REVERSED
NVVDYYYNRLRLEVAAFGPRNEVDYTWCLNMLDYMERPCGAPCGMREGKELMATVESGKMGRYPKQGYSFAEWMLVGFSW
VDSKSSFKYYNICEPAYWKVPWKGHTQAKYYNEDARLAKSLGFDSIKAYHQTVLLVNRAALDRHVFNSEELYKMGMSVQH
VLEIINKDKVHRNQQLYKNLPGLEAMEMVLMWSEAECIGIMRVIYPNDLQQMVNAEALLEDKLAPDNAENKLIKVAVTKV
VKKMQYYGKKVTGFNGSGLEKDELTLLKRDLYVEKPRIEEPDAYPSEYVETDMPLAERQPGKDAAWPALEPEYPNFSVTS
EQRNGQAPSSKRHGPKPFSYSKIRSIIGGASWTAPHSGPLQPRGGFNVNGQTGIKQCPVTLVRLLGDAKYSYHEVLQWLT
DFKKGEPISLKGTKDKDIRYHLVKGEHLLCLAYSGNNDRARILFKGNTKSGILVIQESEERSIKGHFWPMKEHATTAILK
ELQPKQSIIAQELAQGQLNWTQKVYERILNEKLDEFPGTKPQVGQPRNFPKKLLCVLGDSEQSHYHCLDAPSAHTRGGAI
AYTGNLEREITYHHAKRGHAVSLAFGGLYNRSQRLLYLGDSMGGQVLYDEAEERTINGFFFPLHNASDAMGSSAM
>MINK1(1-320)|NM_015716|MINK1
MGDPAPARSLDDIDLSALRDPAGIFELVEVVGNGTYGQVYKGRHVKTGQLAAIKVMDVTEDEEEEIKQEINMLKKYSHHR
NIATYYGAFIKKSPPGNDDQLWLVMEFCGAGSVTDLVKNTKGNALKEDCIAYICREILRGLAHLHAHKVIHRDIKGQNVL
LTENAEVKLVDFGVSAQLDRTVGRRNTFIGTPYWMAPEVIACDENPDATYDYRSDIWSLGITAIEMAEGAPPLCDMHPMR
ALFLIPRNPPPRLKSKKWSKKFIDFIDTCLIKTYLSRPPTEQLLKFPFIRDQPTERQVRIQLKDHIDRSRKKRGEKEETE
>NM_015716_REVERSED
ETEEKEGRKKRSRDIHDKLQIRVQRETPQDRIFPFKLLQETPPRSLYTKILCTDIFDIFKKSWKKSKLRPPPNRPILFLA
RMPHMDCLPPAGEAMEIATIGLSWIDSRYDYTADPNEDCAIVEPAMWYPTGIFTNRRGVTRDLQASVGFDVLKVEANETL
LVNQGKIDRHIVKHAHLHALGRLIERCIYAICDEKLANGKTNKVLDTVSGAGCFEMVLWLQDDNGPPSKKIFAGYYTAIN
RHHSYKKLMNIEQKIEEEEDETVDMVKIAALQGTKVHRGKYVQGYTGNGVVEVLEFIGAPDRLASLDIDDLSRAPAPDGM
>MST4(1-416)|NM_016542.3|MST4
MAHSPVAVQVPGMQNNIADPEELFTKLERIGKGSFGEVFKGIDNRTQQVVAIKIIDLEEAEDEIEDIQQEITVLSQCDSS
YVTKYYGSYLKGSKLWIIMEYLGGGSALDLLRAGPFDEFQIATMLKEILKGLDYLHSEKKIHRDIKAANVLLSEQGDVKL
ADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIQQSAYDSKADIWSLGITAIELAKGEPPNSDMHPMRVLFLIPKNNPPTLV
GDFTKSFKEFIDACLNKDPSFRPTAKELLKHKFIVKNSKKTSYLTELIDRFKRWKAEGHSDDESDSEGSDSESTSRENNT
HPEWSFTTVRKKPDPKKVQNGAEQDLVQTLSCLSMIITPAFAELKQQDENNASRNQAIEELEKSIAVAEAACPGITDKMV
KKLIEKFQKCSADESP
>NM_016542.3_REVERSED
PSEDASCKQFKEILKKVMKDTIGPCAAEAVAISKELEEIAQNRSANNEDQQKLEAFAPTIIMSLCSLTQVLDQEAGNQVK
KPDPKKRVTTFSWEPHTNNERSTSESDSGESDSEDDSHGEAKWRKFRDILETLYSTKKSNKVIFKHKLLEKATPRFSPDK
NLCADIFEKFSKTFDGVLTPPNNKPILFLVRMPHMDSNPPEGKALEIATIGLSWIDAKSDYASQQIVEPAMWFPTGVFTN
RKIQTDTLQGAVGFDALKVDGQESLLVNAAKIDRHIKKESHLYDLGKLIEKLMTAIQFEDFPGARLLDLASGGGLYEMII
WLKSGKLYSGYYKTVYSSDCQSLVTIEQQIDEIEDEAEELDIIKIAVVQQTRNDIGKFVEGFSGKGIRELKTFLEEPDAI
NNQMGPVQVAVPSHAM

Original issue reported on code.google.com by [email protected] on 5 Feb 2014 at 4:25

importing data canceled.

> What steps will reproduce the problem?
When I import 104 mascot and xtandem searching results from 52 mgf files

> What is the expected output? What do you see instead?


> What version of the product are you using? On what operating system?
V 0.27.0 windows 7 64bit

> Please provide any additional information below.
I have gave peptideshaker 12GB memory and I notice that memory consumption is 
always stay at 13GB.

> 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).

Original issue reported on code.google.com by [email protected] on 27 Mar 2014 at 3:23

Problem with peptideshaker - import canceled

> What steps will reproduce the problem?
starting new project

> What is the expected output? What do you see instead?
protein list

> What version of the product are you using? On what operating system?
0.17.3 Windows XP

> Please provide any additional information below.
Import is canceled when I try to visualize my SearchGUI search.

Spectrum files import failed when trying to import xxx.pkl

The report file is included as an attachment.

Yours,

Jukka Sund
[email protected]

> 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 [email protected] on 19 Jun 2012 at 11:53

Error loading large files

> What steps will reproduce the problem?
Loading large data files. These can be Mascot, Tandem, or OMSSA. The problem 
seems to be related to the size of the files (or combined size) rather than the 
source of the file.

> What is the expected output? What do you see instead?
Typically the error I get is something like; A string constant starting with 
''A0EVJ8_cus_A0EVJ9_cus_A0EVK0_cus_A0EVK1_cus_A0FKC4_cus_A0FK&' is too long.

> What version of the product are you using? On what operating system?
0.22.6, CentOS, 64-bit

> Please provide any additional information below.
I have not been able to work out what the size threshold is, or maybe, for the 
problem to occur. I have recently started searching very large data sets and 
routinely end up with DATs that are over 250 MB. Loading these files has been 
my problem. I can load around 2 at a time, but above that doesn't work.

> 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).

The log follows;


Mon Nov 04 07:32:50 EST 2013: PeptideShaker version 0.22.6.

Total amount of memory in the Java virtual machine: 128647168.

Java version: 1.7.0_19.

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_19
os.name: Linux
memory: 22.5/128.6
processors available: 32
useCommandThread: false
Reindexing: ICKP_140_IS_human_concatenated_target_decoy.fasta.
File I:/MassspecCoreGroup/Search 
Engine/DB/SearchGUI/ICKP_140_seq_concatenated_target_decoy.fasta was not found. 
Please select a different FASTA file.
java.io.FileNotFoundException: 
/home/phains/bin/PeptideShaker-0.22.6/I:/MassspecCoreGroup/Search 
Engine/DB/SearchGUI/ICKP_140_seq_concatenated_target_decoy.fasta (No such file 
or directory)
    at java.io.RandomAccessFile.open(Native Method)
    at java.io.RandomAccessFile.<init>(RandomAccessFile.java:233)
    at java.io.RandomAccessFile.<init>(RandomAccessFile.java:118)
    at uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile.<init>(BufferedRandomAccessFile.java:45)
    at uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile.<init>(BufferedRandomAccessFile.java:53)
    at com.compomics.util.experiment.identification.SequenceFactory.loadFastaFile(SequenceFactory.java:357)
    at eu.isas.peptideshaker.fileimport.FileImporter.importSequences(FileImporter.java:171)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:511)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:476)
    at javax.swing.SwingWorker$1.call(SwingWorker.java:296)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
    at java.util.concurrent.FutureTask.run(FutureTask.java:166)
    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:722)
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
<CompomicsError> PeptideShaker processing failed. See the PeptideShaker log for 
details. </CompomicsError>
java.sql.SQLException: A string constant starting with 
''A0EVJ8_cus_A0EVJ9_cus_A0EVK0_cus_A0EVK1_cus_A0FKC4_cus_A0FK&' is too long.
    at org.apache.derby.impl.jdbc.SQLExceptionFactory40.getSQLException(Unknown Source)
    at org.apache.derby.impl.jdbc.Util.generateCsSQLException(Unknown Source)
    at org.apache.derby.impl.jdbc.TransactionResourceImpl.wrapInSQLException(Unknown Source)
    at org.apache.derby.impl.jdbc.TransactionResourceImpl.handleException(Unknown Source)
    at org.apache.derby.impl.jdbc.EmbedConnection.handleException(Unknown Source)
    at org.apache.derby.impl.jdbc.ConnectionChild.handleException(Unknown Source)
    at org.apache.derby.impl.jdbc.EmbedStatement.execute(Unknown Source)
    at org.apache.derby.impl.jdbc.EmbedStatement.executeLargeUpdate(Unknown Source)
    at org.apache.derby.impl.jdbc.EmbedStatement.executeUpdate(Unknown Source)
    at com.compomics.util.db.ObjectsDB.deleteObject(ObjectsDB.java:664)
    at com.compomics.util.experiment.identification.IdentificationDB.removeProteinMatch(IdentificationDB.java:263)
    at com.compomics.util.experiment.identification.Identification.removeProteinMatch(Identification.java:832)
    at eu.isas.peptideshaker.PeptideShaker.cleanProteinGroups(PeptideShaker.java:2363)
    at eu.isas.peptideshaker.PeptideShaker.processIdentifications(PeptideShaker.java:339)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:574)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:476)
    at javax.swing.SwingWorker$1.call(SwingWorker.java:296)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
    at java.util.concurrent.FutureTask.run(FutureTask.java:166)
    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:722)
Caused by: java.sql.SQLException: A string constant starting with 
''A0EVJ8_cus_A0EVJ9_cus_A0EVK0_cus_A0EVK1_cus_A0FKC4_cus_A0FK&' is too long.
    at org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source)
    at org.apache.derby.impl.jdbc.SQLExceptionFactory40.wrapArgsForTransportAcrossDRDA(Unknown Source)
    ... 23 more
Caused by: ERROR 54002: A string constant starting with 
''A0EVJ8_cus_A0EVJ9_cus_A0EVK0_cus_A0EVK1_cus_A0FKC4_cus_A0FK&' is too long.
    at org.apache.derby.iapi.error.StandardException.newException(Unknown Source)
    at org.apache.derby.impl.sql.compile.SQLParser.stringLiteral(Unknown Source)
    at org.apache.derby.impl.sql.compile.SQLParser.literal(Unknown Source)
    at org.apache.derby.impl.sql.compile.SQLParser.valueSpecification(Unknown Source)
    at org.apache.derby.impl.sql.compile.SQLParser.valueExpressionPrimary(Unknown Source)
    at org.apache.derby.impl.sql.compile.SQLParser.primary(Unknown Source)
    at org.apache.derby.impl.sql.compile.SQLParser.primaryExpressionXX(Unknown Source)
    at org.apache.derby.impl.sql.compile.SQLParser.primaryExpression(Unknown Source)
    at org.apache.derby.impl.sql.compile.SQLParser.unaryExpression(Unknown Source)
    at org.apache.derby.impl.sql.compile.SQLParser.multiplicativeExpression(Unknown Source)
    at org.apache.derby.impl.sql.compile.SQLParser.additiveExpression(Unknown Source)
    at org.apache.derby.impl.sql.compile.SQLParser.remainingNonNegatablePredicate(Unknown Source)
    at org.apache.derby.impl.sql.compile.SQLParser.remainingPredicate(Unknown Source)
    at org.apache.derby.impl.sql.compile.SQLParser.predicate(Unknown Source)
    at org.apache.derby.impl.sql.compile.SQLParser.booleanPrimary(Unknown Source)
    at org.apache.derby.impl.sql.compile.SQLParser.isSearchCondition(Unknown Source)
    at org.apache.derby.impl.sql.compile.SQLParser.andExpression(Unknown Source)
    at org.apache.derby.impl.sql.compile.SQLParser.orExpression(Unknown Source)
    at org.apache.derby.impl.sql.compile.SQLParser.valueExpression(Unknown Source)
    at org.apache.derby.impl.sql.compile.SQLParser.whereClause(Unknown Source)
    at org.apache.derby.impl.sql.compile.SQLParser.deleteBody(Unknown Source)
    at org.apache.derby.impl.sql.compile.SQLParser.preparableDeleteStatement(Unknown Source)
    at org.apache.derby.impl.sql.compile.SQLParser.preparableSQLDataStatement(Unknown Source)
    at org.apache.derby.impl.sql.compile.SQLParser.StatementPart(Unknown Source)
    at org.apache.derby.impl.sql.compile.SQLParser.Statement(Unknown Source)
    at org.apache.derby.impl.sql.compile.ParserImpl.parseStatement(Unknown Source)
    at org.apache.derby.impl.sql.GenericStatement.prepMinion(Unknown Source)
    at org.apache.derby.impl.sql.GenericStatement.prepare(Unknown Source)
    at org.apache.derby.impl.sql.conn.GenericLanguageConnectionContext.prepareInternalStatement(Unknown Source)
    ... 17 more
Free memory: 4280350536

Original issue reported on code.google.com by [email protected] on 3 Nov 2013 at 11:50

Can peptide-shaker run on command line?

Hi all,
Can peptide-shaker run on command line?
If not , will it support the command line mode？

Best

Bo

Original issue reported on code.google.com by [email protected] on 4 Jan 2012 at 2:09

OMSSA results import prpoblem

Dear all,
I experienced a problem with OMSSA data import into Peptide-shaker.
I used an home-made DB that work properly with xtandem. The search with OMSSA 
works fine but Peptide-shaker is unable to import the data.

Here you have the Peptide-shaker.log:

Thu Nov 21 14:22:06 CET 2013: PeptideShaker version 0.22.6.

Total amount of memory in the Java virtual machine: 129761280.

Java version: 1.7.0_25.

java.lang.IllegalArgumentException: Protein not found: BL_ORD_ID:158089.
    at com.compomics.util.experiment.identification.SequenceFactory.getProtein(SequenceFactory.java:180)
    at com.compomics.util.experiment.identification.SequenceFactory.getProtein(SequenceFactory.java:178)
    at com.compomics.util.experiment.identification.SequenceFactory.getProtein(SequenceFactory.java:140)
    at eu.isas.peptideshaker.PeptideShaker.cleanProteinGroups(PeptideShaker.java:2389)
    at eu.isas.peptideshaker.PeptideShaker.processIdentifications(PeptideShaker.java:339)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:574)
    at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:153)
    at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:217)
    at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:363)
    at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:124)
    at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:635)
Free memory: 67857832

I'm using OsX.

Original issue reported on code.google.com by [email protected] on 21 Nov 2013 at 2:09

Failure to load DAT files

> What steps will reproduce the problem?
Loading any Mascot DAT files, including ones I have loaded successfully in 
previous PeptideShaker versions.

> What is the expected output? What do you see instead?
The import process halts at 4%. I have left the program "running" for over a 
day with no change. I have to cancel the import or it will stay in that state. 
PeptideShaker does not report an error.

> What version of the product are you using? On what operating system?
The problem first appeared with 0.24.0, but is still present with 0.24.3. I am 
using Win7, 64-bit, 32 GB RAM.

> Please provide any additional information below.
I can load OMSSA and X!Tandem searches done with the same MGF, settings and 
database. I only have issues when loading Mascot files, currently version 2.4.0.

> 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).
Mon Jan 20 09:46:31 EST 2014
Import process for APSDAT (Sample: APS4DAT, Replicate: 0)  Mon Jan 20 09:46:31 
EST 2014
Importing sequences from uniprot_homo_sapiens_concatenated_target_decoy.fasta. 
Mon Jan 20 09:46:39 EST 2014
Expected import time: 12 minutes. (See Protein Inference.) Mon Jan 20 09:59:37 
EST 2014
FASTA file import completed. Mon Jan 20 09:59:37 EST 2014
Establishing local database connection. Mon Jan 20 09:59:47 EST 2014
Reading identification files. Mon Jan 20 09:59:47 EST 2014
Parsing APS4_A_Ti_E_01_F023657.dat.  Mon Jan 20 10:46:13 EST 2014
Importing Data Canceled! 



Mon Jan 20 09:44:51 EST 2014: PeptideShaker version 0.24.3.

Total amount of memory in the Java virtual machine: 129499136.

Java version: 1.7.0_45.

jshortcut.dll loaded via tmp generated pathname: 
C:\Users\phains\AppData\Local\Temp\jshortcut-2967493841186453377.dll
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_45
os.name: Windows 7
memory: 19.3/129.5
processors available: 8
useCommandThread: false
No Decoy section found!!

Original issue reported on code.google.com by [email protected] on 20 Jan 2014 at 12:34

Problem with my own database

> 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 [email protected] on 6 Mar 2013 at 3:52

Importing Data Cancelled

> What steps will reproduce the problem?
Loading the identification file - a fasta file containing UniProt protein 
sequence and a MS spectrum of appropriate format and clicking load data

> What is the expected output? What do you see instead?
Information on crosslinked peptides


> What version of the product are you using? On what operating system?
0.27.4


> Please provide any additional information below.
Please see the errors as taken from error log:
Mon Apr 07 11:28:50 BST 2014: PeptideShaker version 0.27.4.
Memory given to the Java virtual machine: 1037959168.
Total amount of memory in the Java virtual machine: 129761280.
Free memory: 114646056.
Java version: 1.7.0_51.
java.net.UnknownHostException: genesis.ugent.be
    at java.net.AbstractPlainSocketImpl.connect(Unknown Source)
    at java.net.PlainSocketImpl.connect(Unknown Source)
    at java.net.SocksSocketImpl.connect(Unknown Source)
    at java.net.Socket.connect(Unknown Source)
    at java.net.Socket.connect(Unknown Source)
    at sun.net.NetworkClient.doConnect(Unknown Source)
    at sun.net.www.http.HttpClient.openServer(Unknown Source)
    at sun.net.www.http.HttpClient.openServer(Unknown Source)
    at sun.net.www.http.HttpClient.<init>(Unknown Source)
    at sun.net.www.http.HttpClient.New(Unknown Source)
    at sun.net.www.http.HttpClient.New(Unknown Source)
    at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(Unknown Source)
    at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source)
    at sun.net.www.protocol.http.HttpURLConnection.connect(Unknown Source)
    at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
    at java.net.URL.openStream(Unknown Source)
    at com.compomics.software.autoupdater.WebDAO.getLatestVersionNumberFromRemoteRepo(WebDAO.java:34)
    at com.compomics.software.autoupdater.WebDAO.newVersionReleased(WebDAO.java:105)
    at com.compomics.software.CompomicsWrapper.checkForNewDeployedVersion(CompomicsWrapper.java:509)
    at eu.isas.peptideshaker.gui.PeptideShakerGUI.checkForNewVersion(PeptideShakerGUI.java:6539)
    at eu.isas.peptideshaker.gui.PeptideShakerGUI.<init>(PeptideShakerGUI.java:424)
    at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:400)
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: Windows 8
memory: 31.4/129.8
processors available: 4
useCommandThread: false
Reindexing: 140331_101.mgf. (Reason: 
com.compomics.util.experiment.io.massspectrometry.MgfIndex; local class 
incompatible: stream classdesc serialVersionUID = 4769401753928606746, local 
class serialVersionUID = 1490481272256514169)
<CompomicsError>PeptideShaker processing failed. See the PeptideShaker log for 
details.</CompomicsError>
java.lang.NullPointerException
    at com.compomics.util.experiment.biology.Peptide.getPotentialModificationSites(Peptide.java:724)
    at com.compomics.util.experiment.biology.PTMFactory.getExpectedPTMs(PTMFactory.java:876)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:881)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:489)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:457)
    at javax.swing.SwingWorker$1.call(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at javax.swing.SwingWorker.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
Free memory: 348023024


Mon Apr 07 11:44:44 BST 2014: PeptideShaker version 0.27.4.
Memory given to the Java virtual machine: 1037959168.
Total amount of memory in the Java virtual machine: 129761280.
Free memory: 114554896.
Java version: 1.7.0_51.
java.net.UnknownHostException: genesis.ugent.be
    at java.net.AbstractPlainSocketImpl.connect(Unknown Source)
    at java.net.PlainSocketImpl.connect(Unknown Source)
    at java.net.SocksSocketImpl.connect(Unknown Source)
    at java.net.Socket.connect(Unknown Source)
    at java.net.Socket.connect(Unknown Source)
    at sun.net.NetworkClient.doConnect(Unknown Source)
    at sun.net.www.http.HttpClient.openServer(Unknown Source)
    at sun.net.www.http.HttpClient.openServer(Unknown Source)
    at sun.net.www.http.HttpClient.<init>(Unknown Source)
    at sun.net.www.http.HttpClient.New(Unknown Source)
    at sun.net.www.http.HttpClient.New(Unknown Source)
    at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(Unknown Source)
    at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source)
    at sun.net.www.protocol.http.HttpURLConnection.connect(Unknown Source)
    at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
    at java.net.URL.openStream(Unknown Source)
    at com.compomics.software.autoupdater.WebDAO.getLatestVersionNumberFromRemoteRepo(WebDAO.java:34)
    at com.compomics.software.autoupdater.WebDAO.newVersionReleased(WebDAO.java:105)
    at com.compomics.software.CompomicsWrapper.checkForNewDeployedVersion(CompomicsWrapper.java:509)
    at eu.isas.peptideshaker.gui.PeptideShakerGUI.checkForNewVersion(PeptideShakerGUI.java:6539)
    at eu.isas.peptideshaker.gui.PeptideShakerGUI.<init>(PeptideShakerGUI.java:424)
    at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:400)
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: Windows 8
memory: 32.1/129.8
processors available: 4
useCommandThread: false

> 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).

Original issue reported on code.google.com by [email protected] on 8 Apr 2014 at 9:02

Amino acid J not supported

> What steps will reproduce the problem?
During import of identifications, the error "amino acid not supported" shows up.

> What is the expected output? What do you see instead?
Guess, J stands for Isoleucine or Leucine as a wildcard in some FASTA files. 
Pride toolsuite does support it, just wanted to ask whether it could be 
included as well in peptide-shaker.

> What version of the product are you using? On what operating system?
Peptide-shaker 0.17.1

> Please provide any additional information below.
Thilo just wanted to do some metaproteomics searches on his laptop and now he 
is bothering you guys. :-)

> 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 [email protected] on 31 May 2012 at 11:24

Program crashes when %FDR is changed in the validation tab

What steps will reproduce the problem?
1.
2.
3.

What is the expected output? What do you see instead?

Peptide shaker reported my results with a Nmax value of 38 and a FDR of 0% at 
the protein level. I tried to change the FDR % to 10% and pressed the validate 
tab. Whilst I expected a list with a set of proteins scored differently, I got 
an error message instead saying "Error while loading null. This message will be 
displayed only once. Please contact the developers".

What version of the product are you using? On what operating system?

I am using Peptide shaker 0.12.0 on a Windows 7 OS.

Please provide any additional information below.

When I changed the FDR% to 2% I got a different error message saying "Invalid 
range. Please contact developers".

Original issue reported on code.google.com by [email protected] on 20 Dec 2011 at 7:34

Importing Data Cancelled

> What steps will reproduce the problem?
Loading the identification file - a fasta file containing UniProt protein 
sequence and a MS spectrum of appropriate format and clicking load data

> What is the expected output? What do you see instead?
Information on crosslinked peptides


> What version of the product are you using? On what operating system?
0.27.4


> Please provide any additional information below.
Please see the errors as taken from error log:
Mon Apr 07 11:28:50 BST 2014: PeptideShaker version 0.27.4.
Memory given to the Java virtual machine: 1037959168.
Total amount of memory in the Java virtual machine: 129761280.
Free memory: 114646056.
Java version: 1.7.0_51.
java.net.UnknownHostException: genesis.ugent.be
    at java.net.AbstractPlainSocketImpl.connect(Unknown Source)
    at java.net.PlainSocketImpl.connect(Unknown Source)
    at java.net.SocksSocketImpl.connect(Unknown Source)
    at java.net.Socket.connect(Unknown Source)
    at java.net.Socket.connect(Unknown Source)
    at sun.net.NetworkClient.doConnect(Unknown Source)
    at sun.net.www.http.HttpClient.openServer(Unknown Source)
    at sun.net.www.http.HttpClient.openServer(Unknown Source)
    at sun.net.www.http.HttpClient.<init>(Unknown Source)
    at sun.net.www.http.HttpClient.New(Unknown Source)
    at sun.net.www.http.HttpClient.New(Unknown Source)
    at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(Unknown Source)
    at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source)
    at sun.net.www.protocol.http.HttpURLConnection.connect(Unknown Source)
    at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
    at java.net.URL.openStream(Unknown Source)
    at com.compomics.software.autoupdater.WebDAO.getLatestVersionNumberFromRemoteRepo(WebDAO.java:34)
    at com.compomics.software.autoupdater.WebDAO.newVersionReleased(WebDAO.java:105)
    at com.compomics.software.CompomicsWrapper.checkForNewDeployedVersion(CompomicsWrapper.java:509)
    at eu.isas.peptideshaker.gui.PeptideShakerGUI.checkForNewVersion(PeptideShakerGUI.java:6539)
    at eu.isas.peptideshaker.gui.PeptideShakerGUI.<init>(PeptideShakerGUI.java:424)
    at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:400)
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: Windows 8
memory: 31.4/129.8
processors available: 4
useCommandThread: false
Reindexing: 140331_101.mgf. (Reason: 
com.compomics.util.experiment.io.massspectrometry.MgfIndex; local class 
incompatible: stream classdesc serialVersionUID = 4769401753928606746, local 
class serialVersionUID = 1490481272256514169)
<CompomicsError>PeptideShaker processing failed. See the PeptideShaker log for 
details.</CompomicsError>
java.lang.NullPointerException
    at com.compomics.util.experiment.biology.Peptide.getPotentialModificationSites(Peptide.java:724)
    at com.compomics.util.experiment.biology.PTMFactory.getExpectedPTMs(PTMFactory.java:876)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:881)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:489)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:457)
    at javax.swing.SwingWorker$1.call(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at javax.swing.SwingWorker.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
Free memory: 348023024


Mon Apr 07 11:44:44 BST 2014: PeptideShaker version 0.27.4.
Memory given to the Java virtual machine: 1037959168.
Total amount of memory in the Java virtual machine: 129761280.
Free memory: 114554896.
Java version: 1.7.0_51.
java.net.UnknownHostException: genesis.ugent.be
    at java.net.AbstractPlainSocketImpl.connect(Unknown Source)
    at java.net.PlainSocketImpl.connect(Unknown Source)
    at java.net.SocksSocketImpl.connect(Unknown Source)
    at java.net.Socket.connect(Unknown Source)
    at java.net.Socket.connect(Unknown Source)
    at sun.net.NetworkClient.doConnect(Unknown Source)
    at sun.net.www.http.HttpClient.openServer(Unknown Source)
    at sun.net.www.http.HttpClient.openServer(Unknown Source)
    at sun.net.www.http.HttpClient.<init>(Unknown Source)
    at sun.net.www.http.HttpClient.New(Unknown Source)
    at sun.net.www.http.HttpClient.New(Unknown Source)
    at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(Unknown Source)
    at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source)
    at sun.net.www.protocol.http.HttpURLConnection.connect(Unknown Source)
    at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
    at java.net.URL.openStream(Unknown Source)
    at com.compomics.software.autoupdater.WebDAO.getLatestVersionNumberFromRemoteRepo(WebDAO.java:34)
    at com.compomics.software.autoupdater.WebDAO.newVersionReleased(WebDAO.java:105)
    at com.compomics.software.CompomicsWrapper.checkForNewDeployedVersion(CompomicsWrapper.java:509)
    at eu.isas.peptideshaker.gui.PeptideShakerGUI.checkForNewVersion(PeptideShakerGUI.java:6539)
    at eu.isas.peptideshaker.gui.PeptideShakerGUI.<init>(PeptideShakerGUI.java:424)
    at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:400)
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: Windows 8
memory: 32.1/129.8
processors available: 4
useCommandThread: false

> 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).

Original issue reported on code.google.com by [email protected] on 7 Apr 2014 at 1:15

missing mgf and fasta files

> What steps will reproduce the problem?
when loading input files a message pops up about missing mgf and FASTA file and 
i get prompted to load them manually.

> What is the expected output? What do you see instead?
when i add the missing files manually and i run the program, i get the message 
that importing data is cancelled and an error occured while loading spectrum 
matches.

> What version of the product are you using? On what operating system?
0.22.2

> Please provide any additional information 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).

Original issue reported on code.google.com by [email protected] on 26 Jun 2013 at 11:54

Cannot find spectrum in MGF file

> What steps will reproduce the problem?

Do the SearchGUI search
Try to use Peptide Shaker after

> What is the expected output? What do you see instead?

i expect to see the identified peptides and proteins
instead:

An error occured while loading the identification files:
Fri Mar 29 09:46:31 CDT 2013    Spectrum '031413_01_HC.1052.1052.5 
RTINSECONDS=1334.9848' in mgf file '031413_01_HC.mgf' not found.

... Import cancelled
(logfile attached)

> What version of the product are you using? On what operating system?
peptide shaker 0.19.2
SearchGUI 1.12.1

Windows XP, 32-bit.
I use msconvert to create .mgf files
I had no problems with previous versions of the peptide-shaker.
> Please provide any additional information 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\conf folder).

Original issue reported on code.google.com by [email protected] on 29 Mar 2013 at 3:03

Trouble while loading Mascot DAT file

> What steps will reproduce the problem?
Loading a Mascot Dat file in peptide-shaker

> What is the expected output? What do you see instead?
Expect identifications from the Mascot.dat file

> What version of the product are you using? On what operating system?
Peptide-shaker 0.18.3
searchGUI 1.10.4
Mascot 2.2
Windows XP sp3 32bits

> Please provide any additional information below.
Hi everybody,
I'm using peptide shaker for month and it use to work
well with X!Tandem and OMSSA (SearchGUI's results), however I'm having issues 
with importing my Mascot results.  I have read about parsing rules and mascot 
configuration (no decoy, same database, rule to parse accession 
">..|\([^|]*\)", parse description ">[^ ]* \(.*\)", but even with this good 
advices, when I add a Mascot.dat file the report say:

Mon Oct 15 13:03:34 CEST 2012   Parsing F002981.dat.
Mon Oct 15 13:03:36 CEST 2012   An error occured while loading the identification 
files:
Mon Oct 15 13:03:36 CEST 2012   For input string: "M"

Mon Oct 15 13:03:36 CEST 2012   Importing Data Canceled!

Log say: 

Mon Oct 15 13:38:46 CEST 2012: PeptideShaker version 0.18.3.

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_07
os.name: Windows XP
memory: 26.1/129.8
processors available: 2
useCommandThread: false
No Decoy section found!!
java.lang.NumberFormatException: For input string: "M"
    at java.lang.NumberFormatException.forInputString(Unknown Source)
    at java.lang.Integer.parseInt(Unknown Source)
    at java.lang.Integer.valueOf(Unknown Source)
    at com.compomics.mascotdatfile.util.io.MascotIdfileReader.getAllSpectrumMatches(MascotIdfileReader.java:172)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:714)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:605)
    at javax.swing.SwingWorker$1.call(Unknown Source)
    at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at javax.swing.SwingWorker.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)

Do you have any helpful idea or suggestion?



> 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 [email protected] on 15 Oct 2012 at 11:46

Loading local PDB files

Can local PBD files be used in peptideshaker?

Original issue reported on code.google.com by [email protected] on 1 Mar 2012 at 8:13

Incompatibility with MSDA (https://msda.u-strasbg.fr/index.php)

What steps will reproduce the problem?
1. identification
2.
3.

What is the expected output? What do you see instead?

Wed Sep 28 11:38:15 CEST 2011        Importing sequences from SWISSPROT.fasta.
Wed Sep 28 11:39:04 CEST 2011        FASTA file import completed.
Wed Sep 28 11:39:04 CEST 2011        Reading identification files.
Wed Sep 28 11:39:04 CEST 2011        Reading file: 163.omx
Wed Sep 28 11:39:20 CEST 2011        No identifications retained.
Wed Sep 28 11:39:21 CEST 2011        Your peptides have been shaken!

What version of the product are you using? On what operating system?
peptideShaker 0.9.3

Please provide any additional information below.

Original issue reported on code.google.com by [email protected] on 28 Sep 2011 at 9:57

Peptideshaker eorror when importing fasta database file

> What steps will reproduce the problem?
When building new project, importing fasta database file failed.

> What is the expected output? What do you see instead?
Peptideshaker canceled protein sequences importing.

> What version of the product are you using? On what operating system?
PeptideShaker 0.26, windows 7 64bit.

> Please provide any additional information below.
log file information:
Jmol Version: 12.0.43  2011-05-03 14:21
java.vendor: Oracle Corporation
java.version: 1.7.0_40
os.name: Windows 7
memory: 31.3/129.8
processors available: 8
useCommandThread: false
Reindexing: Uniprot_MOUSE_iRT_20130626_concatenated_target_decoy.fasta. 
(Reason: com.compomics.util.experiment.identification.FastaIndex; local class 
incompatible: stream classdesc serialVersionUID = -5858706212745992648, local 
class serialVersionUID = 1089704887553927736)
Reindexing: Uniprot_MOUSE_iRT_20130626_concatenated_target_decoy.fasta.
An error occured while loading 
C:\SearchGUI-1.14.4\resources\database\Uniprot_MOUSE_iRT_20130626_concatenated_t
arget_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:266)
    at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.indexProteinsSingleThread(ProteinTree.java:612)
    at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.loadTags(ProteinTree.java:534)
    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:1188)
    at com.compomics.util.experiment.identification.SequenceFactory.getDefaultProteinTree(SequenceFactory.java:1155)
    at eu.isas.peptideshaker.fileimport.FileImporter.importSequences(FileImporter.java:195)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:399)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:388)
    at javax.swing.SwingWorker$1.call(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at javax.swing.SwingWorker.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)

> 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).

Original issue reported on code.google.com by [email protected] on 6 Mar 2014 at 2:17

data loading cancelled;need advise.

> What steps will reproduce the problem?


> What is the expected output? What do you see instead?


> What version of the product are you using? On what operating system?


> Please provide any additional information 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).

Original issue reported on code.google.com by [email protected] on 5 Mar 2014 at 6:39

Can't proceed from New project dialog

Hey guys, nice project... just wanted to test it, but I was so lucky to find a 
bug. :P

> What steps will reproduce the problem?
Starting a new project and selecting the provided test files (either xml or 
omx) for the Identification Files selection.

> What is the expected output? What do you see instead?
It should work that the color from identification files label turns black and 
the button for Create should be enabled to proceed. But it doesn't work and  so 
I can't see anything "live". 

> What version of the product are you using? On what operating system?
Peptideshaker ver. 0.15 on Win XP 32-bit. 

> Please provide any additional information below.
No further comments... the screenshots look promising by the way!

> 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 [email protected] on 27 Mar 2012 at 7:50

Peptideshaker out of memory

> What steps will reproduce the problem?
When importing 66 searching results from 22 samples

> What is the expected output? What do you see instead?
when importing progress is 86%, peptideshaker crashed.

> What version of the product are you using? On what operating system?
peptideshaker 0.26.1 windows 7 64bit

> Please provide any additional information below.
I have set the 16000 MB memory for peptideshaker, it still crashed. So I want 
to set importing filter to reduce memory consumption, do not know how much 
E-value I should used in OMSSA, Xtandem and Mascot.

> 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).

Original issue reported on code.google.com by [email protected] on 9 Mar 2014 at 11:07

Can't find a protein in the fasta file (but it is present) and cancels the import from a Mascot search.

> What steps will reproduce the problem?
Importing a .dat file

> What is the expected output? What do you see instead?
nothing

> What version of the product are you using? On what operating system?
latest version. Installed on Windows 2003 server

> Please provide any additional information below.
I had this problem over and over so I decided to start fresh. I made a new 
FASTA file from Uniprot. I launched SearchGUI to search my mgf file with OMSSA 
and xTandem. It made a decoy FASTA file for the search. I then used that FASTA 
file to search the same mgf file with MASCOT. I load that DAT file into 
PeptideShaker and I get an error that it can't find a protein. I open the FASTA 
file with Wordpad and the protein is clearly there and appears to be formatted 
correctly. This has happened more than 6 times and each time it has been a 
different protein it couldn't locate. 

The log file says that there is "No Decoy section found" when I know that 
SearchGUI put in reversed sequences. I am not including the entire log file 
because I had several crashes last week with an out of memory error. It 
wouldn't use more than 1 Gb, then I found I how to allocate memory with a 64 
bit system. I didn't think those were relevant. 

I have successfully imported tandem and omssa searches. I have had some 
problems, but none that I have found to be reproducible yet. 


> 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).

Sun Feb 17 00:16:31 EST 2013: PeptideShaker version 0.19.0.

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_13
os.name: Windows 2003
memory: 59.1/257.3
processors available: 8
useCommandThread: false
No Decoy section found!!
java.lang.IllegalArgumentException: Protein not found: sp|P46013-2|KI67_HUMAN.
    at com.compomics.util.experiment.identification.SequenceFactory.getHeader(SequenceFactory.java:206)
    at eu.isas.peptideshaker.PeptideShaker.newDescriptionBetter(PeptideShaker.java:2570)
    at eu.isas.peptideshaker.PeptideShaker.cleanProteinGroups(PeptideShaker.java:2364)
    at eu.isas.peptideshaker.PeptideShaker.processIdentifications(PeptideShaker.java:338)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:550)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:452)
    at javax.swing.SwingWorker$1.call(Unknown Source)
    at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at javax.swing.SwingWorker.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
No Decoy section found!!
java.lang.IllegalArgumentException: Protein not found: sp|Q6DN12-2|MCTP2_HUMAN.
    at com.compomics.util.experiment.identification.SequenceFactory.getHeader(SequenceFactory.java:206)
    at eu.isas.peptideshaker.PeptideShaker.newDescriptionBetter(PeptideShaker.java:2570)
    at eu.isas.peptideshaker.PeptideShaker.cleanProteinGroups(PeptideShaker.java:2364)
    at eu.isas.peptideshaker.PeptideShaker.processIdentifications(PeptideShaker.java:338)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:550)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:452)
    at javax.swing.SwingWorker$1.call(Unknown Source)
    at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at javax.swing.SwingWorker.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
No Decoy section found!!
java.lang.IllegalArgumentException: Protein not found: tr|B9PYT3|B9PYT3_TOXGO.
    at com.compomics.util.experiment.identification.SequenceFactory.getHeader(SequenceFactory.java:206)
    at eu.isas.peptideshaker.PeptideShaker.newDescriptionBetter(PeptideShaker.java:2570)
    at eu.isas.peptideshaker.PeptideShaker.cleanProteinGroups(PeptideShaker.java:2364)
    at eu.isas.peptideshaker.PeptideShaker.processIdentifications(PeptideShaker.java:338)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:550)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:452)
    at javax.swing.SwingWorker$1.call(Unknown Source)
    at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at javax.swing.SwingWorker.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
No Decoy section found!!
java.lang.IllegalArgumentException: Protein not found: tr|B9PT45|B9PT45_TOXGO.
    at com.compomics.util.experiment.identification.SequenceFactory.getHeader(SequenceFactory.java:206)
    at eu.isas.peptideshaker.PeptideShaker.newDescriptionBetter(PeptideShaker.java:2570)
    at eu.isas.peptideshaker.PeptideShaker.cleanProteinGroups(PeptideShaker.java:2364)
    at eu.isas.peptideshaker.PeptideShaker.processIdentifications(PeptideShaker.java:338)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:550)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:452)
    at javax.swing.SwingWorker$1.call(Unknown Source)
    at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at javax.swing.SwingWorker.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
No Decoy section found!!
java.lang.IllegalArgumentException: Protein not found: sw|Q86UA1-2|PRP39_HUMAN.
    at com.compomics.util.experiment.identification.SequenceFactory.getHeader(SequenceFactory.java:206)
    at eu.isas.peptideshaker.PeptideShaker.newDescriptionBetter(PeptideShaker.java:2570)
    at eu.isas.peptideshaker.PeptideShaker.cleanProteinGroups(PeptideShaker.java:2364)
    at eu.isas.peptideshaker.PeptideShaker.processIdentifications(PeptideShaker.java:338)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:550)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:452)
    at javax.swing.SwingWorker$1.call(Unknown Source)
    at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at javax.swing.SwingWorker.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)


Mon Feb 18 12:04:02 EST 2013: PeptideShaker version 0.19.0.

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_13
os.name: Windows 2003
memory: 57.8/257.3
processors available: 8
useCommandThread: false
No Decoy section found!!
java.lang.IllegalArgumentException: Protein not found: tr|H0YHH0|H0YHH0_HUMAN.
    at com.compomics.util.experiment.identification.SequenceFactory.getHeader(SequenceFactory.java:206)
    at eu.isas.peptideshaker.PeptideShaker.newDescriptionBetter(PeptideShaker.java:2570)
    at eu.isas.peptideshaker.PeptideShaker.cleanProteinGroups(PeptideShaker.java:2364)
    at eu.isas.peptideshaker.PeptideShaker.processIdentifications(PeptideShaker.java:338)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:550)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:452)
    at javax.swing.SwingWorker$1.call(Unknown Source)
    at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at javax.swing.SwingWorker.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)

Original issue reported on code.google.com by [email protected] on 18 Feb 2013 at 5:41

Peptide shaker is not accepting my custom database

> What steps will reproduce the problem?
1.Searchgui seems to accepts my database file 

2.peptide shaker seems not to like my database file (see attached)


> What is the expected output? What do you see instead?
please see attached for details

> What version of the product are you using? On what operating system?

v0.19.0
> Please provide any additional information below.
I have attached the error report i am getting.
I suspect that my db is not in the format acceptable by peptide shaker. If so, 
how do I solve the problem? Could it be because my database headings are 
non-standard? Is there any program in place that can automatically make it 
acceptable for PeptideShaker?
Warm regards,
Ryman

> 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 [email protected] on 20 Feb 2013 at 12:59

How to include "protein description" in a customized peptidesummary export?

> What steps will reproduce the problem?
Export a customized peptidesummary result.

> What is the expected output? What do you see instead?
I want to include "protein description" in the customized peptidesummary export.

> What version of the product are you using? On what operating system?
V0.26.1 windows 7 64bit

> Please provide any additional information below.
I noticed that there is "protein description" can be exported in default 
peptidesummary export, but I can not find this attribute in peptidesummary 
section in the custom tab.

> 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).

Original issue reported on code.google.com by [email protected] on 20 Mar 2014 at 1:22

Error with Validating Results

> 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 [email protected] on 26 Feb 2014 at 12:50

Export Identification Features

> What steps will reproduce the problem?
Not too sure if this is a issue or me missing something.

My FASTA file contains contains decoy sequences which were added by the 
SearchGUI software. I do my search and open the results in Peptideshaker. I 
then export the identification features via peptides tab, with the following 
criteria selected:

- Protein Accession
- Protein Description
- Peptide Sequence
- Modification Status
- Precursor Charges 

I then select export. Here is where I think there is an issue. In my exported 
results it contains Reverse matches. But in the peptide shaker GUI (under 
protein window in description) there are not any hits with the reverse 
sequence. I this an issue or a setting I need to select?


> What is the expected output? What do you see instead?
No reversed sequences in my exported output. 

> What version of the product are you using? On what operating system?


> Please provide any additional information 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).

Original issue reported on code.google.com by [email protected] on 27 Feb 2014 at 4:40

Error when opening project

> What steps will reproduce the problem?
I used SearchGUI 1.16.3 to generate the .xml files required for the protein 
shaker search, which was successful. When I opened the peptide shaker to open a 
project, upon opening the project and error occured, instructing me to raise it 
as an issue. 

> What is the expected output? What do you see instead?
I have not used peptide shaker before and so I do not know what to expect. 
Other than a list of modified peptides.

> What version of the product are you using? On what operating system?
I am using Peptide Shaker 0.27.4 on Windows 8

> Please provide any additional information 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).

The error from the log is too long to paste in full so I have pasted the frst 
and last sections with an explanation as to what is missing:

Thu Apr 10 09:31:36 BST 2014: PeptideShaker version 0.27.4.
Memory given to the Java virtual machine: 1037959168.
Total amount of memory in the Java virtual machine: 129761280.
Free memory: 114550736.
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: Windows 8
memory: 32.9/129.8
processors available: 4
useCommandThread: false
Exception in thread "AWT-EventQueue-0" 
java.lang.ArrayIndexOutOfBoundsException: 8 >= 7
    at java.util.Vector.elementAt(Unknown Source)
    at javax.swing.table.DefaultTableColumnModel.getColumn(Unknown Source)
    at javax.swing.plaf.basic.BasicTableHeaderUI.paint(Unknown Source)
    at javax.swing.plaf.synth.SynthTableHeaderUI.paint(Unknown Source)
    at javax.swing.plaf.synth.SynthTableHeaderUI.update(Unknown Source)
    at javax.swing.JComponent.paintComponent(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintToOffscreen(Unknown Source)
    at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(Unknown Source)
    at javax.swing.RepaintManager$PaintManager.paint(Unknown Source)
    at javax.swing.RepaintManager.paint(Unknown Source)
    at javax.swing.JComponent._paintImmediately(Unknown Source)
    at javax.swing.JComponent.paintImmediately(Unknown Source)
    at javax.swing.RepaintManager$3.run(Unknown Source)
    at javax.swing.RepaintManager$3.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
    at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source)
    at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source)
    at javax.swing.RepaintManager.prePaintDirtyRegions(Unknown Source)
    at javax.swing.RepaintManager.access$1100(Unknown Source)
    at javax.swing.RepaintManager$ProcessingRunnable.run(Unknown Source)
    at java.awt.event.InvocationEvent.dispatch(Unknown Source)
    at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
    at java.awt.EventQueue.access$200(Unknown Source)
    at java.awt.EventQueue$3.run(Unknown Source)
    at java.awt.EventQueue$3.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
    at java.awt.EventQueue.dispatchEvent(Unknown Source)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    at java.awt.WaitDispatchSupport$2.run(Unknown Source)
    at java.awt.event.InvocationEvent.dispatch(Unknown Source)
    at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
    at java.awt.EventQueue.access$200(Unknown Source)
    at java.awt.EventQueue$3.run(Unknown Source)
    at java.awt.EventQueue$3.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
    at java.awt.EventQueue.dispatchEvent(Unknown Source)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    at java.awt.EventDispatchThread.run(Unknown Source)
No protein found:

There was a list a proteins and no protein found repeated a number of times. 

It finished with:
java.lang.NullPointerException
    at eu.isas.peptideshaker.utils.IdentificationFeaturesGenerator.estimateSequenceCoverage(IdentificationFeaturesGenerator.java:344)
    at eu.isas.peptideshaker.utils.IdentificationFeaturesGenerator.getSequenceCoverage(IdentificationFeaturesGenerator.java:223)
    at eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel.loadDataForRows(ProteinTableModel.java:477)
    at com.compomics.util.gui.tablemodels.SelfUpdatingTableModel$LoadingRunnable.run(SelfUpdatingTableModel.java:485)
    at java.lang.Thread.run(Unknown Source)

Original issue reported on code.google.com by [email protected] on 10 Apr 2014 at 8:49

Importing Mascot.dat results

What steps will reproduce the problem?
1. Loading a Mascot.Dat file into peptide shaker
2.
3.

What is the expected output? What do you see instead?
Expect identifications from the Mascot.dat file to be carried into peptide 
shaker but none are retained.

What version of the product are you using? On what operating system?
PeptideShaker 0.9.3 with Windows 32 bit OS

Please provide any additional information below.

I have recently installed peptide shaker and I can get this to work
well with X!Tandem and OMSSA results generated in SearchGUI, however I
am having issues with importing Mascot results.  Whenever I add a
Mascot.dat file no identifications are carried into peptide shaker.
Do you have any helpful ideas or suggestions?

Many thanks

Original issue reported on code.google.com by aad100%[email protected] on 3 Oct 2011 at 2:23

a bug in custom output

> What steps will reproduce the problem?
When output a custom peptidesummary

> What is the expected output? What do you see instead?
In the end of the first line, there is no tab.
In the end of the reset lines, there have a additional tab.

> What version of the product are you using? On what operating system?

Version 0.27.3 windows 64 bit
> Please provide any additional information 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).

Original issue reported on code.google.com by [email protected] on 14 Apr 2014 at 12:51

PeptideShaker does not start

> What steps will reproduce the problem?
Double-click on PeptideShaker.jar

> What is the expected output? What do you see instead?
Start PeptideShaker

> What version of the product are you using? On what operating system?
14.5 or 14.6 - both do not work

> Please provide any additional information below.
That's what I get in the error log file:

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  EXCEPTION_ACCESS_VIOLATION (0xc0000005) at pc=0x6d0ae53d, pid=3264, tid=2112
#
# JRE version: 6.0_31-b05
# Java VM: Java HotSpot(TM) Client VM (20.6-b01 mixed mode windows-x86 )
# Problematic frame:
# C  [awt.dll+0xae53d]
#
# If you would like to submit a bug report, please visit:
#   http://java.sun.com/webapps/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#

---------------  T H R E A D  ---------------

Current thread (0x66d23400):  JavaThread "AWT-Windows" daemon 
[_thread_in_native, id=2112, stack(0x66f40000,0x66f90000)]

siginfo: ExceptionCode=0xc0000005, writing address 0xe23bf4ac

Registers:
EAX=0xe23bf4ac, EBX=0x0000001b, ECX=0x00000020, EDX=0x66e10ce0
ESP=0x66f8f784, EBP=0x00000080, ESI=0x66e10ce0, EDI=0xe23bf4ac
EIP=0x6d0ae53d, EFLAGS=0x00010202

Top of Stack: (sp=0x66f8f784)
0x66f8f784:   66dd8718 00000001 00000020 000c55c0
0x66f8f794:   00148cc0 00000400 e23bf4ac 00000000
0x66f8f7a4:   00000000 00000020 0000001b 6d0b07d3
0x66f8f7b4:   00000000 66e10ce0 00000000 00000000
0x66f8f7c4:   00000000 00000080 00000020 0000001b
0x66f8f7d4:   00000080 00000004 00000000 00000000
0x66f8f7e4:   66e10ce0 0000001b 00000003 66f8f95c
0x66f8f7f4:   698199e8 437f8000 6d0b24f2 6d0b3d2f 

Instructions: (pc=0x6d0ae53d)
0x6d0ae51d:   18 8d 0c ad 00 00 00 00 89 4c 24 44 8d a4 24 00
0x6d0ae52d:   00 00 00 8b 4c 24 44 8b e9 c1 e9 02 8b f2 8b f8
0x6d0ae53d:   f3 a5 8b cd 8b 6c 24 50 83 e1 03 f3 a4 8b 7c 24
0x6d0ae54d:   14 03 d5 03 c7 4b 85 db 7f d9 8b 44 24 58 85 c0 


Register to memory mapping:

EAX=0xe23bf4ac is an unknown value
EBX=0x0000001b is an unknown value
ECX=0x00000020 is an unknown value
EDX=0x66e10ce0 is an unknown value
ESP=0x66f8f784 is pointing into the stack for thread: 0x66d23400
EBP=0x00000080 is an unknown value
ESI=0x66e10ce0 is an unknown value
EDI=0xe23bf4ac is an unknown value


Stack: [0x66f40000,0x66f90000],  sp=0x66f8f784,  free space=317k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
C  [awt.dll+0xae53d]  D3DContext::UploadTileToTexture+0x42d

[error occurred during error reporting (printing native stack), id 0xc0000005]

Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
j  sun.awt.windows.WToolkit.eventLoop()V+0
j  sun.awt.windows.WToolkit.run()V+52
j  java.lang.Thread.run()V+11
v  ~StubRoutines::call_stub

---------------  P R O C E S S  ---------------

Java Threads: ( => current thread )
  0x69814800 JavaThread "D3D Screen Updater" daemon [_thread_blocked, id=3988, stack(0x67510000,0x67560000)]
  0x66e30400 JavaThread "AWT-EventQueue-0" [_thread_in_native, id=816, stack(0x67420000,0x67470000)]
=>0x66d23400 JavaThread "AWT-Windows" daemon [_thread_in_native, id=2112, 
stack(0x66f40000,0x66f90000)]
  0x66db4400 JavaThread "AWT-Shutdown" [_thread_blocked, id=1716, stack(0x66ef0000,0x66f40000)]
  0x66dc4400 JavaThread "Java2D Disposer" daemon [_thread_blocked, id=1972, stack(0x66ea0000,0x66ef0000)]
  0x66971000 JavaThread "Low Memory Detector" daemon [_thread_blocked, id=1940, stack(0x66bc0000,0x66c10000)]
  0x6696e800 JavaThread "C1 CompilerThread0" daemon [_thread_blocked, id=2516, stack(0x66b70000,0x66bc0000)]
  0x66969c00 JavaThread "Attach Listener" daemon [_thread_blocked, id=2220, stack(0x66b20000,0x66b70000)]
  0x66968400 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=2140, stack(0x66ad0000,0x66b20000)]
  0x6695a800 JavaThread "Finalizer" daemon [_thread_blocked, id=2692, stack(0x66a80000,0x66ad0000)]
  0x66955c00 JavaThread "Reference Handler" daemon [_thread_blocked, id=1856, stack(0x66a30000,0x66a80000)]
  0x002b6c00 JavaThread "main" [_thread_blocked, id=1132, stack(0x008c0000,0x00910000)]

Other Threads:
  0x66952000 VMThread [stack: 0x669e0000,0x66a30000] [id=2488]
  0x6697c000 WatcherThread [stack: 0x66c10000,0x66c60000] [id=1684]

VM state:not at safepoint (normal execution)

VM Mutex/Monitor currently owned by a thread: None

Heap
 def new generation   total 39296K, used 9362K [0x02990000, 0x05430000, 0x21d90000)
  eden space 34944K,  26% used [0x02990000, 0x032b4a90, 0x04bb0000)
  from space 4352K,   0% used [0x04bb0000, 0x04bb0000, 0x04ff0000)
  to   space 4352K,   0% used [0x04ff0000, 0x04ff0000, 0x05430000)
 tenured generation   total 87424K, used 0K [0x21d90000, 0x272f0000, 0x60590000)
   the space 87424K,   0% used [0x21d90000, 0x21d90000, 0x21d90200, 0x272f0000)
 compacting perm gen  total 12288K, used 9889K [0x60590000, 0x61190000, 0x64590000)
   the space 12288K,  80% used [0x60590000, 0x60f38790, 0x60f38800, 0x61190000)
No shared spaces configured.

Code Cache  [0x00910000, 0x009c8000, 0x02910000)
 total_blobs=389 nmethods=155 adapters=170 free_code_cache=32810880 largest_free_block=0

Dynamic libraries:
0x00400000 - 0x00425000     C:\Program Files\Java\jre6\bin\java.exe
0x7c900000 - 0x7c9b2000     C:\WINDOWS\system32\ntdll.dll
0x7c800000 - 0x7c8f6000     C:\WINDOWS\system32\kernel32.dll
0x77dd0000 - 0x77e6b000     C:\WINDOWS\system32\ADVAPI32.dll
0x77e70000 - 0x77f03000     C:\WINDOWS\system32\RPCRT4.dll
0x77fe0000 - 0x77ff1000     C:\WINDOWS\system32\Secur32.dll
0x7c340000 - 0x7c396000     C:\Program Files\Java\jre6\bin\msvcr71.dll
0x6d7f0000 - 0x6da9f000     C:\Program Files\Java\jre6\bin\client\jvm.dll
0x7e410000 - 0x7e4a1000     C:\WINDOWS\system32\USER32.dll
0x77f10000 - 0x77f59000     C:\WINDOWS\system32\GDI32.dll
0x76b40000 - 0x76b6d000     C:\WINDOWS\system32\WINMM.dll
0x76390000 - 0x763ad000     C:\WINDOWS\system32\IMM32.DLL
0x6d7a0000 - 0x6d7ac000     C:\Program Files\Java\jre6\bin\verify.dll
0x6d320000 - 0x6d33f000     C:\Program Files\Java\jre6\bin\java.dll
0x6d7e0000 - 0x6d7ef000     C:\Program Files\Java\jre6\bin\zip.dll
0x6d000000 - 0x6d14c000     C:\Program Files\Java\jre6\bin\awt.dll
0x73000000 - 0x73026000     C:\WINDOWS\system32\WINSPOOL.DRV
0x77c10000 - 0x77c68000     C:\WINDOWS\system32\msvcrt.dll
0x774e0000 - 0x7761e000     C:\WINDOWS\system32\ole32.dll
0x773d0000 - 0x774d3000 
    C:\WINDOWS\WinSxS\x86_Microsoft.Windows.Common-Controls_6595b64144ccf1df_6.0.26
00.6028_x-ww_61e65202\COMCTL32.dll
0x77f60000 - 0x77fd6000     C:\WINDOWS\system32\SHLWAPI.dll
0x74720000 - 0x7476c000     C:\WINDOWS\system32\MSCTF.dll
0x755c0000 - 0x755ee000     C:\WINDOWS\system32\msctfime.ime
0x7c9c0000 - 0x7d1d7000     C:\WINDOWS\system32\shell32.dll
0x6d230000 - 0x6d27f000     C:\Program Files\Java\jre6\bin\fontmanager.dll
0x66fd0000 - 0x67176000     C:\WINDOWS\system32\d3d9.dll
0x67180000 - 0x67186000     C:\WINDOWS\system32\d3d8thk.dll
0x77c00000 - 0x77c08000     C:\WINDOWS\system32\VERSION.dll
0x6d600000 - 0x6d613000     C:\Program Files\Java\jre6\bin\net.dll
0x71ab0000 - 0x71ac7000     C:\WINDOWS\system32\WS2_32.dll
0x71aa0000 - 0x71aa8000     C:\WINDOWS\system32\WS2HELP.dll
0x71a50000 - 0x71a8f000     C:\WINDOWS\System32\mswsock.dll
0x76f20000 - 0x76f47000     C:\WINDOWS\system32\DNSAPI.dll
0x76d60000 - 0x76d79000     C:\WINDOWS\system32\iphlpapi.dll
0x76fb0000 - 0x76fb8000     C:\WINDOWS\System32\winrnr.dll
0x76f60000 - 0x76f8c000     C:\WINDOWS\system32\WLDAP32.dll
0x67240000 - 0x67249000     C:\WINDOWS\system32\netware\NWWS2NDS.DLL
0x67250000 - 0x67298000     C:\WINDOWS\system32\NETWIN32.DLL
0x672a0000 - 0x672b5000     C:\WINDOWS\system32\CLNWIN32.DLL
0x672c0000 - 0x672e0000     C:\WINDOWS\system32\LOCWIN32.DLL
0x672e0000 - 0x6730b000     C:\WINDOWS\system32\NCPWIN32.dll
0x71ad0000 - 0x71ad9000     C:\WINDOWS\system32\WSOCK32.dll
0x67350000 - 0x6735c000     C:\WINDOWS\system32\netware\NWWS2SLP.DLL
0x67360000 - 0x67367000     C:\WINDOWS\system32\NWSRVLOC.dll
0x76fc0000 - 0x76fc6000     C:\WINDOWS\system32\rasadhlp.dll
0x673c0000 - 0x67418000     C:\WINDOWS\system32\hnetcfg.dll
0x71a90000 - 0x71a98000     C:\WINDOWS\System32\wshtcpip.dll
0x6d620000 - 0x6d629000     C:\Program Files\Java\jre6\bin\nio.dll
0x77120000 - 0x771ab000     C:\WINDOWS\system32\OLEAUT32.DLL
0x6d1a0000 - 0x6d1c3000     C:\Program Files\Java\jre6\bin\dcpr.dll
0x76bf0000 - 0x76bfb000     C:\WINDOWS\system32\PSAPI.DLL
0x67560000 - 0x67601000     C:\WINDOWS\system32\dbghelp.dll

VM Arguments:
jvm_args: -Xms128M -Xmx1500M 
java_command: eu.isas.peptideshaker.gui.PeptideShakerGUI
Launcher Type: SUN_STANDARD

Environment Variables:
CLASSPATH=C:\Program Files\HostExplorer.nt\hcljrcsv.jar;C:\Program 
Files\HostExplorer.nt\;
PATH=C:\Xcalibur\system\programs;C:\Program Files\Thermo\Foundation;C:\Program 
Files\Agilent\MassHunter\Workstation\Bin\;C:\Program 
Files\Agilent\MassHunter\Workstation\Quant\Bin\;C:\Program 
Files\Agilent\MassHunter\Workstation\Qual\Bin\;C:\Program 
Files\Agilent\MassHunter\Workstation\Acq\Bin\release\;C:\Perl\bin\;C:\oracle\ora
92\bin;C:\Program Files\Oracle\jre\1.3.1\bin;C:\Program 
Files\Oracle\jre\1.1.8\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wb
em;C:\Program Files\Common Files\Adaptec 
Shared\System;C:\WINDOWS\system32\nls;C:\WINDOWS\system32\nls\ENGLISH;C:\Program
 Files\ATI Technologies\ATI Control Panel;C:\Program Files\Common Files\Bruker 
Daltonik\NTDS\Bin;C:\cygwin\usr\X11R6\bin;C:\cygwin\bin;Y:.;Z:.
USERNAME=poliakov
OS=Windows_NT
PROCESSOR_IDENTIFIER=x86 Family 15 Model 4 Stepping 10, GenuineIntel



---------------  S Y S T E M  ---------------

OS: Windows XP Build 2600 Service Pack 3

CPU:total 2 (1 cores per cpu, 2 threads per core) family 15 model 4 stepping 
10, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ht

Memory: 4k page, physical 3668036k(2921304k free), swap 5552508k(4845412k free)

vm_info: Java HotSpot(TM) Client VM (20.6-b01) for windows-x86 JRE 
(1.6.0_31-b05), built on Feb  3 2012 18:44:09 by "java_re" with MS VC++ 7.1 
(VS2003)

time: Wed Feb 29 11:31:56 2012
elapsed time: 1 seconds



> 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 [email protected] on 29 Feb 2012 at 4:37

Error loading spectrum file

> What steps will reproduce the problem?

Trying to load a fasta file (containing only 2 proprietary proteins - no 
database), X!Tandem output, and an mgf file (of only the proprietary proteins).

> What is the expected output? What do you see instead?

I expected to see my X!Tandem search results. Instead I get an error that 
changes each time I attempt to load the same exact files?

Tue Nov 20 18:35:07 EST 2012        Import process for test4 (Sample: test4, 
Replicate: 0)
Tue Nov 20 18:35:07 EST 2012        Establishing database connection.
Tue Nov 20 18:35:07 EST 2012        Importing sequences from avastin.fasta.
Tue Nov 20 18:35:09 EST 2012        Creating peptide to protein map.
Tue Nov 20 18:35:09 EST 2012        FASTA file import completed.
Tue Nov 20 18:35:09 EST 2012        Reading identification files.
Tue Nov 20 18:35:09 EST 2012        Parsing 
new_output.2012_11_20_18_32_00.t.xml.
Tue Nov 20 18:35:09 EST 2012        Spectrum test.2129.2129.2 File:"test.wiff", 
NativeID:"sample=2 period=1 cycle=1325 experiment=3" RTINSECONDS=2161.974 
number 246 not found in file test.mgf.
Tue Nov 20 18:35:09 EST 2012        Importing Data Canceled!
Tue Nov 20 18:35:09 EST 2012        No identifications retained.
Tue Nov 20 18:35:09 EST 2012        Importing Data Canceled!

When I started to look at the mgf file for something obvious, I ended up trying 
to reload the same files multiple times. To my surprise, the error changes each 
time, for the same files! What would cause the same input to produce different 
output?

Tue Nov 20 18:32:26 EST 2012        Spectrum 'test.1899.1899.2 
File:"test.wiff", NativeID:"sample=2 period=1 cycle=1239 experiment=4" 
RTINSECONDS=1932.501' in mgf file 'test.mgf' not found!

Tue Nov 20 18:33:28 EST 2012        Spectrum test.1985.1985.2 File:"test.wiff", 
NativeID:"sample=2 period=1 cycle=1275 experiment=3" RTINSECONDS=2016.637 
number 201 not found in file test.mgf.

Tue Nov 20 18:34:14 EST 2012        Spectrum test.3317.3317.3 File:"test.wiff", 
NativeID:"sample=2 period=1 cycle=1748 experiment=3" RTINSECONDS=3360.343 
number 589 not found in file test.mgf.


> What version of the product are you using? On what operating system?
Latest copy, fresh download, Windows XP SP3

> Please provide any additional information below.

Browsing the X!Tandem results by hand shows that it did find expected peptides 
and fragments.

I used MSConvert to convert my *wiff file to an *mgf file. X!Tandem had no 
problems reading it, and I can't see anything obviously wrong with the file 
itself.

Previously, I was able to load files from a different experiment on the same 
proteins, using the exact same process.

Original issue reported on code.google.com by [email protected] on 20 Nov 2012 at 11:52

OMSSA results import prpoblem

Dear all,
I experienced a problem with OMSSA data import into Peptide-shaker.
I used an home-made DB that work properly with xtandem. The search with OMSSA 
works fine but Peptide-shaker is unable to import the data.

Here you have the Peptide-shaker.log:

Thu Nov 21 14:22:06 CET 2013: PeptideShaker version 0.22.6.

Total amount of memory in the Java virtual machine: 129761280.

Java version: 1.7.0_25.

java.lang.IllegalArgumentException: Protein not found: BL_ORD_ID:158089.
    at com.compomics.util.experiment.identification.SequenceFactory.getProtein(SequenceFactory.java:180)
    at com.compomics.util.experiment.identification.SequenceFactory.getProtein(SequenceFactory.java:178)
    at com.compomics.util.experiment.identification.SequenceFactory.getProtein(SequenceFactory.java:140)
    at eu.isas.peptideshaker.PeptideShaker.cleanProteinGroups(PeptideShaker.java:2389)
    at eu.isas.peptideshaker.PeptideShaker.processIdentifications(PeptideShaker.java:339)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:574)
    at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:153)
    at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:217)
    at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:363)
    at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:124)
    at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:635)
Free memory: 67857832

I'm using OsX.

Thanks in advance for the help.
Marco

Original issue reported on code.google.com by [email protected] on 21 Nov 2013 at 2:10

Interfering protein and PI status and number of PTMs

Hi.

I use peptide shaker to (in addition to "normal" proteomics) to also search my 
standard synthetic peptides and other known small peptides not necessary from 
proteins. I do this by adding them as new proteins in a normal FASTA file. In 
previous versions this worked out very nicely, no problem at all. However, in 
you latest version (0.21.0) this is no longer possible as I during import of 
data to Peptide Shaker I get a error message stating "Resolving protein 
inference status, inferring peptide and protein PI status" - "Importing data 
canceled". I guess that this is somehow due to me finding the whole "protein" 
in one peptide.  Do you have any solution to this?

regarding another issue: can shaker and/or search gui only handle up to 3 PTMs 
pr peptide. The last version I tried this on was 18.something, due to the error 
of importing data where the peptide and the protein is the same...

Please contact me off line if more details are required

best,
Terkel







> What steps will reproduce the problem?


> What is the expected output? What do you see instead?


> What version of the product are you using? On what operating system?


> Please provide any additional information 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).

Original issue reported on code.google.com by [email protected] on 4 Jun 2013 at 11:51

Attachments:

Shaker.png

Parsing protein descriptions

What steps will reproduce the problem?

1. Running of any omx etc.. other than the test files provided by peptide 
shaker which function correctly. Omx files are created using SearchGUI and the 
omx file outputted is operable in omssa-Parser's Omssa Viewer. 
2.
3.

What is the expected output? What do you see instead?

Results after completion of Data import progress. Instead error message says 
Display problem: A problem occurred while displaying results. Please send the 
log file to the developers.
Having looked in the conf file I cannot identify a peptideshaker.log file.



What version of the product are you using? On what operating system?

I'm using peptide shaker 0.9.3 run on windows 7 32bit with java version 6 
update 26 installed.

Please provide any additional information below.

The test files run fine and results are displayed. Samples i run myself through 
searchGUI using a mgf created in DataAnalysis and a FASTA downloaded from 
Uniprot does not work. 

This software looks great and would be really useful. I'm sure its a simple 
fault with what I'm doing but can't identify what.
Thank you in advance for any assistance.

Joseph Longworth 
[email protected]

Original issue reported on code.google.com by [email protected] on 4 Oct 2011 at 1:31

Database and memory issues

> What steps will reproduce the problem?
First, we donwloaded UniProtKB/SwissProt and uniProtKB/TrEMBL databases from 
UniProt download page in the decoy version. 
Then, since these database were not uploaded correctly by PeptideShaker, we 
tried to assemble a target-decoy DB using the Database Processing Tool, 
starting from the original UniProt DB versions (no decoy).

> What is the expected output? What do you see instead?
Only SwissProt DB obtained using the Database Processing Tool did work, while 
TrEMBL gave errors (see log file attached). In both cases, the original UniProt 
decoy DB files were not recognized correctly.
Moreover, when using the only functioning DB (SwissProt), an additional issue 
occurred (Out of Memory Error).
We tried to install both 32- and 64-bit versions of Java (also separately), as 
well as to extend the Java memory limit (up to 2 GB or more, as suggested) 
without success.
How can these issues be fixed?

> What version of the product are you using? On what operating system?
0.20.1 on a Windows 7 Professional 64-bit OS

> Please provide any additional information below.
The file extension of the decoy database downloaded from UniProt is .decoy, but 
this format is not recognized by PeptideShaker. We tried to modify the 
extension in .fasta either manually or using the Database Processing Tool but 
in both cases the database didn't work.

> 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).

Original issue reported on code.google.com by [email protected] on 17 May 2013 at 2:28

Attachments:

PeptideShaker.log

Plant species

> What steps will reproduce the problem?

I'm working with a database composed of sequences from multiple legumes and 
Arabidopsis thaliana.  The list of available species does not appear to contain 
any of them.
> What is the expected output? What do you see instead?


> What version of the product are you using? On what operating system?


> Please provide any additional information 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).

Original issue reported on code.google.com by [email protected] on 25 Jun 2013 at 8:40

Strange Java errors with Mascot import. Worked once, but not anymore

> What steps will reproduce the problem?
I am repeatedly trying to import a dat file. It worked once but gave very few 
IDs (less than 1/4 of what Scaffold reports). I changed the settings in PS very 
slightly because they didn't match Mascot exactly (28 vs. 25 ppm, 2 vs. 1 
missed cleavage). Now I can't get the same file to import. 

> What is the expected output? What do you see instead?
I get a series of Java errors  (see log file)

> What version of the product are you using? On what operating system?
0.19.0, Windows Server 2003, 64 bit, 14 Gb RAM

> Please provide any additional information 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\conf folder).

I am attaching the log file. There are some initial errors that were related to 
parsing the dat file. I fixed those and the new errors start later on Monday, 
Feb 18 (ignore the parsing errors early in the day).  If you just scroll 
through the file, about 1/3 of the way through, one of the errors will become 
very obvious. The errors all appear to be similar, but they aren't exactly the 
same.

Original issue reported on code.google.com by [email protected] on 19 Feb 2013 at 6:11

protein export option not working

What steps will reproduce the problem?
1. open any .omx file generated by searchgui 
2. export, protein, select all, export 
3.

What is the expected output? What do you see instead?
textfile containing details but we see text file containing only headers and no 
protein information

What version of the product are you using? On what operating system?
peptide shaker 12.2. Windows XP with service pack3

Please provide any additional information below.

Original issue reported on code.google.com by [email protected] on 29 Dec 2011 at 8:30

Failure to create Peptide Shaker project

> What steps will reproduce the problem?
trying to create a project using Omssa and XTandem searches from Progenesis 
LC-MS exported .mgf file

> What is the expected output? What do you see instead?

Finished file with protein info - get error message.

> What version of the product are you using? On what operating system?
0.22.5 on Windows 7 Enterprise 64bit OS

> Please provide any additional information below.
I have gotten the warning about having duplicate spectrum titles, but I have 
not been able to create Peptide Shaker projects even when I do rename titles so 
that they are unique. I see Java exceptions in the error log, but I am not 
savvy enough to figure out what they mean. I checked, and I do have the latest 
version of Java.

Also of potential interest to you: I have contacted Progenesis LC-MS about the 
duplicate spectrum issue, and they are trying to find a way to resolve it. They 
were also going to contact you, I think.

> 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).

Original issue reported on code.google.com by [email protected] on 1 Aug 2013 at 1:31

Attachments:

PeptideShaker.log

Memory issues

When trying to start the jar file, the program crashes with an error warning.  
By setting the memory limit below 1100M, program will start.  however, trying 
to load and x!tandem results in the progess bar being stuck at 25% and in an 
eventual crash of the software.

Does the jar require 64 bit java?  I only have the 32 bit java installed.

THe x!tandem results were from the test mgf file included with x!tandem so 
memory should not be a problem.

What version of the product are you using? On what operating system?
0.9 on windows server 2008 R2 (64 bit) with 32 GB of memory and 4 cpus (32 
cores total)

Please provide any additional information below.
trying to use your software to view the results of x!tandem searches

Original issue reported on code.google.com by [email protected] on 13 Jul 2011 at 5:50

Failure loading X!Tandem

> What steps will reproduce the problem?

Loading X!Tandem files fails. IT says it's going to skip that file, but it just 
cancels the entire importation process.

I'm using PeptideShaker 0.19.1 with SearchGUI 1.12.0. I was using 1.11.0, but I 
updated it and redid the X!tandem searches. No joy. These files are currently 
loading fine with Scaffold, but Scaffold is not as good as PeptideShaker.

> What version of the product are you using? On what operating system?
Versions noted above. They are running on Windows Server 2007, SP2 applied, 
32-bit. I can try Win7, 32-bit if required, but I've never seen a difference 
when run on the different OS.

> 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).

Tue Mar 26 07:37:09 EST 2013: PeptideShaker version 0.19.1.

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_15
os.name: Windows Server 2008
memory: 29.8/129.8
processors available: 4
useCommandThread: false
java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
    at java.lang.reflect.Constructor.newInstance(Unknown Source)
    at com.compomics.util.experiment.io.identifications.IdfileReaderFactory.getFileReader(IdfileReaderFactory.java:142)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:627)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:507)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:465)
    at javax.swing.SwingWorker$1.call(Unknown Source)
    at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at javax.swing.SwingWorker.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.OutOfMemoryError: Java heap space
    at java.util.Arrays.copyOfRange(Unknown Source)
    at java.lang.String.<init>(Unknown Source)
    at java.lang.StringBuffer.toString(Unknown Source)
    at org.apache.xerces.dom.ParentNode.getTextContent(Unknown Source)
    at de.proteinms.xtandemparser.parser.XTandemParser.parseXTandemFile(XTandemParser.java:928)
    at de.proteinms.xtandemparser.parser.XTandemParser.<init>(XTandemParser.java:82)
    at de.proteinms.xtandemparser.xtandem.XTandemFile.<init>(XTandemFile.java:89)
    at de.proteinms.xtandemparser.parser.XTandemIdfileReader.<init>(XTandemIdfileReader.java:67)
    ... 15 more
java.lang.NullPointerException
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:633)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:507)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:465)
    at javax.swing.SwingWorker$1.call(Unknown Source)
    at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at javax.swing.SwingWorker.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
java.lang.NullPointerException
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:641)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:507)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:465)
    at javax.swing.SwingWorker$1.call(Unknown Source)
    at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at javax.swing.SwingWorker.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)

Original issue reported on code.google.com by [email protected] on 25 Mar 2013 at 9:29

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