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Failure loading MASCOT and X! Tandem files #16

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
> 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 snoor...@gmail.com on 14 Aug 2012 at 12:53

GoogleCodeExporter commented 9 years ago 
Thanks for telling us about this issue. Seems to be a problem with the parsing 
of the mgf file. Could you send us the file 'MEF4_5_FT_03.mgf' so that we can 
do some testing?

Original comment by harald.b...@gmail.com on 14 Aug 2012 at 7:09

GoogleCodeExporter commented 9 years ago 
Actually, if you could upload the files from MEF4_10_FT_03_F022745.dat, 
MEF4_10_FT_03.2012_08_09_17_32_02.t.xml, MEF4_10_FT_03.mgf and 
LM_rodentia_concatenated_target_decoy.fasta we could do the tests directly on 
your data.

Original comment by harald.b...@gmail.com on 14 Aug 2012 at 7:17

GoogleCodeExporter commented 9 years ago 
Hi,

I've placed all the files (along with additional OMX, DAT, XML and MGFs) on
Dropbox <https://dl.dropbox.com/u/3533588/Not_shaking.zip>. Everything was
working perfectly and then the wheels fell off. It's quite frustrating as I
have some data I'm keen to finish analysing. The only thing that may have
changed here is a Java update, we are still using the same Mascot version
etc.

Thanks for your help,

Peter

Original comment by snoor...@gmail.com on 14 Aug 2012 at 9:38

GoogleCodeExporter commented 9 years ago 
Thanks for the files. The problem seems to be related to the parsing of the 
spectrum titles. In particular the path to the wiff file at the end.

Example mgf spectrum title:
TITLE=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]

The path we are trying to find:
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] 

Note that the second path only has one "\" in front of "cmri-as\...", while the 
first one has two, thus resulting in the spectrum not being found.

Which also explains why the parsing works fine on other files not containing 
"\\" in the spectrum titles.

A fix has been implemented and I'll release a beta version for you to test has 
soon as possible. Hopefully by the end of the week.

Original comment by harald.b...@gmail.com on 15 Aug 2012 at 1:22

GoogleCodeExporter commented 9 years ago 
Okay, glad to hear. I was wondering if some of my issues were related to
file locations, so I've been working with all the files located on my PC.
That said, I have not moved the wiff files as I didn't know these were
required once I'd generated the MGF.

Original comment by snoor...@gmail.com on 15 Aug 2012 at 2:19

GoogleCodeExporter commented 9 years ago 
The wiff files are not required once the MGFs are generated. (At least not in 
PeptideShaker.) But given that they were part of the spectrum titles we had to 
parse them to get at the spectra. We never look for the files though, so the 
actual location is not important.

And yes, it is recommended keeping all the files used in a 
SearchGUI/PeptideShaker project on the same machine. Mainly for faster 
performance. However, if a file has been moved or is not found were it was 
supposed to be located, PeptideShaker will detect this an allow you to locate 
the file(s) manually.

If you plan to move a project from one machine to another I'd recommend saving 
the project and then exporting it via Export > PeptideShaker Project. You'll 
then get a single zip file with all the required files, which can be directly 
opened (after unzipping of course) on any computer where PeptideShaker is 
installed. This feature will be much improved (and faster) in the next release 
btw.

Original comment by harald.b...@gmail.com on 15 Aug 2012 at 2:38

GoogleCodeExporter commented 9 years ago 
Sorry for the delay. PeptideShaker v0.18.0-beta is now available online: 
http://code.google.com/p/peptide-shaker/downloads/detail?name=PeptideShaker-0.18
.0-beta.zip.

Note that this is a beta release and that projects generated in this version 
will not be compatible with the the propper v0.18.0 released in the near future.

But at least you should now be able to load the data not supported in v0.17.3.

Please let us know if you experience any other issues.

Original comment by harald.b...@gmail.com on 22 Aug 2012 at 6:14

GoogleCodeExporter commented 9 years ago 
No problems, thanks for taking the time to fix the problem. It all imports
fine now, but since you have the files, you know that. There was some
general spectra display weirdness (the spectra don't load when I go to the
"Spectrum ID" tab), but I'm guessing that is a "beta release" thing. I look
forward to the new version, it looks like you've adding some interesting
stuff.

Thanks again,

Peter

Original comment by snoor...@gmail.com on 23 Aug 2012 at 4:09

GoogleCodeExporter commented 9 years ago 
Well, it is a beta release, but you should still get the spectra displayed and 
the Spectrum IDs tab should load. Could you please tell me a bit more about 
what goes wrong? And is there anyting in your error log?

Original comment by harald.b...@gmail.com on 23 Aug 2012 at 8:13

GoogleCodeExporter commented 9 years ago 
Oddly, it seems to be related to the order I do things. I "shake" the
samples and they are all fine. If I go directly to the "Spectrum IDs" tab,
before doing anything else, then I get the error "An error occurred, please
contact the developers". When this occurs, I don't see anything (literally
nothing other than the empty window outlines) on the Spectrum IDs tab page.
If I then go back to the "Overview" tab then the spectra have disappeared.

It seems critical that I go to the "Fractions" tab prior to the IDs tab. I
tried various tabs prior to the IDs tab, but they all give the same
failure. So if I go to QC, or Validation first, then IDs, I get the same
error. As long as I go to Fractions prior to IDs, it all works out fine.
Weird.

My error log is as follows;

Fri Aug 24 07:17:08 EST 2012: PeptideShaker version 0.18.0-beta.

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: 19.5/129.9
processors available: 2
useCommandThread: false
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
java.lang.NullPointerException
    at
eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel$53.run(SpectrumI
dentificationPanel.java:2515)

Peter

Original comment by snoor...@gmail.com on 23 Aug 2012 at 10:12

GoogleCodeExporter commented 9 years ago 
That is indeed a bit strange. I'm able to load your data without any problems 
though. Both in the online beta version and in my updated beta version without 
any such issues.

It could be that you have some older files causing issues. Can you verify that 
you get the same problem if you make a new folder with just the files you sent 
me via Dropbox? Perhaps some old SearchGUI or indexing files (the .cui files) 
are responsible.

Original comment by harald.b...@gmail.com on 23 Aug 2012 at 10:44

GoogleCodeExporter commented 9 years ago 
Bingo, got it in one. I deleted the *.cui files and everything behaves as
expected. I'll keep that solution in mind.

Original comment by snoor...@gmail.com on 23 Aug 2012 at 11:30

GoogleCodeExporter commented 9 years ago 
Great! Deleting the indexing files should not be required. But glad you were 
able to solve the problem. Thanks for helping us improve PeptideShaker. 

The new official version of PeptideShaker v0.18.0 should be available soon. 
Keep in mind that projects created in the beta version will not be compatible 
with the official release, as we want to make some additional minor backend 
changes. Projects from v0.17.3 will be possible to open though.

Original comment by harald.b...@gmail.com on 23 Aug 2012 at 11:46

GoogleCodeExporter commented 9 years ago 
Sorry to be a pain again, but I am seeing the same odd behaviour with
v0.18.0. To be specific, the spectra don't load if I go straight to
Spectrum IDs. I've just determined this only happens if I don't save the
project first. So if I load, save, then go to Spectrum IDs all is fine, if
I skip saving, I get the error message about contacting the developers. I
thought you should know. Deleting the "old" *.cui files does not work the
way it did with the beta version.

Whilst I'm reporting errors, the proxy fix is no longer working with the
uniprotjapi.properties file. The proxy is still correctly set (I'm just
copying this from the old versions, could that be the cause?), but when I
go to the Annotation tab, I get an error telling me the software can't
reach Uniprot.

The log file follows.

Thanks,

Peter

***log start***

Tue Sep 11 14:18:42 EST 2012: PeptideShaker version 0.18.0.

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: 11.6/129.9
processors available: 2
useCommandThread: false
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!!
java.lang.NullPointerException
    at
eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel$53.run(SpectrumI
dentificationPanel.java:2516)
org.springframework.remoting.RemoteAccessException: Could not access HTTP
invoker remote service at [
http://www.ebi.ac.uk/uniprot/remotingAPI/remotingAPI/queryService]; nested
exception is java.net.SocketException: Connection reset
    at
org.springframework.remoting.httpinvoker.HttpInvokerClientInterceptor.convertHtt
pInvokerAccessException(HttpInvokerClientInterceptor.java:212)
    at
org.springframework.remoting.httpinvoker.HttpInvokerClientInterceptor.invoke(Htt
pInvokerClientInterceptor.java:145)
    at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveM
ethodInvocation.java:172)
    at
org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.j
ava:202)
    at $Proxy0.getEntryIterator(Unknown Source)
    at
uk.ac.ebi.kraken.uuw.services.remoting.UniProtQueryServiceClientImpl.getEntryIte
rator(Unknown
Source)
    at
uk.ac.ebi.kraken.uuw.services.remoting.UniProtQueryServiceClientImpl.getEntryIte
rator(Unknown
Source)
    at
eu.isas.peptideshaker.gui.tabpanels.AnnotationPanel$20.run(AnnotationPanel.java:
1216)
Caused by: java.net.SocketException: Connection reset
    at java.net.SocketInputStream.read(Unknown Source)
    at java.io.BufferedInputStream.fill(Unknown Source)
    at java.io.BufferedInputStream.read(Unknown Source)
    at
org.apache.commons.httpclient.HttpParser.readRawLine(HttpParser.java:77)
    at
org.apache.commons.httpclient.HttpParser.readLine(HttpParser.java:105)
    at
org.apache.commons.httpclient.HttpConnection.readLine(HttpConnection.java:1115)
    at
org.apache.commons.httpclient.MultiThreadedHttpConnectionManager$HttpConnectionA
dapter.readLine(MultiThreadedHttpConnectionManager.java:1373)
    at
org.apache.commons.httpclient.HttpMethodBase.readStatusLine(HttpMethodBase.java:
1832)
    at
org.apache.commons.httpclient.HttpMethodBase.readResponse(HttpMethodBase.java:15
90)
    at
org.apache.commons.httpclient.HttpMethodBase.execute(HttpMethodBase.java:995)
    at
org.apache.commons.httpclient.HttpMethodDirector.executeWithRetry(HttpMethodDire
ctor.java:397)
    at
org.apache.commons.httpclient.HttpMethodDirector.executeMethod(HttpMethodDirecto
r.java:170)
    at
org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:396)
    at
org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:324)
    at
org.springframework.remoting.httpinvoker.CommonsHttpInvokerRequestExecutor.execu
tePostMethod(CommonsHttpInvokerRequestExecutor.java:196)
    at
org.springframework.remoting.httpinvoker.CommonsHttpInvokerRequestExecutor.doExe
cuteRequest(CommonsHttpInvokerRequestExecutor.java:130)
    at
org.springframework.remoting.httpinvoker.AbstractHttpInvokerRequestExecutor.exec
uteRequest(AbstractHttpInvokerRequestExecutor.java:136)
    at
org.springframework.remoting.httpinvoker.HttpInvokerClientInterceptor.executeReq
uest(HttpInvokerClientInterceptor.java:192)
    at
org.springframework.remoting.httpinvoker.HttpInvokerClientInterceptor.executeReq
uest(HttpInvokerClientInterceptor.java:174)
    at
org.springframework.remoting.httpinvoker.HttpInvokerClientInterceptor.invoke(Htt
pInvokerClientInterceptor.java:142)
    ... 6 more

***log end***

Original comment by snoor...@gmail.com on 11 Sep 2012 at 4:50

GoogleCodeExporter commented 9 years ago 
Keep in mind that projects created in the beta version are _not_ compatible 
with the official release of v0.18.0. So delete the .cui files and create a new 
project in the released v0.18.0. This should hopefully fix the missing spectrum 
problem.

As for the proxy settings, I'm not sure wich file you are copying? All you need 
to do is open the file resources/conf/JavaOptions.txt and add the proxy 
settings as detailed here: 
http://code.google.com/p/peptide-shaker/#Troubleshooting.

If this doesn't work please send me the contents of the file startup.log 
located in the same folder. This will show us if the proxy settings are set or 
not during startup.

And don't worry about reporting bugs. We much rather know about them than be 
left in the dark. ;)

Original comment by harald.b...@gmail.com on 11 Sep 2012 at 9:22

GoogleCodeExporter commented 9 years ago 
I know beta projects aren't compatible. I'm working with the same OMSSA,
X!Tandem and Mascot files, but I deleted the *.cui prior to loading the
data into 0.18.0. So I'm not opening an existing project, I'm making a new
one. As I said, the error doesn't occur if I save the file first.

The proxy settings, I'm copying the file "uniprotjapi.properties" that
lives in the "PeptideShaker-0.18.0\resources\conf\proxy" directory. My
understanding is that EBI needed a special file when going through a proxy
server, and this was the solution. I also have my "JavaOptions.txt" file in
the "PeptideShaker-0.18.0\resources\conf" directory with the proxy set as
required.

Startup.log follows;

Memory settings read from the user preferences: 1500
original java.home: C:\Program Files\Java\jre6\bin\
new java.home: C:\Program Files\Java\jre6\bin\

Command line: C:\Program Files\Java\jre6\bin\java
-splash:"C:\Users\phains\Apps\PeptideShaker-0.18.0\resources\conf\peptide-shaker
-splash.png"
-Xms128M  -Dhttp.proxyHost=cmri-proxy.cmri.com.au -Dhttp.proxyPort=8080
-Xmx1500M -cp
"C:\Users\phains\Apps\PeptideShaker-0.18.0\PeptideShaker-0.18.0.jar";"C:\Users\p
hains\Apps\PeptideShaker-0.18.0\resources\confproxy"
eu.isas.peptideshaker.gui.PeptideShakerGUI

Process exitValue: 0

Original comment by snoor...@gmail.com on 11 Sep 2012 at 10:04

GoogleCodeExporter commented 9 years ago 
Ok, lets take the last thing first, the proxy settings. Seems like there's a 
"\" missing in the path to the proxy settings file ("\resources\confproxy" 
should be "\resources\conf\proxy"). Easy to fix. Test v0.18.2 in the downloads 
section to see if it solves the problem.

As for the missing spectra, seems like this is unrelated to the .cui files. I 
need to look at this in more detail and get back to you with a fix. Should work 
to load the data without issues in v0.18.2 though. But I had to disable some 
new and improved PTM site determination code.

Original comment by harald.b...@gmail.com on 12 Sep 2012 at 12:52

GoogleCodeExporter commented 9 years ago 
Yep, Uniprot now works.

As always, thanks...

Original comment by snoor...@gmail.com on 12 Sep 2012 at 1:18

GoogleCodeExporter commented 9 years ago 
And I assume you're now able to load the data without having to go via the 
Spectrum IDs tab as well?

Original comment by harald.b...@gmail.com on 12 Sep 2012 at 11:13

GoogleCodeExporter commented 9 years ago 
I'm using 0.18.2 now. Oddly, I can load the individual files with no
problems. As in, I can load all OMSSA searches, or all X!Tandem searches,
or all Mascot searches. I don't need to save, I can go straight to IDs
without any issues. If, I then load those exact files, but at the same
time, I see the error when I go directly to the IDs tab.

Original comment by snoor...@gmail.com on 12 Sep 2012 at 10:11

GoogleCodeExporter commented 9 years ago 
And the error is the same as before? Can you send me the error log?

Original comment by harald.b...@gmail.com on 12 Sep 2012 at 10:20

GoogleCodeExporter commented 9 years ago 
Yes, same error, it's a bit nondescript and tells me to contact the
developers. I've attached the log file. I'm not sure where the error is, I
was doing a lot of stuff yesterday.

Peter

Original comment by snoor...@gmail.com on 13 Sep 2012 at 6:43

GoogleCodeExporter commented 9 years ago 
Seems like you forgot to attach the log file..?

Original comment by harald.b...@gmail.com on 13 Sep 2012 at 8:31

GoogleCodeExporter commented 9 years ago 
Mmm, I did attach it. I'll send it again tomorrow.

On 13/09/2012, at 6:31 PM, "peptide-shaker@googlecode.com"
<peptide-shaker@googlecode.com> wrote:

Original comment by snoor...@gmail.com on 13 Sep 2012 at 9:31

GoogleCodeExporter commented 9 years ago 
Yep, file was attached, not sure why you're not seeing it. I've just pasted
the text below;

***begin log***

Wed Sep 12 11:05:05 EST 2012: PeptideShaker version 0.18.2.

jshortcut.dll loaded via tmp generated pathname:
C:\Users\phains\AppData\Local\Temp\jshortcut-6225089518494661726.dll
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: 18.6/129.9
processors available: 2
useCommandThread: false
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
Number format exception for pdb alignment!
Number format exception for pdb alignment!
Number format exception for pdb alignment!
Number format exception for pdb alignment!

FileManager.getAtomSetCollectionFromFile(
http://www.rcsb.org/pdb/files/1JTI.pdb)
FileManager opening http://www.rcsb.org/pdb/files/1JTI.pdb
Exception in thread "AWT-EventQueue-0" java.lang.IllegalArgumentException:
Lower interval range >= upper interval range! 188.0>=188.0
    at
no.uib.jsparklines.renderers.JSparklinesIntervalChartTableCellRenderer.getTableC
ellRendererComponent(JSparklinesIntervalChartTableCellRenderer.java:678)
    at javax.swing.JTable.prepareRenderer(Unknown Source)
    at javax.swing.plaf.synth.SynthTableUI.paintCell(Unknown Source)
    at javax.swing.plaf.synth.SynthTableUI.paintCells(Unknown Source)
    at javax.swing.plaf.synth.SynthTableUI.paint(Unknown Source)
    at javax.swing.plaf.synth.SynthTableUI.update(Unknown Source)
    at javax.swing.JComponent.paintComponent(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JViewport.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JLayeredPane.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(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.paintDirtyRegions(Unknown Source)
    at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source)
    at javax.swing.RepaintManager.seqPaintDirtyRegions(Unknown Source)
    at
javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(Unknown
Source)
    at java.awt.event.InvocationEvent.dispatch(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)
The Resolver thinks Pdb
biomolecule 1: number of transforms: 1
biomolecule 2: number of transforms: 1
Setting space group name to P 1
openFile(http://www.rcsb.org/pdb/files/1JTI.pdb): 6365 ms
reading 6049 atoms
ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty
"auxiliaryInfo" to inspect them.
Default Van der Waals type for model set to Jmol
Time to autoBond: 62 ms
ModelSet: autobonding; use  autobond=false  to not generate bonds
automatically
spinY = 20
spinFPS is set too fast (30.0) -- can't keep up!
Exception in thread "AWT-EventQueue-0" java.lang.IllegalArgumentException:
Lower interval range >= upper interval range! 188.0>=188.0
    at
no.uib.jsparklines.renderers.JSparklinesIntervalChartTableCellRenderer.getTableC
ellRendererComponent(JSparklinesIntervalChartTableCellRenderer.java:678)
    at javax.swing.JTable.prepareRenderer(Unknown Source)
    at javax.swing.plaf.synth.SynthTableUI.paintCell(Unknown Source)
    at javax.swing.plaf.synth.SynthTableUI.paintCells(Unknown Source)
    at javax.swing.plaf.synth.SynthTableUI.paint(Unknown Source)
    at javax.swing.plaf.synth.SynthTableUI.update(Unknown Source)
    at javax.swing.JComponent.paintComponent(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JViewport.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JLayeredPane.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(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$PaintManager.paint(Unknown Source)
    at javax.swing.RepaintManager.paint(Unknown Source)
    at javax.swing.JComponent._paintImmediately(Unknown Source)
    at javax.swing.JComponent.paintImmediately(Unknown Source)
    at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source)
    at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source)
    at javax.swing.RepaintManager.seqPaintDirtyRegions(Unknown Source)
    at
javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(Unknown
Source)
    at java.awt.event.InvocationEvent.dispatch(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)
(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: 218.7/398.7
processors available: 2
useCommandThread: false
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
java.sql.SQLException: Cannot close a connection while a transaction is
still active.
    at
org.apache.derby.impl.jdbc.SQLExceptionFactory40.getSQLException(Unknown
Source)
    at org.apache.derby.impl.jdbc.Util.newEmbedSQLException(Unknown Source)
    at org.apache.derby.impl.jdbc.Util.newEmbedSQLException(Unknown Source)
    at org.apache.derby.impl.jdbc.Util.generateCsSQLException(Unknown
Source)
    at org.apache.derby.impl.jdbc.EmbedConnection.newSQLException(Unknown
Source)
    at
org.apache.derby.impl.jdbc.EmbedConnection.checkForTransactionInProgress(Unknown
Source)
    at org.apache.derby.impl.jdbc.EmbedConnection.close(Unknown Source)
    at com.compomics.util.db.ObjectsDB.close(ObjectsDB.java:539)
    at
com.compomics.util.experiment.identification.IdentificationDB.close(Identificati
onDB.java:742)
    at
com.compomics.util.experiment.identification.Identification.close(Identification
.java:995)
    at
eu.isas.peptideshaker.gui.PeptideShakerGUI.clearDatabaseFolder(PeptideShakerGUI.
java:3973)
    at
eu.isas.peptideshaker.gui.PeptideShakerGUI.clearData(PeptideShakerGUI.java:3944)
    at
eu.isas.peptideshaker.gui.NewDialog.openButtonActionPerformed(NewDialog.java:616
)
    at eu.isas.peptideshaker.gui.NewDialog.access$100(NewDialog.java:42)
    at
eu.isas.peptideshaker.gui.NewDialog$2.actionPerformed(NewDialog.java:228)
    at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
    at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
    at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
    at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
    at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown
Source)
    at java.awt.Component.processMouseEvent(Unknown Source)
    at javax.swing.JComponent.processMouseEvent(Unknown Source)
    at java.awt.Component.processEvent(Unknown Source)
    at java.awt.Container.processEvent(Unknown Source)
    at java.awt.Component.dispatchEventImpl(Unknown Source)
    at java.awt.Container.dispatchEventImpl(Unknown Source)
    at java.awt.Component.dispatchEvent(Unknown Source)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
    at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
    at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
    at java.awt.Container.dispatchEventImpl(Unknown Source)
    at java.awt.Window.dispatchEventImpl(Unknown Source)
    at java.awt.Component.dispatchEvent(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.Dialog$1.run(Unknown Source)
    at java.awt.event.InvocationEvent.dispatch(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.Dialog$1.run(Unknown Source)
    at java.awt.Dialog$3.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.awt.Dialog.show(Unknown Source)
    at java.awt.Component.show(Unknown Source)
    at java.awt.Component.setVisible(Unknown Source)
    at java.awt.Window.setVisible(Unknown Source)
    at java.awt.Dialog.setVisible(Unknown Source)
    at
eu.isas.peptideshaker.gui.PeptideShakerGUI.newJMenuItemActionPerformed(PeptideSh
akerGUI.java:1610)
    at
eu.isas.peptideshaker.gui.PeptideShakerGUI.access$3200(PeptideShakerGUI.java:107
)
    at
eu.isas.peptideshaker.gui.PeptideShakerGUI$33.actionPerformed(PeptideShakerGUI.j
ava:1170)
    at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
    at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
    at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
    at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
    at javax.swing.AbstractButton.doClick(Unknown Source)
    at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
    at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown
Source)
    at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
    at java.awt.Component.processMouseEvent(Unknown Source)
    at javax.swing.JComponent.processMouseEvent(Unknown Source)
    at java.awt.Component.processEvent(Unknown Source)
    at java.awt.Container.processEvent(Unknown Source)
    at java.awt.Component.dispatchEventImpl(Unknown Source)
    at java.awt.Container.dispatchEventImpl(Unknown Source)
    at java.awt.Component.dispatchEvent(Unknown Source)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
    at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
    at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
    at java.awt.Container.dispatchEventImpl(Unknown Source)
    at java.awt.Window.dispatchEventImpl(Unknown Source)
    at java.awt.Component.dispatchEvent(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)
Caused by: java.sql.SQLException: Cannot close a connection while a
transaction is still active.
    at
org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown
Source)
    at
org.apache.derby.impl.jdbc.SQLExceptionFactory40.wrapArgsForTransportAcrossDRDA(
Unknown
Source)
    ... 82 more
java.lang.NullPointerException
    at com.compomics.util.db.ObjectsDB.retrieveObject(ObjectsDB.java:329)
    at
com.compomics.util.experiment.identification.IdentificationDB.getSpectrumMatch(I
dentificationDB.java:330)
    at
com.compomics.util.experiment.identification.Identification.getSpectrumMatch(Ide
ntification.java:644)
    at
eu.isas.peptideshaker.gui.tablemodels.PsmTableModel.getValueAt(PsmTableModel.jav
a:149)
    at javax.swing.JTable.getValueAt(Unknown Source)
    at javax.swing.JTable.prepareRenderer(Unknown Source)
    at javax.swing.plaf.synth.SynthTableUI.paintCell(Unknown Source)
    at javax.swing.plaf.synth.SynthTableUI.paintCells(Unknown Source)
    at javax.swing.plaf.synth.SynthTableUI.paint(Unknown Source)
    at javax.swing.plaf.synth.SynthTableUI.update(Unknown Source)
    at javax.swing.JComponent.paintComponent(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JViewport.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JLayeredPane.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JSplitPane.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JSplitPane.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JSplitPane.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JSplitPane.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JLayeredPane.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at javax.swing.JLayeredPane.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(Unknown Source)
    at javax.swing.JComponent.paintToOffscreen(Unknown Source)
    at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(Unknown
Source)
    at javax.swing.RepaintManager$PaintManager.paint(Unknown Source)
    at javax.swing.RepaintManager.paint(Unknown Source)
    at javax.swing.JComponent.paint(Unknown Source)
    at java.awt.GraphicsCallback$PaintCallback.run(Unknown Source)
    at sun.awt.SunGraphicsCallback.runOneComponent(Unknown Source)
    at sun.awt.SunGraphicsCallback.runComponents(Unknown Source)
    at java.awt.Container.paint(Unknown Source)
    at java.awt.Window.paint(Unknown Source)
    at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source)
    at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source)
    at javax.swing.RepaintManager.seqPaintDirtyRegions(Unknown Source)
    at
javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(Unknown
Source)
    at java.awt.event.InvocationEvent.dispatch(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.Dialog$1.run(Unknown Source)
    at java.awt.Dialog$3.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.awt.Dialog.show(Unknown Source)
    at javax.swing.JOptionPane.showOptionDialog(Unknown Source)
    at javax.swing.JOptionPane.showMessageDialog(Unknown Source)
    at javax.swing.JOptionPane.showMessageDialog(Unknown Source)
    at
eu.isas.peptideshaker.gui.PeptideShakerGUI.clearDatabaseFolder(PeptideShakerGUI.
java:3978)
    at
eu.isas.peptideshaker.gui.PeptideShakerGUI.clearData(PeptideShakerGUI.java:3944)
    at
eu.isas.peptideshaker.gui.NewDialog.openButtonActionPerformed(NewDialog.java:616
)
    at eu.isas.peptideshaker.gui.NewDialog.access$100(NewDialog.java:42)
    at
eu.isas.peptideshaker.gui.NewDialog$2.actionPerformed(NewDialog.java:228)
    at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
    at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
    at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
    at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
    at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown
Source)
    at java.awt.Component.processMouseEvent(Unknown Source)
    at javax.swing.JComponent.processMouseEvent(Unknown Source)
    at java.awt.Component.processEvent(Unknown Source)
    at java.awt.Container.processEvent(Unknown Source)
    at java.awt.Component.dispatchEventImpl(Unknown Source)
    at java.awt.Container.dispatchEventImpl(Unknown Source)
    at java.awt.Component.dispatchEvent(Unknown Source)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
    at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
    at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
    at java.awt.Container.dispatchEventImpl(Unknown Source)
    at java.awt.Window.dispatchEventImpl(Unknown Source)
    at java.awt.Component.dispatchEvent(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.Dialog$1.run(Unknown Source)
    at java.awt.event.InvocationEvent.dispatch(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.Dialog$1.run(Unknown Source)
    at java.awt.Dialog$3.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.awt.Dialog.show(Unknown Source)
    at java.awt.Component.show(Unknown Source)
    at java.awt.Component.setVisible(Unknown Source)
    at java.awt.Window.setVisible(Unknown Source)
    at java.awt.Dialog.setVisible(Unknown Source)
    at
eu.isas.peptideshaker.gui.PeptideShakerGUI.newJMenuItemActionPerformed(PeptideSh
akerGUI.java:1610)
    at
eu.isas.peptideshaker.gui.PeptideShakerGUI.access$3200(PeptideShakerGUI.java:107
)
    at
eu.isas.peptideshaker.gui.PeptideShakerGUI$33.actionPerformed(PeptideShakerGUI.j
ava:1170)
    at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
    at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
    at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
    at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
    at javax.swing.AbstractButton.doClick(Unknown Source)
    at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
    at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown
Source)
    at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
    at java.awt.Component.processMouseEvent(Unknown Source)
    at javax.swing.JComponent.processMouseEvent(Unknown Source)
    at java.awt.Component.processEvent(Unknown Source)
    at java.awt.Container.processEvent(Unknown Source)
    at java.awt.Component.dispatchEventImpl(Unknown Source)
    at java.awt.Container.dispatchEventImpl(Unknown Source)
    at java.awt.Component.dispatchEvent(Unknown Source)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
    at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
    at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
    at java.awt.Container.dispatchEventImpl(Unknown Source)
    at java.awt.Window.dispatchEventImpl(Unknown Source)
    at java.awt.Component.dispatchEvent(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)
java.lang.NullPointerException
    at com.compomics.util.db.ObjectsDB.insertObjects(ObjectsDB.java:226)
    at com.compomics.util.db.ObjectsCache.saveCache(ObjectsCache.java:526)
    at
eu.isas.peptideshaker.gui.PeptideShakerGUI.saveProjectProcess(PeptideShakerGUI.j
ava:6061)
    at
eu.isas.peptideshaker.gui.PeptideShakerGUI.access$8600(PeptideShakerGUI.java:107
)
    at
eu.isas.peptideshaker.gui.PeptideShakerGUI$89.run(PeptideShakerGUI.java:5827)
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
java.io.IOException: Spectrum '19: Scan 107812 (rt=36.9352, p=0, c=6738,
e=3) [\cmri-nas\massspecdata2\Data\5600\PGH\300512\MEF4_Ti_FT_10_01.wiff]'
in mgf file 'MEF2_Ti_FT_10_01.wiff.-1.mgf' not found!
    at
com.compomics.util.experiment.massspectrometry.SpectrumFactory.getPrecursor(Spec
trumFactory.java:479)
    at
com.compomics.util.experiment.massspectrometry.SpectrumFactory.getPrecursor(Spec
trumFactory.java:410)
    at
com.compomics.util.experiment.massspectrometry.SpectrumFactory.getPrecursor(Spec
trumFactory.java:223)
    at
eu.isas.peptideshaker.fileimport.IdFilter.validateId(IdFilter.java:150)
    at
eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(Fil
eImporter.java:775)
    at
eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground
(FileImporter.java:636)
    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)

Wed Sep 12 11:52:57 EST 2012: PeptideShaker version 0.18.2.

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: 11.8/129.9
processors available: 2
useCommandThread: false
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!!
java.io.FileNotFoundException:
K:\Data\5600\PGH\260612\MEF4_Ti_FT_10_02.wiff.-1.mgf (The system cannot
find the file specified)
    at java.io.RandomAccessFile.open(Native Method)
    at java.io.RandomAccessFile.<init>(Unknown Source)
    at java.io.RandomAccessFile.<init>(Unknown Source)
    at
uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile.<init>(BufferedRandomAccessF
ile.java:45)
    at
uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile.<init>(BufferedRandomAccessF
ile.java:53)
    at
com.compomics.util.experiment.massspectrometry.SpectrumFactory.addSpectra(Spectr
umFactory.java:184)
    at
eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importSpectra(
FileImporter.java:899)
    at
eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(Fil
eImporter.java:755)
    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$Worker.runTask(Unknown
Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
java.lang.NullPointerException
    at
com.compomics.util.experiment.massspectrometry.SpectrumFactory.getNSpectra(Spect
rumFactory.java:369)
    at
eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(Fil
eImporter.java:759)
    at
eu.isas.peptideshaker.fileimport.FileImporter$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$Worker.runTask(Unknown
Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)

Wed Sep 12 14:12:51 EST 2012: PeptideShaker version 0.18.2.

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: 11.8/129.9
processors available: 2
useCommandThread: false
No Decoy section found!!
java.io.IOException: Spectrum '675: Sum of 2 scans in range 92067
(rt=47.0693, p=0, c=5754, e=2) to 92084 (rt=47.0976, p=0, c=5755, e=3)
[\cmri-nas\massspecdata2\Data\5600\PGH\260612\MEF4_2_FT_03.wiff]' in mgf
file 'MEF4_2_FT_03.wiff.-1.mgf' not found!
    at
com.compomics.util.experiment.massspectrometry.SpectrumFactory.getPrecursor(Spec
trumFactory.java:479)
    at
com.compomics.util.experiment.massspectrometry.SpectrumFactory.getPrecursor(Spec
trumFactory.java:410)
    at
com.compomics.util.experiment.massspectrometry.SpectrumFactory.getPrecursor(Spec
trumFactory.java:223)
    at
eu.isas.peptideshaker.fileimport.IdFilter.validateId(IdFilter.java:150)
    at
eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(Fil
eImporter.java:775)
    at
eu.isas.peptideshaker.fileimport.FileImporter$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$Worker.runTask(Unknown
Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)

Wed Sep 12 14:15:27 EST 2012: PeptideShaker version 0.18.2.

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: 11.8/129.9
processors available: 2
useCommandThread: false
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!!
java.lang.NullPointerException
    at
eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel$53.run(SpectrumI
dentificationPanel.java:2521)

Wed Sep 12 14:31:10 EST 2012: PeptideShaker version 0.18.2.

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: 11.8/129.9
processors available: 2
useCommandThread: false
Exception in thread "AWT-EventQueue-0" java.lang.ClassCastException:
java.lang.Boolean cannot be cast to java.awt.Font
    at com.sun.java.swing.plaf.nimbus.NimbusStyle.getFontForState(Unknown
Source)
    at javax.swing.plaf.synth.SynthStyle.installDefaults(Unknown Source)
    at com.sun.java.swing.plaf.nimbus.NimbusStyle.installDefaults(Unknown
Source)
    at javax.swing.plaf.synth.SynthStyle.installDefaults(Unknown Source)
    at javax.swing.plaf.synth.SynthLookAndFeel.updateStyle(Unknown Source)
    at javax.swing.plaf.synth.SynthPanelUI.updateStyle(Unknown Source)
    at javax.swing.plaf.synth.SynthPanelUI.installDefaults(Unknown Source)
    at javax.swing.plaf.basic.BasicPanelUI.installUI(Unknown Source)
    at javax.swing.plaf.synth.SynthPanelUI.installUI(Unknown Source)
    at javax.swing.JComponent.setUI(Unknown Source)
    at javax.swing.JPanel.setUI(Unknown Source)
    at javax.swing.JPanel.updateUI(Unknown Source)
    at
eu.isas.peptideshaker.gui.tabpanels.PtmPanel$51.run(PtmPanel.java:1818)
    at java.awt.event.InvocationEvent.dispatch(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)
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
    at javax.swing.plaf.synth.SynthPanelUI.uninstallDefaults(Unknown Source)
    at javax.swing.plaf.basic.BasicPanelUI.uninstallUI(Unknown Source)
    at javax.swing.plaf.synth.SynthPanelUI.uninstallUI(Unknown Source)
    at javax.swing.JComponent.setUI(Unknown Source)
    at javax.swing.JPanel.setUI(Unknown Source)
    at javax.swing.JPanel.updateUI(Unknown Source)
    at
eu.isas.peptideshaker.gui.tabpanels.PtmPanel$51.run(PtmPanel.java:1818)
    at java.awt.event.InvocationEvent.dispatch(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)
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
    at javax.swing.plaf.synth.SynthPanelUI.uninstallDefaults(Unknown Source)
    at javax.swing.plaf.basic.BasicPanelUI.uninstallUI(Unknown Source)
    at javax.swing.plaf.synth.SynthPanelUI.uninstallUI(Unknown Source)
    at javax.swing.JComponent.setUI(Unknown Source)
    at javax.swing.JPanel.setUI(Unknown Source)
    at javax.swing.JPanel.updateUI(Unknown Source)
    at
eu.isas.peptideshaker.gui.tabpanels.PtmPanel$51.run(PtmPanel.java:1818)
    at java.awt.event.InvocationEvent.dispatch(Unknown Source)
    at java.awt.EventQueue.dispatchEvent(Unknown Source)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    at java.awt.EventDispatchThread.run(Unknown Source)
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
java.io.IOException: Spectrum '1045: Sum of 2 scans in range 107316
(rt=60.1191, p=0, c=6707, e=3) to 107333 (rt=60.1557, p=0, c=6708, e=4)
[\cmri-nas\massspecdata2\Data\5600\PGH\260612\MEF4_2_FT_03.wiff]' in mgf
file 'MEF4_2_FT_03.wiff.-1.mgf' not found!
    at
com.compomics.util.experiment.massspectrometry.SpectrumFactory.getPrecursor(Spec
trumFactory.java:479)
    at
com.compomics.util.experiment.massspectrometry.SpectrumFactory.getPrecursor(Spec
trumFactory.java:410)
    at
com.compomics.util.experiment.massspectrometry.SpectrumFactory.getPrecursor(Spec
trumFactory.java:223)
    at
eu.isas.peptideshaker.fileimport.IdFilter.validateId(IdFilter.java:150)
    at
eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(Fil
eImporter.java:775)
    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$Worker.runTask(Unknown
Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)

Wed Sep 12 14:49:02 EST 2012: PeptideShaker version 0.18.2.

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: 11.9/129.9
processors available: 2
useCommandThread: false
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!!

***end log***

Original comment by snoor...@gmail.com on 13 Sep 2012 at 9:27

GoogleCodeExporter commented 9 years ago 
This part is for me the most interesting:

Spectrum '1045: Sum of 2 scans in range 107316
(rt=60.1191, p=0, c=6707, e=3) to 107333 (rt=60.1557, p=0, c=6708, e=4)
[\cmri-nas\massspecdata2\Data\5600\PGH\260612\MEF4_2_FT_03.wiff]' in mgf
file 'MEF4_2_FT_03.wiff.-1.mgf' not found!

as 'MEF4_2_FT_03.wiff.-1.mgf' is not one if the files you sent me. I have a 
similarly named file called just 'MEF4_2_FT_03.mgf'. So perhaps we are testing 
with different files?

I re-uploaded the files you sent me here: 
http://vedlegg.uib.no/?id=2fbf4be7f15988c179440e78ed24e8c5

Could you try loading these files? This I'm able to do without issues using 
PeptideShaker version 0.18.2.

If we're testing on a different set of files that could explain why we're get 
different results. :)

Original comment by harald.b...@gmail.com on 13 Sep 2012 at 9:52

GoogleCodeExporter commented 9 years ago 
File in Dropbox; https://dl.dropbox.com/u/3533588/MEF4_5_FT_03.zip

Peter

Original comment by snoor...@gmail.com on 13 Sep 2012 at 11:53

GoogleCodeExporter commented 9 years ago 
Ah sorry, missed this e-mail. Some of the problem may be me doing something
silly, I didn't think of this at the time. I searched these files over a
fair amount of time and it's possible that I've renamed an MGF file after
searching with Mascot (long story). PeptideShaker has been having issues
finding some of the MGFs when loading Mascot searches, but only for the
'MEF' searches. I can't recall exactly when I renamed some of the files. I
have been able to get around this problem, but I'm reasonably confident
that the parsing of MGF file upon loading is not the problem.

I don't see any errors when loading the files, it's only when I go to IDs
and if I don't save. Maybe it's something stupid with the setup of my
system? Like I said, the PCs are tied up pretty tightly and the settings
have caused numerous issues in the past with various MS software.

I've grabbed the ZIP file and I'll load that and let you know how it goes.

Original comment by snoor...@gmail.com on 14 Sep 2012 at 12:01

GoogleCodeExporter commented 9 years ago 
It could be a matter of PeptideShaker trying to be clever and select too many 
mgf files when loading the data in the new project dialog. (Due to SearchGUI 
settings files in the folder(s).) To avoid this it is always best to choose an 
empty folder for the SearchGUI output.

So to do a clean test with your data I recommend that you move all of the 
search result files, the fasta file (the target-decoy one) and the required 
mgfs that you want to analyze into an empty folder. Delete all the .cui files, 
and then try to load the files from this folder.

This is what I did with the zip file I re-uploaded.

Original comment by harald.b...@gmail.com on 14 Sep 2012 at 12:12

GoogleCodeExporter commented 9 years ago 
I've noticed that PeptideShaker automatically selects all the MGFs as
detailed in the SearchGUI file. I usually clear that and load what I really
need.

I tested the "Not Shaking" files. I initially used it with the *cui that
you had generated. First load, all good until I went to the IDs tab. The
same error about contacting the developers. The second time all I did was
load, save and then went to the IDs tab. All worked perfectly. The final
time, I deleted the *.cui files and loaded the data again. I then went to
the IDs tab without saving. The same error message.

My guess is it's something with my system since it works fine on your
system. I'd be willing to bet if I tried it on my PC at home all would be
well, it has always worked well at home (64-bit Win 7). I know a work
around, so I'm not too concerned. The log file follows.

***start log***

Fri Sep 14 10:25:37 EST 2012: PeptideShaker version 0.18.2.

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: 11.9/129.9
processors available: 2
useCommandThread: false
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
java.lang.NullPointerException
    at
eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel$53.run(SpectrumI
dentificationPanel.java:2526)

    Fri Sep 14 10:30:00 EST 2012: PeptideShaker version 0.18.2.

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: 11.8/129.9
processors available: 2
useCommandThread: false
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!

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: 11.8/129.9
processors available: 2
useCommandThread: false
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
No Decoy section found!!
java.lang.NullPointerException
    at
eu.isas.peptideshaker.gui.tabpanels.SpectrumIdentificationPanel$53.run(SpectrumI
dentificationPanel.java:2516)

***end log***

Original comment by snoor...@gmail.com on 14 Sep 2012 at 12:46

GoogleCodeExporter commented 9 years ago 
I'm finally able to reproduce the issue! It seems to be related to the memory 
you give to PeptideShaker. I usually give it 5000MB (to get it to run faster), 
but if I reduce it to 1500M (which seems to be your setup) I get the same error 
as you.

This shouldn't happen of course. But now that I'm able to reproduce the error I 
should be able to fix it. I'll let you know when I've found a fix that works.

Original comment by harald.b...@gmail.com on 14 Sep 2012 at 1:03

GoogleCodeExporter commented 9 years ago 
Ah, well done. I used to tell PeptideShaker to take 1500 MB, but I've had
trouble making that much available in recent times, so I've left the option
as the default now (-Xmx****M). I hate the fact that we are stuck using
32-bit systems when the world has moved on... So much of the MS software is
so RAM intensive.

Original comment by snoor...@gmail.com on 14 Sep 2012 at 1:15

GoogleCodeExporter commented 9 years ago 
PeptideShaker 0.18.3 has just been released. This should fix the problem with 
using PeptideShaker when limited memory is available, and you should thus be 
able to load all your files at the same time without getting the null pointer 
when moving to the Spectrum IDs tab. Let me know if this is not the case.

And thanks for telling us about this issue btw. We would not have found this 
ourselves as we usually test on machines were more memory is available.

Original comment by harald.b...@gmail.com on 15 Sep 2012 at 1:22

GoogleCodeExporter commented 9 years ago 
Happy to help! Even if it was "creating" problems for you. I'm happy to say
that I tested 0.18.3 and it's all fine, no error messages, even without
saving the project.

Thanks for all your efforts, PeptideShaker and SearchGUI are definitely two
of the best and most useful applications out there.

Original comment by snoor...@gmail.com on 16 Sep 2012 at 10:10