compomics/denovogui

Graphical user interface for de novo sequencing of tandem mass spectra

denovogui's Issues

Got .out files, can't see them

What steps will reproduce the problem?
1. Load 30 spectra (.mgf)
2. Stablished different parameters (fixed modifications - carboxymethyl, 
variable modifications - oxidation M, phosphorylation Ser, Thr, Tyr) 
3. Results didn't show but .out files were generated

What is the expected output? What do you see instead?
Expected to see peptides for each ms.ms spectra. All 30 spectra run well but at 
the end all boxes were empty and a message appeared (An error occured. If the 
problem persists, please contact developers)

What version of the product are you using? On what operating system?
DeNovo Gui v1.3.7
Mac OS X 10.7.5

Please provide any additional information below.

Original issue reported on code.google.com by [email protected] on 28 Apr 2014 at 2:33

Attachments:

• [Captura de pantalla 2014-04-28 a la(s) 9.25.25.png](https://storage.googleapis.com/google-code-attachments/denovogui/issue-8/comment-0/Captura de pantalla 2014-04-28 a la%28s%29 9.25.25.png)

license has expired - pNovo+

Greetings,

I am trying to use pNovo+ via De Novo-GUI. But the licensing had expired. I have provied the error message below for your reference. Lastly, thank you go for handling my request.

Regards,
Ben

Mon Apr 25 00:26:08 SGT 2022 Starting DeNovoGUI.

Mon Apr 25 00:26:08 SGT 2022 Loading the spectra.
Mon Apr 25 00:27:00 SGT 2022 Done loading the spectra.

Mon Apr 25 00:27:00 SGT 2022 Starting de novo sequencing: 23629 spectra in 1 file using 24 threads.

Mon Apr 25 00:27:00 SGT 2022 Sequencing 20180507_OR16_Ag6_5607264_SA_MHC_HCD_clone1-IP1.mgf using pNovo+.

Sorry, the license has expired. Please visit http://pfind.ict.ac.cn/software/pNovo/ and download the newest version.

Mon Apr 25 00:27:00 SGT 2022 Sequencing 20180507_OR16_Ag6_5607264_SA_MHC_HCD_clone1-IP1.mgf using pNovo+ completed (279.0 milliseconds).

Mon Apr 25 00:27:00 SGT 2022 De novo sequencing completed (280.0 milliseconds).

Mon Apr 25 00:27:00 SGT 2022 The de novo sequencing did not generate any output files!

Mon Apr 25 00:27:00 SGT 2022 Sequencing Canceled.

Mon Apr 25 00:27:00 SGT 2022 De Novo Sequencing Canceled!

Peptide matches export does not work in 1.5.2

What steps will reproduce the problem?
1. Run deNovoGUI on spectra (all three algorithms)
2. Click Export -> Peptide Matches (Beta)
3. Fill out required fields, click OK

What is the expected output? What do you see instead?
A text file with peptide match information.  Instead the best I get is a text 
file that has only header information (1 line long) and nothing after it.  Some 
attempts don't even generate the 1-line text file.

What version of the product are you using? On what operating system?
1.5.2 in Windows 7.  

Please provide any additional information below.
The peptide matching pops up a window saying "A protein mapping was already 
found; use the previous results?", with yes and no options.  My answer to this 
does not seem to impact the results in the peptide matches export file.

Original issue reported on code.google.com by [email protected] on 14 Jul 2015 at 8:55

Not updating Settings file

What steps will reproduce the problem?
1. I change the No. of Solutions to: 2 
2. Save the Parameters File
3. Reopen the File, but No. of Solution has turned back to default value of 10

What is the expected output? What do you see instead?
When i run pepnovo, after changing  No. of Solutions to: 2 , I still get the 
default value of 10, even after changing and saving the Parameters File

What version of the product are you using? On what operating system?
1.2.3 on Windows 7, 64bit

Please provide any additional information below.
Great piece of software!!! I'm an old 'de-novo' user, dating back from the 
Lutefisk era. This is great program, but I want to change the No. of Solutions 
to 2 because if not, the Blast files are too big.
ALTERNATIVELY, it would be great if you could implement to ONLY export the Nth 
most highest match for each peptide.

Thanks and hope to hear back from you!!!

Alex

Original issue reported on code.google.com by [email protected] on 14 Mar 2014 at 1:24

output file converting?

Hi,

is it possible to get the output files in one this openacces format?
mzIdentML
mzTab

Or is maybe a converter known for the mgf.out and pnovo.txt files?

Thanks,
HP

problems of installation

Hi, I got some problems when using the DeNovoGUI 1.16.6. It works if I don't choose any setting file. But when choosing any parameter file even the original denovo.par, I got the error from de novo parameters.

Maybe it's derived from the error of installation. I change the path of denovogui_mathes_directory to get through the path setting, but when I prepare to restart the computer, there is an error.

And the following is my path settings.
original path that can't be written: C:\Windows\System32\resources
final path that I set: C:\Users\sun.compomics

It would be grateful if you would be so kind to help me solve the problems above.

Sincerely,
Dandan Liu

I cannot change the spectrum file

What steps will reproduce the problem?
1. analyse Several mgf files.
2. change spectrum File
3. message "Updating Disply. Please wait," is shown, but the message does not 
leave, and I cannot operate denovogui.

What is the expected output? What do you see instead?
Usually, the message was disappear, and I can continue to analyze other data.

What version of the product are you using? On what operating system?
I use denovogui on MacOS X 10.10.4. The version is 1.5.2, and Java version is 
built 1.8.0_51b-b16.


Please provide any additional information below.

Original issue reported on code.google.com by [email protected] on 11 Aug 2015 at 1:12

Problems adding reporter ions to custom modifications

Hi,
I'm using denovogui 1.15.11 and have created several custom modifications. I've been trying to add reporter ions to these modifications and have had an issue:

• The reporter ion editor doesn't seem to handle masses greater than 200 Da. For one modification, I was able to add multiple reporter ions (all under 200 Da) with no problems. For another modification, I was able to add one reporter ion (mass 156.1) with no problems, but after creating a second one (mass 201.1), the reporter ions field became red and I was unable to save the settings. I tried recreating the reporter ion multiple times and the issue reoccurred. My successful and unsuccessfully saved reporter ions were made in the same way; the only difference I can find is the mass.

Thanks for any assistance you can provide.

A Rizzo

Edit: first issue resolved, second remains.

NullPointerException in DeNovoGUI-1.16.4 IdentificationParametersCLI

Hello! I encounter an error when attempting to generate a parameters file using DeNovoGUI v1.16.3 and v1.16.4 (Linux), but not v1.16.2.

>java -cp /path/to/DeNovoGUI-1.16.4/DeNovoGUI-1.16.4.jar com.compomics.denovogui.cmd.IdentificationParametersCLI -out /path/to/params.out -prec_tol 20 -frag_tol 0.5 -fixed_mods "Carbamidomethylation of C" -variable_mods "Oxidation of M" -pepnovo_hitlist_length 20 -novor_fragmentation HCD -novor_mass_analyzer FT

java.lang.NullPointerException at com.compomics.denovogui.cmd.PathSettingsCLI.setPathSettings(PathSettingsCLI.java:106) at com.compomics.denovogui.cmd.PathSettingsCLI.extractAndUpdatePathOptions(PathSettingsCLI.java:240) at com.compomics.denovogui.cmd.IdentificationParametersCLI.<init>(IdentificationParametersCLI.java:34) at com.compomics.denovogui.cmd.IdentificationParametersCLI.main(IdentificationParametersCLI.java:50)

Thank you very much,
Sam

Blast export fails in denovogui 1.5.1

What steps will reproduce the problem?
1. Run a denovogui search of my mgf files
2. Export -> Blast -> click OK and enter file name for text file output
3. Click OK, error comes up "Export error" "An error occurred while exporting 
the results"

What is the expected output? What do you see instead?
I expect it to create a file with useful information on the peptide sequences 
that were derived by denovogui.  Instead I get a zero byte text file and an 
error that doesn't tell me anything.  

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

Please provide any additional information below.

Original issue reported on code.google.com by [email protected] on 9 Jul 2015 at 3:44

No output denovoGUI

What steps will reproduce the problem?
1. Analyze my MGF file ( already sent to Marc Vaudel )
2.
3.

What is the expected output? What do you see instead?
Expect to see some peptide sequences. The program works through all 4736 and 
completes OK. The crash occurrs when it is trying to make the output file. The 
results screen shows up with all boxes empty and an error message saying to 
contact the developers. ( I have the Java memory set at 8000 )

What version of the product are you using? On what operating system?
DenovoGUI1.3.6
Windows 7 

Please provide any additional information below.

Original issue reported on code.google.com by [email protected] on 9 Apr 2014 at 10:05

unable to give pepnovo+ search settings

What steps will reproduce the problem?
1. unable to define modifications settings for pepnovo+
2. .out file does not open, although all the other dialogue boxes before 
opening are displayed i.e) retereiving, loading results etc.
3.

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


What version of the product are you using? On what operating system?
1.5.1

Please provide any additional information below.

Original issue reported on code.google.com by [email protected] on 8 Jul 2015 at 9:57

error when exporting peptide matches

Hi,
an error (image attached) occurred, when exporting peptide matches.
I am using the latest version: DeNovoGUI-1.4.8

The database is the human uniprot one, 2014 August version. 
The raw file is a 2hrs raw from OrbitrapXL. I used proteoWizard to convert to 
mgf format. All good for the denovo, until export to the tags. Just cannot 
export to peptide matches. 

Original issue reported on code.google.com by [email protected] on 11 Sep 2014 at 2:33

Attachments:

• error.png

pNovo licence expired

Hi,

since mid of march I got the message, if I try to run pNovo+:
Sorry, the license has expired. Please visit http://pfind.ict.ac.cn/software/pNovo/ and download the newest version.

Will you get a new license? (I would prefer it, because your interface is a much nicer to view through the data)

Best,
HPooky

Trojan Virus on download?

Hi, i am getting this error when i try to download the program from this link (windows) http://compomics.github.io/projects/denovogui.html

Gateway Anti-Virus Alert
This request is blocked by the Firewall Gateway Anti-Virus Service. Name: JavaAGNT.AVC (Trojan)

Any ideas or can i get a "clean" link

"An error ocurred: No current connection"

What steps will reproduce the problem?
1. Open the output files
2. Go to "Export", then "Peptide Matches (Beta)"
3. Load my costum database

What is the expected output? What do you see instead?
Identification of a protein according to the spectra but an error ocurred "An 
error ocurred: No current connection"

What version of the product are you using? On what operating system?
1.4.0

Please provide any additional information below.

Thanks

Original issue reported on code.google.com by [email protected] on 2 May 2014 at 8:37

Attachments:

• denovo.png

PepNovo PTM +42 not recognised

Facing an error while running denovogui for the pepnovo+

File size max for De Novo gui?

What steps will reproduce the problem?
1. Open any results file
2.
3.

What is the expected output? What do you see instead?
Expected: eventual opened & visible file, but opening completed search results 
takes as long as running a search.

What version of the product are you using? On what operating system?
version 1.5.0 on Windows 7 Ultimate.

Please provide any additional information below.
Opening any results file in the GUI takes upwards of several hours, whether the 
output is with one algorithm (e.g. just DirecTag) or several. Is this 
unavoidable/typical? Is there an upper limit on file size that the program can 
handle? Or is this basically a problem with my machine?

Original issue reported on code.google.com by [email protected] on 7 Jul 2015 at 4:28

no peptide or spectrum display

What steps will reproduce the problem?
1. I couldn't reproduce the same error. After this error display error 
(attached) nothing on spectrum viewer and denovo peptides. 
3.

What is the expected output? What do you see instead?
Expected output is some spectra and peptides as in the example denovoGUI output 
file.

What version of the product are you using? On what operating system?
Denovo1.2.3, Windows 7

Please provide any additional information below.
java.io.IOException: Error while writing match 
HIV2_3.mgf_cus_Locus:1.1.1.6099.14 File:"HIV2_3.wiff" in table 
"HIV2_3.mgf_psms" in databaseDeNovoGUI_sample reference_0_id.
    at com.compomics.util.db.ObjectsCache.saveObject(ObjectsCache.java:429)
    at com.compomics.util.db.ObjectsCache.saveObject(ObjectsCache.java:393)
    at com.compomics.util.db.ObjectsCache.updateCache(ObjectsCache.java:461)
    at com.compomics.util.db.ObjectsCache.addObject(ObjectsCache.java:252)
    at com.compomics.util.db.ObjectsDB.insertObject(ObjectsDB.java:208)
    at com.compomics.util.experiment.identification.IdentificationDB.addSpectrumMatch(IdentificationDB.java:353)
    at com.compomics.util.experiment.identification.Identification.addSpectrumMatch(Identification.java:1190)
    at com.compomics.util.experiment.identification.Identification.addSpectrumMatch(Identification.java:1348)
    at com.compomics.denovogui.gui.ResultsFrame.importPepNovoResults(ResultsFrame.java:2451)
    at com.compomics.denovogui.gui.ResultsFrame$46.run(ResultsFrame.java:2013)

Original issue reported on code.google.com by [email protected] on 3 Apr 2014 at 9:31

Attachments:

• HIV2_3.png

Download link doesnt work

Hi,
Recently when running de novo gui (or peptide shaker and search gui) application doesnt ask to upgrade the software. In addition when trying to download the executables the the site http://genesis.ugent.be/maven2/com/compomics/denovogui/DeNovoGUI/1.10.1/DeNovoGUI-1.10.1-windows.zip tmes out.
Thanks,
DD

pNovo Results Top 1

Dear Authors,

Thank you very much for providing this nice tool. I was trying to run pNovo using your wrapper. I could successfully run the tool and produce the results. According to the user-guide from pNovo one can choose between top1 and top10 results, this case will be when I use the pNovo3_Search.exe ( I already tried to do so but the tool keeps running for hours without any progress) so I decided to use your DeNovoGUI instead. By running pNovo3 using DeNovoGUI, the produced results file are the top 10 (sample_pnovo.res.txt). Is there any setting in your GUI to produce the top1 results? The top10 results file doesn't contain aaScore and some other values, which I need for downstream analysis. Thank you very much!

Best,
Ahmad

DeNovoCLI blast generation

Hello,

I am running DeNovoCLI but the blast file is not being generated. It has to be generated via the server becuase they are 2-3 GB files and I don't have the computing power to run it via the GUI. Any thoughts? These are my command line arguments:

java -cp DeNovoGUI-1.15.0.jar com.compomics.denovogui.cmd.IdentificationParametersCLI -out "HCD_par_decoy.par" -db uniprot_all_concatenated_target_decoy.fastaprot_all.fasta -mc 2 -fixed_mods "Carbamidomethylation of C" -variable_mods "Oxidation of M" -pepnovo_hitlist_length 1 -pepnovo_generate_blast 1 -pnovo_activation HCD -pnovo_num_peptides 1 -novor_fragmentation HCD

Thank you very much!

Best wishes from the Mexico science rebellion,

Carla Uranga

can't install denovogui

I've tried everything. nothing works.
Java is updated
I click on the jar file to open the following screen but when I click on open nothing happens.
the jar file (latest version July 2022) shows up as a Microsoft Internet Explorer program, which is confusing

DirecTag search fails in version 1.4.6 in Windows

What steps will reproduce the problem?
1. DirecTag search using default settings and the example Ecoli_30.mgf MS/MS 
file
2. Start
3. Message: An error occured: If the problem persists... 

What is the expected output? What do you see instead?
Run de novo sequencing of the mgf file and see the peptides.
DeNovo sequencing using DirecTag algorithm does no work.

What version of the product are you using? On what operating system?
DeNovoGUI 1.4.6 for windows.

Please provide any additional information below.

Original issue reported on code.google.com by [email protected] on 27 Aug 2014 at 12:34

Attachments:

• Captura.PNG

Exporting tag matches fails

I get an error message when I'm trying to export tag matches and the resulting output file is empty except for the header line.

The following stack trace is reported in the log file:

java.lang.NullPointerException
	at com.compomics.util.experiment.massspectrometry.SpectrumFactory.fixMgfTitle(SpectrumFactory.java:1007)
	at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getPrecursor(SpectrumFactory.java:627)
	at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getPrecursor(SpectrumFactory.java:293)
	at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getPrecursor(SpectrumFactory.java:554)
	at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getPrecursor(SpectrumFactory.java:308)
	at com.compomics.denovogui.io.TextExporter.exportTags(TextExporter.java:311)
	at com.compomics.denovogui.gui.ResultsFrame$49.run(ResultsFrame.java:2329)

The de novo identification was initially done using DeNovoGUI v1.16.0 on a Windows machine after which the identification results were imported in DeNovoGUI v1.16.0 on Mac to try to export the tag matches.

An error occured: Index: 14192, Size: 14192

Hi,

i run the software on windows platform with 30G ram, but error:

"An error occured: Index: 14192, Size: 14192"

Can't Add in Modification not Present in UniMod

What steps will reproduce the problem?
1. Attempting to add a fixed modification
2. Typing in all necessary information
3. Not being able to click OK in the new modification dialogue box.

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

I would like to make a custom modification that does not have a unimod 
accession number.  The dialogue box does not allow me to click "OK" and add the 
modification.

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

This is on denovoGUI1.3.4 on Windows 7 (64 bit)

Please provide any additional information below.

Attached is a screen 

Original issue reported on code.google.com by [email protected] on 3 Apr 2014 at 3:15

Attachments:

• AMCA.png

Peptide match: missing results

What steps will reproduce the problem?
1. Run peptide match (cutoff >100 for 1 peptide sequence per spectrum)
2. Run mouse Fasta DB


What is the expected output? What do you see instead?
I expected to see the results (peptide matches) in the .txt file, but instead 
see an empty file (just the column headers!) 

What version of the product are you using? On what operating system?
1.3.6 on Windows 7 64bit

Please provide any additional information below.
No error was genetated in the bug report

Original issue reported on code.google.com by [email protected] on 9 Apr 2014 at 7:10

max number of sequences / amino acids in fasta DB

I got an error while doing the export of Peptide matches using a rather large fasta DB. Regretfully I don't have the log, but the error mentioned that there were too many sequences / amino acids in my database. Is this a memory issue or is there in general a max of sequences / amino acids that can be matched? I used Novor

An error occured: Index: 2, Size: 2.

Hi All,

I am loading an mgf file converted from a .wiff (from a 5600+) through 
MSConvert with peakpicking and using the default parameters. After the search 
completes the results are starting to load when this error appears:

An error occured: Index: 2, Size: 2.
If the problem persists, contact etc.

This happens every time with this file. It doesn't happen on another replicate 
from the batch, however. What is wrong, and how can I work around it? Are there 
settings I can alter to avoid seeing this?

Best regards,
Matt



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

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.

Original issue reported on code.google.com by [email protected] on 24 Mar 2015 at 2:02

DeNovoGUI 1.7.0 An error occured: No amino acid found for letter *. when exporting Peptide matches

Hi,
DeNovoGUI 1.7.0 Throws "error occured: No amino acid found for letter *." when exporting Peptide matches. I have never gotten this function to work in any ver. of the SW.

Love all the SW you guys are putting out there for the community.

De novo database matching fails

What steps will reproduce the problem?
1. Database mapping of de novo results
2.
3.

What is the expected output? What do you see instead?
Matches between fasta file and de novo results.  No amino acid sequence longer 
than 3 was found for tag W.

What version of the product are you using? On what operating system?
1.1.12

Please provide any additional information below.

none

Original issue reported on code.google.com by [email protected] on 11 Feb 2015 at 12:30

Incorporating PepNovo RankScore?

(Transferred from https://groups.google.com/forum/#!topic/denovogui/tk8XCRWXQ2A)

For some time now, PepNovo+ has included a rank score for ranking PSMs in addition to the PepNovo score. This score, as detailed in Frank (2009), is significantly better at selecting between PSMs for a given spectrum. Currently DeNovoGUI ranks PepNovo+ results within each spectrum by PepNovo Score, not by the Rank Score. As it is now, this can result in top-ranking PSMs being excluded from results files if one is exporting fewer PSMs to a text file than were returned by the search. In the attached example, exporting the top 5 matches/spectrum would exclude the best match (by Rank Score criteria) for this spectrum.

Would you consider either 1) ranking (the "Rank" field in DeNovo GUI) PSMs within spectra by Rank Score, the better criterion, rather than PepNovo score as is done currently or 2) passing on the rank score index from .out files ("#Index") to DeNovoGUI as a separate field in addition to the current DeNovoGUI ranking? It would be helpful to have some sort of embedded ranking index based on Rank Score for each spectrum instead of/in addition to the PepNovo Score-based indexing currently present.

This is just a suggestion for a new feature if you are willing. DeNovoGUI works great as it is, but this kind of feature would save me a lot of time downstream, as I have been using Rank Score to select matches.

Thanks,
Adriana

Unable to add custom modification

Hi,

I would like to add TMTpro 16-plex and a custom modification. I was able to add them as user-modifications and save them into user modifications.txt file. But I did not find a way to add the user modifications into the default modification list, how do I do that? version (DeNovoGUI 1.16.8)

Thank you very much!!

Cannot download

Hi,

I am wondering why the DeNoveGUI is unable to be downloaded?

Thank you,

Chen

Export values

When exporting the Novor score and other values are not exported along. It would be helpful to have these values in the export as well!

Thanks,
An

pepnovo+ parameters

What steps will reproduce the problem?
1. unable to edit pepnovo + configuration settings in version 1.5.1
2.
3.

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.

Original issue reported on code.google.com by [email protected] on 8 Jul 2015 at 11:03

pNovo+ license expired

The license of pNovo+ seemingly expired with the new year.
Are you in planning to release an updated version of DenovoGUI with renewed license of pNovo+?

While it was still working I also had some issues with pNovo+ stopping to work during analysis of certain files, where i couldn't really pinpoint to where the error might come from, as it occured just in some files of the same batch.
I will try to reproduce that once the license is renewed, but anyway I guess in that case it would be better to contact the pNovo+ developers directly.

Other than that I want to thank you for your great work and constant improvements!

An error occured: Table/View 'NIST_digest.mgf_assumptions' already exists in Schema 'APP'. If the problem persists, please contact the developers.

What steps will reproduce the problem?
1. Trying to export peptide list, after choosing DB and pressing OK
2.
3.

What is the expected output? What do you see instead? A txt file matching to 
the DB.


What version of the product are you using? On what operating system?
1.5.2

Please provide any additional information below.

W7 machine

Original issue reported on code.google.com by [email protected] on 22 Jul 2015 at 4:19

• Merged into: #20

Error when saving settings

What steps will reproduce the problem?
1. Error when saving settings, even when using default settings
2.
3.

What is the expected output? What do you see instead?
Settings should be saved to path provided,however, instead a previously 
established path (not present on the computer) is called and cannot be found

What version of the product are you using? On what operating system?
DeNovoGUI1.2.3(?); Windows 7 64-bit

Please provide any additional information below.
see attached screenshot

Original issue reported on code.google.com by [email protected] on 13 Mar 2014 at 9:59

Attachments:

• DeNovoGUI_params.JPG

unable to decrease or increase the size of the denovo parameters, cursor options absent

What steps will reproduce the problem?
1. during declaration of denovo settings
2. window size is more than the screen size
3. all the window can be moved, unable to resize/ scroll down the settings 
window for saving the settings

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


What version of the product are you using? On what operating system?
denovo gui 1.5.0

Please provide any additional information below.

Original issue reported on code.google.com by [email protected] on 3 Jul 2015 at 8:55

Novor column empty

No scores show up in Novor column, is it because it needs to be licensed?

Suggestion: Score cut-off and 'top N-sequences' for Peptide Search (Beta)

What steps will reproduce the problem?

No real problem, just a suggestion. It would be nice to add a score cut-off 
threshold and 'top n-sequences' for the new Peptide Search (Beta), just like 
the Blast option has included. This would considerably reduce search times and 
file sizes,

Thanks!

Alex

Original issue reported on code.google.com by [email protected] on 3 Apr 2014 at 7:02

Contaminant list

Hi, is there an option to filter common contaminants from the results on DenovoGUI?

DeNovoGUI1.4.12 running DirecTag only, with supplied test data and parameters, gives DirecTag error on OSX Yosemite system

What steps will reproduce the problem?

1. Install DeNovoGUI 1.4.12 on macbook pro with OSX Yosemite/16GB RAM/Java for 
OSX 2014-001, load Ecoli_30.mgf, denovo.parameters
2. click Start Sequencing!
3. starts, loads spectra ok, processes .mgf ok, then "An error occured running 
DirecTag. See error log for details. null Sequencing Canceled. De Novo 
Sequencing Canceled!"

Please provide any additional information below.

Bug Report:
Fri Mar 06 13:27:41 EST 2015: DeNovoGUI version 1.4.12.
java.lang.NullPointerException  at 
com.compomics.denovogui.execution.jobs.DirecTagJob.initJob(DirecTagJob.java:93) 
at 
com.compomics.denovogui.execution.jobs.DirecTagJob.<init>(DirecTagJob.java:79)
    at com.compomics.denovogui.DeNovoSequencingHandler.startSequencing(DeNovoSequencingHandler.java:277)
    at com.compomics.denovogui.DeNovoSequencingHandler.startSequencing(DeNovoSequencingHandler.java:183)
    at com.compomics.denovogui.gui.DeNovoGUI$SequencingWorker.doInBackground(DeNovoGUI.java:1774)
    at javax.swing.SwingWorker$1.call(SwingWorker.java:295)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at javax.swing.SwingWorker.run(SwingWorker.java:334)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)

Original issue reported on code.google.com by [email protected] on 6 Mar 2015 at 6:54

PepNovo doesn't apply fixed modifications correctly

In PepNovo results generated with DeNovo GUI (latest version), fixed modifications are applied like variable modifications and only show up some of the time, despite being specified as fixed. For example, in the results below (from the PepNovo .out file), which was run with parameters specifying the fixed modifications n-terminal dimethylation and carbamidomethylated cysteine, many spectra show up with sequences containing neither. With these specifications, every single result should have the dimethylation and every cysteine should be modified.

Modifications worked as expected for a Novor analysis run in the same session (same spectra and settings files). I'm wondering if there is a bug in how the GUI passes on modification info to PepNovo.

Non-application of fixed modifications:

>> 0 9747 File: "D:\Orbitrap data\2015\10-Oct2015\16Oct2015\DvH1-IPTL-18Oto16O-Oct16-6.raw"; SpectrumID: "2878"; scans: "9747" (SQS 0.996)
#Index	RnkScr	PnvScr	N-Gap	C-Gap	[M+H]	Charge	Sequence
0	-1.215	68.328	275.094	0.000	1317.678	2	TSHTCVPLK
1	-1.710	68.424	293.198	0.000	1317.678	2	SSHELNPLK
2	-1.929	71.508	188.052	0.000	1317.678	2	STSHTCVPLK
3	-1.947	75.181	293.198	0.000	1317.678	2	SSHEAGVPLK
4	-2.058	71.230	248.153	0.000	1317.678	2	QSHTCVPLK
5	-2.204	68.000	188.052	0.000	1317.678	2	CVELGDVPLK
6	-2.414	68.999	0.000	0.000	1317.678	2	STSTAELDRPLK
7	-2.420	20.453	345.160	0.000	1314.683	2	VFTLTEQM
8	-2.470	22.932	345.160	0.000	1314.683	2	VFTTLEQM
9	-2.513	74.233	275.094	0.000	1317.678	2	TAELGDVPLK

Inconsistent application of fixed modifications:

>> 0 9750 File: "D:\Orbitrap data\2015\10-Oct2015\16Oct2015\DvH1-IPTL-18Oto16O-Oct16-6.raw"; SpectrumID: "2880"; scans: "9750" (SQS 0.676)
#Index	RnkScr	PnvScr	N-Gap	C-Gap	[M+H]	Charge	Sequence
0	0.249	-21.184	130.600	0.000	1320.584	3	AMAGSFYCQR
1	0.078	-21.314	130.600	0.000	1320.584	3	AMASGFYCQR
2	-0.068	-24.494	130.600	0.000	1320.584	3	AMAGSFYCKR
3	-2.339	23.939	0.000	0.000	1323.580	3	AACTVADATGSGSR
4	-2.356	33.587	0.000	0.000	1323.580	3	Q^+28EEHHATGGSSR
5	-2.510	33.238	0.000	0.000	1323.580	3	Q^+28EEHHATGSGSR
6	-2.543	22.780	0.000	0.000	1323.580	3	N^+28CTVADATGVCK
7	-2.547	17.589	0.000	0.000	1323.580	3	ADVEHHACAASR
8	-2.556	17.626	0.000	0.000	1323.580	3	AVDEHHACAASR
9	-2.595	27.553	0.000	0.000	1323.580	3	Y^+28DVPADACTQR