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Immortalin / peptide-shaker

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Custom database error #38

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
> What steps will reproduce the problem?
Using a custom database

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

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

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

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

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

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

LOG FILE***
LOG FILE

Tue Feb 04 18:57:03 CET 2014: PeptideShaker version 0.25.0.
Memory given to the Java virtual machine: 5592449024.
Total amount of memory in the Java virtual machine: 128647168.
Free memory: 115702824.
Java version: 1.7.0_21.
1714 script command tokens
(C) 2009 Jmol Development
Jmol Version: 12.0.43  2011-05-03 14:21
java.vendor: Oracle Corporation
java.version: 1.7.0_21
os.name: Windows 7
memory: 36.5/128.6
processors available: 2
useCommandThread: false

Wed Feb 05 15:08:29 EST 2014: PeptideShaker version 0.25.0.
Memory given to the Java virtual machine: 61084270592.
Total amount of memory in the Java virtual machine: 129499136.
Free memory: 114106352.
Java version: 1.7.0_45.
jshortcut.dll loaded via tmp generated pathname: 
C:\Users\phains\AppData\Local\Temp\3\jshortcut-3262724105231552420.dll
1714 script command tokens
(C) 2009 Jmol Development
Jmol Version: 12.0.43  2011-05-03 14:21
java.vendor: Oracle Corporation
java.version: 1.7.0_45
os.name: Windows Server 2012
memory: 20.2/129.5
processors available: 16
useCommandThread: false
An error occured while loading I:\MassspecCoreGroup\Search 
Engine\DB\SearchGUI\ICKP_140_seq_concatenated_target_decoy.fasta.
java.lang.NullPointerException
    at com.compomics.util.db.ObjectsDB.correctKey(ObjectsDB.java:1048)
    at com.compomics.util.db.ObjectsDB.insertObjects(ObjectsDB.java:270)
    at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory.saveProteinLengths(ProteinTreeComponentsFactory.java:264)
    at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.indexProteins(ProteinTree.java:615)
    at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.loadTags(ProteinTree.java:531)
    at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.importDb(ProteinTree.java:444)
    at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.initiateTree(ProteinTree.java:253)
    at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.initiateTree(ProteinTree.java:189)
    at com.compomics.util.experiment.identification.SequenceFactory.getDefaultProteinTree(SequenceFactory.java:1189)
    at com.compomics.util.experiment.identification.SequenceFactory.getDefaultProteinTree(SequenceFactory.java:1156)
    at eu.isas.peptideshaker.fileimport.FileImporter.importSequences(FileImporter.java:194)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:393)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:382)
    at javax.swing.SwingWorker$1.call(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at javax.swing.SwingWorker.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)

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

Original issue reported on code.google.com by snoor...@gmail.com on 5 Feb 2014 at 4:25

GoogleCodeExporter commented 9 years ago 
For custom databases is it highly recommended to use our generic database 
header format: 
http://code.google.com/p/searchgui/wiki/DatabaseHelp#Non_Standard_FASTA. The 
format of your database headers do not seem to follow these guidelines.

This results in that the reverse/decoy headers not as expected and our new 
protein inference processing fails. 

So please re-format your database headers into the generic database format and 
you should be able to use the database again.

Original comment by harald.b...@gmail.com on 5 Feb 2014 at 9:45

GoogleCodeExporter commented 9 years ago 
Yep, got it working. Sorry, I thought it was in the right format. Clearly
not...

Original comment by snoor...@gmail.com on 5 Feb 2014 at 9:28

GoogleCodeExporter commented 9 years ago

Original comment by harald.b...@gmail.com on 5 Feb 2014 at 9:30