search

compomics / peptide-shaker

Interpretation of proteomics identification results
http://compomics.github.io/projects/peptide-shaker.html
47 stars 19 forks source link

NullPointerException in Peptideshaker (searchGUI runs fine) #497

Closed lukethompson16 closed 1 year ago

lukethompson16 commented 1 year ago

I've used SearchGUI/Peptideshaker successfully several times with several datasets, but when I switched to a new database for a different organism, I have not been able to solve this issue that comes up when I move into peptideshaker.

Wed Nov 09 11:29:39 EST 2022: PeptideShaker version 2.2.17. Memory given to the Java virtual machine: 3817865216. Total amount of memory in the Java virtual machine: 128974848. Free memory: 86654120. Java version: 1.8.0_333. 1714 script command tokens (C) 2009 Jmol Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 1.8.0_333 os.name: Windows 10 memory: 62.8/163.1 processors available: 24 useCommandThread: false

Wed Nov 09 14:57:25 EST 2022: PeptideShaker version 2.2.17. Memory given to the Java virtual machine: 3817865216. Total amount of memory in the Java virtual machine: 128974848. Free memory: 85966504. Java version: 1.8.0_333. 1714 script command tokens (C) 2009 Jmol Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 1.8.0_333 os.name: Windows 10 memory: 63.1/163.1 processors available: 24 useCommandThread: false

PeptideShaker processing failed. See the PeptideShaker log for details.

java.lang.NullPointerException at com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex.addDataToIndex(FMIndex.java:1493) at com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex.init(FMIndex.java:1204) at com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex.(FMIndex.java:590) at eu.isas.peptideshaker.fileimport.FileImporter.importSequences(FileImporter.java:957) at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:219) at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:219) at eu.isas.peptideshaker.gui.NewDialog$20.run(NewDialog.java:736) at java.lang.Thread.run(Unknown Source) Free memory: 624791328

Thu Nov 10 10:28:23 EST 2022: PeptideShaker version 2.2.17. Memory given to the Java virtual machine: 3817865216. Total amount of memory in the Java virtual machine: 128974848. Free memory: 86600216. Java version: 1.8.0_333. 1714 script command tokens (C) 2009 Jmol Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 1.8.0_333 os.name: Windows 10 memory: 63.3/163.1 processors available: 24 useCommandThread: false

Thu Nov 10 11:26:30 EST 2022: PeptideShaker version 2.2.17. Memory given to the Java virtual machine: 3817865216. Total amount of memory in the Java virtual machine: 163053568. Free memory: 118720328. Java version: 1.8.0_351. 1714 script command tokens (C) 2009 Jmol Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 1.8.0_351 os.name: Windows 10 memory: 63.5/163.1 processors available: 24 useCommandThread: false

PeptideShaker processing failed. See the PeptideShaker log for details.

java.lang.NullPointerException at com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex.addDataToIndex(FMIndex.java:1493) at com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex.init(FMIndex.java:1204) at com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex.(FMIndex.java:590) at eu.isas.peptideshaker.fileimport.FileImporter.importSequences(FileImporter.java:957) at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:219) at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:219) at eu.isas.peptideshaker.gui.NewDialog$20.run(NewDialog.java:736) at java.lang.Thread.run(Unknown Source) Free memory: 604892832

Tue Nov 15 15:21:53 EST 2022: PeptideShaker version 2.2.17. Memory given to the Java virtual machine: 3817865216. Total amount of memory in the Java virtual machine: 163053568. Free memory: 118871576. Java version: 1.8.0_351. 1714 script command tokens (C) 2009 Jmol Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 1.8.0_351 os.name: Windows 10 memory: 64.0/163.1 processors available: 24 useCommandThread: false

PeptideShaker processing failed. See the PeptideShaker log for details.

java.lang.NullPointerException at com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex.addDataToIndex(FMIndex.java:1493) at com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex.init(FMIndex.java:1204) at com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex.(FMIndex.java:590) at eu.isas.peptideshaker.fileimport.FileImporter.importSequences(FileImporter.java:957) at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:219) at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:219) at eu.isas.peptideshaker.gui.NewDialog$20.run(NewDialog.java:736) at java.lang.Thread.run(Unknown Source) Free memory: 728298728

hbarsnes commented 1 year ago

Would it be possible for you to share the FASTA file so that we can try to figure out what the problem is?

lukethompson16 commented 1 year ago

Sure, FASTA is here: https://drive.google.com/file/d/1rJvoDHb6Z1FvJLTCA7mQLAjhKq3Sob3n/view?usp=sharing

hbarsnes commented 1 year ago

The problem is these two headers:

>prf||764671A vespakinin M
GRPXGFSPFRID

>prf||764671A_REVERSED vespakinin M_REVERSED
DIRFPSFGXPRG

Simply replacing "||" with "|" solves the problem.

In other words, replace the above with

>prf|764671A vespakinin M
GRPXGFSPFRID

>prf|764671A_REVERSED vespakinin M_REVERSED
DIRFPSFGXPRG

and you should be able to use the FASTA file without any issues.

lukethompson16 commented 1 year ago

Yep, that was the issue. Guess part of an annotation was missing. Works fine now.

Thanks!