Testing of SearchGUI-1.23.0 and PeptideShaker-0.35.2 (outside GalaxyP)
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Pratik Jagtap
Nov 16, 2014, 9:05:57 PM11/16/14
to Galaxy for Proteomics, Marc Vaudel, harald.barsnes, Candace Guerrero, Timothy Griffin
Hello Harald and Marc,
I tested two MGF files against a target-decoy version of Human UniProt database using the latest versions of SearchGUI and PeptideShaker and received the following message:
The PeptideShaker processing failed (see log file in red below). It says - no identifications retained. Is there something wrong in the way I am setting up searches or connectivity (all of these files are on the same PC).
I have copied Candace on this so that she can see how her tests work with the new version. Once we have a working version for features that we are looking for - we will ask Ira or Bjoern to wrap it for GalaxyP testing.
Thanks,
Pratik
# ------------------------------------------------------------------
# SearchGUI 1.23.0 Report File
#
# Originally saved by: pjagtap @ UMN201557439
# on: 16 Nov 2014, 19:57
# as: SearchGUI Report 2014-11-16 07.57.28.html
# ------------------------------------------------------------------
Sun Nov 16 19:53:56 CST 2014 Processing tgriffin_koore004_040511_patient4_control_CA_Fr1.mgf with MS-GF+.
MS-GF+ Beta (v10024) (5/9/2014)
Loading database files...
Loading database finished (elapsed time: 13.47 sec)
Reading spectra...
Ignoring 0 profile spectra.
Ignoring 6 spectra having less than 10 peaks.
Reading spectra finished (elapsed time: 13.70 sec)
Using 1 thread.
Search Parameters:
PrecursorMassTolerance: 10.0ppm
IsotopeError: 0,1
TargetDecoyAnalysis: false
FragmentationMethod: As written in the spectrum or CID if no info
Instrument: LowRes
Enzyme: Tryp
Protocol: Standard
NumTolerableTermini: 2
MinPeptideLength: 6
MaxPeptideLength: 30
NumMatchesPerSpec: 10
Spectrum 0-324 (total: 325)
pool-1-thread-1: Preprocessing spectra...
Loading built-in param file: CID_LowRes_Tryp.param
pool-1-thread-1: Preprocessing spectra finished (elapsed time: 1.00 sec)
pool-1-thread-1: Database search...
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pool-1-thread-1: Database search finished (elapsed time: 17.00 sec)
pool-1-thread-1: Computing spectral E-values...
pool-1-thread-1: Computing spectral E-values finished (elapsed time: 1.00 sec)
Writing results...
Writing results finished (elapsed time: 0.93 sec)
MS-GF+ complete (total elapsed time: 35.21 sec)
Sun Nov 16 19:54:32 CST 2014 MS-GF+ Process Finished.
Sun Nov 16 19:54:32 CST 2014 Processing tgriffin_koore004_040511_patient4_control_CA_Fr2.mgf with MS-GF+.
MS-GF+ Beta (v10024) (5/9/2014)
Loading database files...
Loading database finished (elapsed time: 12.52 sec)
Reading spectra...
Ignoring 0 profile spectra.
Ignoring 18 spectra having less than 10 peaks.
Reading spectra finished (elapsed time: 13.24 sec)
Using 3 threads.
Search Parameters:
PrecursorMassTolerance: 10.0ppm
IsotopeError: 0,1
TargetDecoyAnalysis: false
FragmentationMethod: As written in the spectrum or CID if no info
Instrument: LowRes
Enzyme: Tryp
Protocol: Standard
NumTolerableTermini: 2
MinPeptideLength: 6
MaxPeptideLength: 30
NumMatchesPerSpec: 10
Spectrum 0-3168 (total: 3169)
pool-1-thread-3: Preprocessing spectra...
Loading built-in param file: CID_LowRes_Tryp.param
pool-1-thread-2: Preprocessing spectra...
pool-1-thread-1: Preprocessing spectra...
pool-1-thread-3: Preprocessing spectra finished (elapsed time: 5.00 sec)
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pool-1-thread-2: Database search progress... 99.7% complete
pool-1-thread-2: Database search finished (elapsed time: 21.00 sec)
pool-1-thread-2: Computing spectral E-values...
pool-1-thread-3: Database search progress... 94.0% complete
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pool-1-thread-3: Database search finished (elapsed time: 21.00 sec)
pool-1-thread-3: Computing spectral E-values...
pool-1-thread-1: Database search progress... 99.7% complete
pool-1-thread-1: Database search finished (elapsed time: 21.00 sec)
pool-1-thread-1: Computing spectral E-values...
pool-1-thread-2: Computing spectral E-values... 94.7% complete
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pool-1-thread-2: Computing spectral E-values finished (elapsed time: 11.00 sec)
pool-1-thread-3: Computing spectral E-values finished (elapsed time: 11.00 sec)
pool-1-thread-1: Computing spectral E-values... 94.6% complete
pool-1-thread-1: Computing spectral E-values finished (elapsed time: 11.00 sec)
Writing results...
Writing results finished (elapsed time: 3.91 sec)
MS-GF+ complete (total elapsed time: 56.88 sec)
Sun Nov 16 19:55:29 CST 2014 MS-GF+ Process Finished.
Sun Nov 16 19:55:29 CST 2014 Processing tgriffin_koore004_040511_patient4_control_CA_Fr3.mgf with MS-GF+.
MS-GF+ Beta (v10024) (5/9/2014)
Loading database files...
Loading database finished (elapsed time: 13.21 sec)
Reading spectra...
Ignoring 0 profile spectra.
Ignoring 2 spectra having less than 10 peaks.
Reading spectra finished (elapsed time: 15.49 sec)
Using 6 threads.
Search Parameters:
PrecursorMassTolerance: 10.0ppm
IsotopeError: 0,1
TargetDecoyAnalysis: false
FragmentationMethod: As written in the spectrum or CID if no info
Instrument: LowRes
Enzyme: Tryp
Protocol: Standard
NumTolerableTermini: 2
MinPeptideLength: 6
MaxPeptideLength: 30
NumMatchesPerSpec: 10
Spectrum 0-6042 (total: 6043)
pool-1-thread-2: Preprocessing spectra...
Loading built-in param file: CID_LowRes_Tryp.param
pool-1-thread-5: Preprocessing spectra...
pool-1-thread-6: Preprocessing spectra...
pool-1-thread-4: Preprocessing spectra...
pool-1-thread-3: Preprocessing spectra...
pool-1-thread-1: Preprocessing spectra...
pool-1-thread-2: Preprocessing spectra finished (elapsed time: 11.00 sec)
pool-1-thread-2: Database search...
pool-1-thread-2: Database search progress... 0.0% complete
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pool-1-thread-3: Database search progress... 85.5% complete
pool-1-thread-2: Database search progress... 85.5% complete
pool-1-thread-1: Database search progress... 82.6% complete
pool-1-thread-4: Database search progress... 85.5% complete
pool-1-thread-5: Database search progress... 76.9% complete
pool-1-thread-6: Database search progress... 82.6% complete
pool-1-thread-3: Database search progress... 88.3% complete
pool-1-thread-2: Database search progress... 88.3% complete
pool-1-thread-1: Database search progress... 85.5% complete
pool-1-thread-4: Database search progress... 88.3% complete
pool-1-thread-5: Database search progress... 79.8% complete
pool-1-thread-6: Database search progress... 85.5% complete
pool-1-thread-3: Database search progress... 91.2% complete
pool-1-thread-2: Database search progress... 91.2% complete
pool-1-thread-1: Database search progress... 88.3% complete
pool-1-thread-4: Database search progress... 91.2% complete
pool-1-thread-5: Database search progress... 82.6% complete
pool-1-thread-6: Database search progress... 88.3% complete
pool-1-thread-3: Database search progress... 94.0% complete
pool-1-thread-2: Database search progress... 94.0% complete
pool-1-thread-1: Database search progress... 91.2% complete
pool-1-thread-4: Database search progress... 94.0% complete
pool-1-thread-5: Database search progress... 85.5% complete
pool-1-thread-6: Database search progress... 91.2% complete
pool-1-thread-3: Database search progress... 96.8% complete
pool-1-thread-2: Database search progress... 96.8% complete
pool-1-thread-1: Database search progress... 94.0% complete
pool-1-thread-4: Database search progress... 96.8% complete
pool-1-thread-5: Database search progress... 88.3% complete
pool-1-thread-6: Database search progress... 94.0% complete
pool-1-thread-3: Database search progress... 99.7% complete
pool-1-thread-2: Database search progress... 99.7% complete
pool-1-thread-3: Database search finished (elapsed time: 26.00 sec)
pool-1-thread-3: Computing spectral E-values...
pool-1-thread-2: Database search finished (elapsed time: 27.00 sec)
pool-1-thread-2: Computing spectral E-values...
pool-1-thread-1: Database search progress... 96.8% complete
pool-1-thread-4: Database search progress... 99.7% complete
pool-1-thread-4: Database search finished (elapsed time: 26.00 sec)
pool-1-thread-4: Computing spectral E-values...
pool-1-thread-6: Database search progress... 96.8% complete
pool-1-thread-5: Database search progress... 91.2% complete
pool-1-thread-1: Database search progress... 99.7% complete
pool-1-thread-1: Database search finished (elapsed time: 27.00 sec)
pool-1-thread-1: Computing spectral E-values...
pool-1-thread-6: Database search progress... 99.7% complete
pool-1-thread-6: Database search finished (elapsed time: 27.00 sec)
pool-1-thread-6: Computing spectral E-values...
pool-1-thread-5: Database search progress... 94.0% complete
pool-1-thread-5: Database search progress... 96.8% complete
pool-1-thread-5: Database search progress... 99.7% complete
pool-1-thread-5: Database search finished (elapsed time: 27.00 sec)
pool-1-thread-5: Computing spectral E-values...
pool-1-thread-1: Computing spectral E-values... 99.2% complete
pool-1-thread-1: Computing spectral E-values finished (elapsed time: 7.00 sec)
pool-1-thread-3: Computing spectral E-values... 99.3% complete
pool-1-thread-3: Computing spectral E-values finished (elapsed time: 8.00 sec)
pool-1-thread-2: Computing spectral E-values... 99.3% complete
pool-1-thread-2: Computing spectral E-values finished (elapsed time: 8.00 sec)
pool-1-thread-4: Computing spectral E-values... 99.3% complete
pool-1-thread-4: Computing spectral E-values finished (elapsed time: 8.00 sec)
pool-1-thread-6: Computing spectral E-values... 99.3% complete
pool-1-thread-6: Computing spectral E-values finished (elapsed time: 9.00 sec)
pool-1-thread-5: Computing spectral E-values... 99.3% complete
pool-1-thread-5: Computing spectral E-values finished (elapsed time: 9.00 sec)
Writing results...
Writing results finished (elapsed time: 6.24 sec)
MS-GF+ complete (total elapsed time: 72.00 sec)
Sun Nov 16 19:56:41 CST 2014 MS-GF+ Process Finished.
Sun Nov 16 19:56:41 CST 2014 Zipping output files.
Sun Nov 16 19:56:44 CST 2014 Processing identification files with PeptideShaker.
Sun Nov 16 19:57:28 CST 2014 PeptideShaker processing canceled. See the PeptideShaker log for details.
Sun Nov 16 19:57:28 CST 2014 Search Canceled!
Sun Nov 16 19:57:28 CST 2014 The search or post-processing did not finish properly!
Report:# ------------------------------------------------------------------ # PeptideShaker 0.35.2 Report File # # Originally saved by: pjagtap @ UMN201557439 # on: 16 Nov 2014, 19:57 # ------------------------------------------------------------------ Sun Nov 16 19:56:44 CST 2014 Unzipping searchgui_out.zip. Sun Nov 16 19:56:46 CST 2014 Import process for Test (Sample: Test, Replicate: 0) Sun Nov 16 19:56:46 CST 2014 Importing sequences from Human_UniProt_Isoform_database_with_contaminants_11162014_concatenated_target_decoy.fasta. Sun Nov 16 19:56:49 CST 2014 FASTA file import completed. Sun Nov 16 19:56:49 CST 2014 Establishing local database connection. Sun Nov 16 19:56:51 CST 2014 Reading identification files. Sun Nov 16 19:56:51 CST 2014 Parsing tgriffin_koore004_040511_patient4_control_CA_Fr1.msgf.mzid. Sun Nov 16 19:56:53 CST 2014 Loading spectra for tgriffin_koore004_040511_patient4_control_CA_Fr1.msgf.mzid. Sun Nov 16 19:56:53 CST 2014 Importing tgriffin_koore004_040511_patient4_control_CA_Fr1.mgf Sun Nov 16 19:56:53 CST 2014 tgriffin_koore004_040511_patient4_control_CA_Fr1.mgf imported. Sun Nov 16 19:56:53 CST 2014 Mapping peptides to proteins. Sun Nov 16 19:56:53 CST 2014 No current connection. Sun Nov 16 19:56:53 CST 2014 Please contact the developers (http://code.google.com/p/peptide-shaker/issues/list). Sun Nov 16 19:56:53 CST 2014 Importing PSMs from tgriffin_koore004_040511_patient4_control_CA_Fr1.msgf.mzid Sun Nov 16 19:56:53 CST 2014 Parsing tgriffin_koore004_040511_patient4_control_CA_Fr2.msgf.mzid. Sun Nov 16 19:57:05 CST 2014 Loading spectra for tgriffin_koore004_040511_patient4_control_CA_Fr2.msgf.mzid. Sun Nov 16 19:57:05 CST 2014 Importing tgriffin_koore004_040511_patient4_control_CA_Fr2.mgf Sun Nov 16 19:57:05 CST 2014 tgriffin_koore004_040511_patient4_control_CA_Fr2.mgf imported. Sun Nov 16 19:57:05 CST 2014 Mapping peptides to proteins. Sun Nov 16 19:57:05 CST 2014 Importing PSMs from tgriffin_koore004_040511_patient4_control_CA_Fr2.msgf.mzid Sun Nov 16 19:57:06 CST 2014 Parsing tgriffin_koore004_040511_patient4_control_CA_Fr3.msgf.mzid. Sun Nov 16 19:57:27 CST 2014 Loading spectra for tgriffin_koore004_040511_patient4_control_CA_Fr3.msgf.mzid. Sun Nov 16 19:57:27 CST 2014 Importing tgriffin_koore004_040511_patient4_control_CA_Fr3.mgf Sun Nov 16 19:57:27 CST 2014 tgriffin_koore004_040511_patient4_control_CA_Fr3.mgf imported. Sun Nov 16 19:57:27 CST 2014 Mapping peptides to proteins. Sun Nov 16 19:57:28 CST 2014 Importing PSMs from tgriffin_koore004_040511_patient4_control_CA_Fr3.msgf.mzid Sun Nov 16 19:57:28 CST 2014 No identifications retained. Sun Nov 16 19:57:28 CST 2014 Importing Data Canceled!
Pratik Jagtap,
Managing Director,
Center for Mass Spectrometry and Proteomics,
43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108
1479 Gortner Avenue
St. Paul, MN 55108
Phone: 612-624-9275
Marc Vaudel
Nov 17, 2014, 4:33:28 AM11/17/14
to Pratik Jagtap, Galaxy for Proteomics, harald.barsnes, Candace Guerrero, Timothy Griffin
Dear Pratik,
In order to map peptides to proteins we use an index of the database and it seems that the connection to this index was dropped during processing. Were you working on a server or a computer with specific restrictions?
Can you start PeptideShaker, go to "Help and Settings" -> "Bug Report" and send me the log file you will find there?
Can you start PeptideShaker, go to "Help and Settings" -> "Bug Report" and send me the log file you will find there?
Thank you and sorry for the inconvenience,
Marc
Pratik Jagtap
Nov 17, 2014, 12:08:12 PM11/17/14
to Marc Vaudel, Galaxy for Proteomics, Candace Guerrero
Hello Marc,
Thanks for your reply.
Please see my answers:
> Were you working on a server or a computer with specific restrictions?
I do not think so - but if any log files indicate anything - I can have the restrictions changed.
> Can you start PeptideShaker, go to "Help and Settings" -> "Bug Report" and send me the log file you will find there?
Sun Nov 16 19:56:44 CST 2014: PeptideShaker version 0.35.2.
Memory given to the Java virtual machine: 3817865216.
Total amount of memory in the Java virtual machine: 129499136.
Free memory: 105009128.
Java version: 1.7.0_71.
java.sql.SQLNonTransientConnectionException: No current connection.
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.noCurrentConnection(Unknown Source)
at org.apache.derby.impl.jdbc.EmbedConnection.checkIfClosed(Unknown Source)
at org.apache.derby.impl.jdbc.EmbedConnection.createStatement(Unknown Source)
at org.apache.derby.impl.jdbc.EmbedConnection.createStatement(Unknown Source)
at com.compomics.util.db.ObjectsDB.retrieveObjectSynchronized(ObjectsDB.java:723)
at com.compomics.util.db.ObjectsDB.retrieveObject(ObjectsDB.java:677)
at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory.getNode(ProteinTreeComponentsFactory.java:227)
at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.getNodeSynchronized(ProteinTree.java:1428)
at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.getNode(ProteinTree.java:1407)
at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.getProteinMapping(ProteinTree.java:1008)
at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.getProteinMapping(ProteinTree.java:934)
at com.compomics.util.experiment.biology.Peptide.getParentProteins(Peptide.java:341)
at com.compomics.util.experiment.biology.Peptide.getParentProteins(Peptide.java:281)
at com.compomics.util.experiment.biology.Peptide.getParentProteins(Peptide.java:317)
at eu.isas.peptideshaker.protein_inference.PeptideMapper.mapPeptide(PeptideMapper.java:244)
at eu.isas.peptideshaker.protein_inference.PeptideMapper.access$200(PeptideMapper.java:27)
at eu.isas.peptideshaker.protein_inference.PeptideMapper$PeptideListMapperRunnable.run(PeptideMapper.java:294)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
Caused by: java.sql.SQLException: No current connection.
at org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source)
at org.apache.derby.impl.jdbc.SQLExceptionFactory40.wrapArgsForTransportAcrossDRDA(Unknown Source)
... 25 more
java.sql.SQLNonTransientConnectionException: No current connection.
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.noCurrentConnection(Unknown Source)
at org.apache.derby.impl.jdbc.EmbedConnection.checkIfClosed(Unknown Source)
at org.apache.derby.impl.jdbc.EmbedConnection.getMetaData(Unknown Source)
at com.compomics.util.db.ObjectsDB.hasTable(ObjectsDB.java:220)
at com.compomics.util.db.ObjectsDB.saveLongKeys(ObjectsDB.java:1074)
at com.compomics.util.db.ObjectsDB.close(ObjectsDB.java:1104)
at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory.close(ProteinTreeComponentsFactory.java:149)
at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.close(ProteinTree.java:1466)
at com.compomics.util.experiment.identification.SequenceFactory.closeFile(SequenceFactory.java:844)
at com.compomics.util.experiment.identification.SequenceFactory.clearFactory(SequenceFactory.java:138)
at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:531)
at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:158)
at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:229)
at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:649)
at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:162)
at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:937)
Caused by: java.sql.SQLException: No current connection.
at org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source)
at org.apache.derby.impl.jdbc.SQLExceptionFactory40.wrapArgsForTransportAcrossDRDA(Unknown Source)
... 19 more
Thank you very much,
Pratik
Pratik Jagtap,
Managing Director,
Center for Mass Spectrometry and Proteomics,
43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108
1479 Gortner Avenue
St. Paul, MN 55108
Phone: 612-624-9275
Marc Vaudel
Nov 17, 2014, 3:23:51 PM11/17/14
to Pratik Jagtap, Galaxy for Proteomics, Candace Guerrero
Hi Pratik,
The information in the log confirms that the connection to the fasta file index was broken. The part which puzzles me is that the connection was dropped in the middle of the processing, everything was fine when starting the import. Can it be that another instance of PeptideShaker was working on the same fasta file and closed in the meantime? The database we use in the back-end can become unstable in such cases.
Can you try to reboot your computer and start the PeptideShaker process again? You don't need to rerun ms-gf+ and can simply go to "create project" and provide the searchgui_out.zip file contained in your output folder under "identification files". If this does not work or if you encounter further issues, the best would be to have a short skype and get these things sorted together.
Sorry again for the inconvenience,
Marc
Pratik Jagtap
Nov 17, 2014, 5:01:34 PM11/17/14
to Marc Vaudel, Galaxy for Proteomics, Candace Guerrero
Hello Marc,
It failed again - but with a new error (See below). In particular, I tried to upload a SearchGUI-1.23.0 search to a PeptideShaker-0.35.3 (not .2) and got an error that Protein not found: K1M1_SHEEP_REVERSED. (seems to be a contaminant protein). Should I rerun again and test?
- Pratik
Mon Nov 17 15:32:05 CST 2014 Import process for Test (Sample: Test, Replicate: 0)
Mon Nov 17 15:32:06 CST 2014 Importing sequences from Human_UniProt_Isoform_database_with_contaminants_11162014_concatenated_target_decoy.fasta.
Mon Nov 17 15:32:50 CST 2014 FASTA file import completed.
Mon Nov 17 15:32:50 CST 2014 Establishing local database connection.
Mon Nov 17 15:32:51 CST 2014 Reading identification files.
Mon Nov 17 15:32:51 CST 2014 Parsing tgriffin_koore004_040511_patient4_control_CA_Fr1.msgf.mzid.
Mon Nov 17 15:32:53 CST 2014 Loading spectra for tgriffin_koore004_040511_patient4_control_CA_Fr1.msgf.mzid.
Mon Nov 17 15:32:53 CST 2014 Importing tgriffin_koore004_040511_patient4_control_CA_Fr1.mgf
Mon Nov 17 15:32:53 CST 2014 tgriffin_koore004_040511_patient4_control_CA_Fr1.mgf imported.
Mon Nov 17 15:32:53 CST 2014 Mapping peptides to proteins.
Mon Nov 17 15:33:35 CST 2014 Importing PSMs from tgriffin_koore004_040511_patient4_control_CA_Fr1.msgf.mzid
Mon Nov 17 15:33:35 CST 2014 Parsing tgriffin_koore004_040511_patient4_control_CA_Fr2.msgf.mzid.
Mon Nov 17 15:33:51 CST 2014 Loading spectra for tgriffin_koore004_040511_patient4_control_CA_Fr2.msgf.mzid.
Mon Nov 17 15:33:51 CST 2014 Importing tgriffin_koore004_040511_patient4_control_CA_Fr2.mgf
Mon Nov 17 15:33:51 CST 2014 tgriffin_koore004_040511_patient4_control_CA_Fr2.mgf imported.
Mon Nov 17 15:33:51 CST 2014 Mapping peptides to proteins.
Mon Nov 17 15:33:53 CST 2014 Importing PSMs from tgriffin_koore004_040511_patient4_control_CA_Fr2.msgf.mzid
Mon Nov 17 15:38:46 CST 2014 1 PSMs (0.0%) excluded by the import filters:
Mon Nov 17 15:38:46 CST 2014 - 100.0% peptide mapping to both target and decoy.
Mon Nov 17 15:38:46 CST 2014 Parsing tgriffin_koore004_040511_patient4_control_CA_Fr3.msgf.mzid.
Mon Nov 17 15:39:09 CST 2014 Loading spectra for tgriffin_koore004_040511_patient4_control_CA_Fr3.msgf.mzid.
Mon Nov 17 15:39:09 CST 2014 Importing tgriffin_koore004_040511_patient4_control_CA_Fr3.mgf
Mon Nov 17 15:39:09 CST 2014 tgriffin_koore004_040511_patient4_control_CA_Fr3.mgf imported.
Mon Nov 17 15:39:09 CST 2014 Importing PSMs from tgriffin_koore004_040511_patient4_control_CA_Fr3.msgf.mzid
Mon Nov 17 15:50:57 CST 2014 19 PSMs (0.3%) excluded by the import filters:
Mon Nov 17 15:50:57 CST 2014 - 100.0% peptide mapping to both target and decoy.
Mon Nov 17 15:50:57 CST 2014 File import completed. 8910 first hits imported (73846 secondary) from 9563 spectra.
Mon Nov 17 15:50:57 CST 2014 [8890 first hits passed the initial filtering]
Mon Nov 17 15:50:57 CST 2014 Computing assumptions probabilities.
Mon Nov 17 15:50:57 CST 2014 Saving assumptions probabilities.
Mon Nov 17 15:51:13 CST 2014 Selecting best peptide per spectrum.
Mon Nov 17 15:51:37 CST 2014 Computing PSM probabilities.
Mon Nov 17 15:51:37 CST 2014 Scoring PTMs in PSMs (D-score and PhosphoRS)
Mon Nov 17 15:51:45 CST 2014 Thresholding PTM localizations.
Mon Nov 17 15:51:45 CST 2014 Resolving peptide inference issues.
Mon Nov 17 15:51:46 CST 2014 Saving probabilities, building peptides and proteins.
Mon Nov 17 15:51:47 CST 2014 Simplifying protein groups.
Mon Nov 17 15:51:50 CST 2014 Importing Data Canceled!
Mon Nov 17 15:51:50 CST 2014 An error occurred while loading the identification files:
Mon Nov 17 15:51:50 CST 2014 Protein not found: K1M1_SHEEP_REVERSED.
Mon Nov 17 15:51:50 CST 2014 Please see http://code.google.com/p/searchgui/wiki/DatabaseHelp.
Pratik Jagtap,
Managing Director,
Center for Mass Spectrometry and Proteomics,
43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108
1479 Gortner Avenue
St. Paul, MN 55108
Phone: 612-624-9275
Marc Vaudel
Nov 18, 2014, 3:58:47 AM11/18/14
to Pratik Jagtap, Galaxy for Proteomics, Candace Guerrero
Hi again,
Updating to the new PeptideShaker version should have no effect to that regard, we only released a fix which should make the connection to the database more stable. My best guess on this one is that the header of the contaminant is not parsed properly. Where do you get the contaminants from? Could you share your database with me so that I verify that it is indeed the problem?
Sorry again for the inconvenience. We aim at providing software which work on most setup but it seems that you have been quite unlucky. Hopefully we will get everything sorted out soon.
Marc
Pratik Jagtap
Nov 18, 2014, 7:19:28 AM11/18/14
to Marc Vaudel, Galaxy for Proteomics, Candace Guerrero
Hello Marc,
The contaminants are from the cRAP database from the gpm website.
Here is the entire history. You can download the merged database from here:
Regards,
Pratik
Pratik Jagtap,
Managing Director,
Center for Mass Spectrometry and Proteomics,
43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108
1479 Gortner Avenue
St. Paul, MN 55108
Phone: 612-624-9275
Marc Vaudel
Nov 18, 2014, 7:45:00 AM11/18/14
to Pratik Jagtap, Galaxy for Proteomics, Candace Guerrero
Hi again,
This is strange, we work with cRAP as well and tested the tools for it. I will look into it and come back to you.
Best regards,
Marc
harald.barsnes
Nov 18, 2014, 12:31:54 PM11/18/14
to gal...@umn.edu, pja...@umn.edu, cgue...@umn.edu
Hi Pratik,
The below bug has now been fixed and new versions of both SearchGUI (v1.23.2) and PeptideShaker (v0.35.4) have been released.
Note that you will have to redo the search in SearchGUI as the headers of the cRAP sequences got messed up when adding the decoy sequences, and thus simply reloading in PeptideShaker won't help.
I'd recommend deleting your current FASTA target-decoy files (and the related .fasta.cui indexing files) before retesting.
No other changes compared to the previous versions.
Best regards,
Harald
...
Pratik Jagtap
Nov 18, 2014, 12:36:48 PM11/18/14
to harald.barsnes, Galaxy for Proteomics, Candace Guerrero
Thanks - I will give that a try.
I will also see if I can set up searches with large databases (but that later - after this has worked).
Regards,
Pratik
Pratik Jagtap,
Managing Director,
Center for Mass Spectrometry and Proteomics,
43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108
1479 Gortner Avenue
St. Paul, MN 55108
Phone: 612-624-9275
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Marc Vaudel
Nov 18, 2014, 1:17:10 PM11/18/14
to Pratik Jagtap, harald.barsnes, Galaxy for Proteomics, Candace Guerrero
Hi Pratik,
As a small hint, before starting on very large database, please make sure that you give as much memory as possible to the tool, this will optimize the performance :-) You can edit the memory setting at tool startup under "Settings and Help" -> "Java Parameters" - there make sure that all the memory available on the machine can be allocated to the tool. If you encounter performance issues on your databases, please send me a benchmark dataset, I will be happy to improve the processing.
Hope the tool is happy with your database now :)
Marc
To view this discussion on the web visit https://groups.google.com/a/umn.edu/d/msgid/galaxyp/CAFMfZ42P8%3DhkzS-CFv6KK8SpQ-bWN4AOQBD%2B-q35aTXWgE_Nyw%40mail.gmail.com.
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Pratik Jagtap
Nov 18, 2014, 1:33:13 PM11/18/14
to Marc Vaudel, harald.barsnes, Galaxy for Proteomics, Candace Guerrero
First success ! I saw my first .CPS file after many days ! Thanks so much ! I am going to freeze these numbers in my brain ("SearchGUI-1.23.2" and "PeptideShaker 0.35.4"). :-)
I will follow your instructions on for large db search - later during the day.
Regards,
Pratik
Pratik Jagtap,
Managing Director,
Center for Mass Spectrometry and Proteomics,
43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108
1479 Gortner Avenue
St. Paul, MN 55108
Phone: 612-624-9275
Marc Vaudel
Nov 18, 2014, 1:45:49 PM11/18/14
to Pratik Jagtap, harald.barsnes, Galaxy for Proteomics, Candace Guerrero
Congratulations! I feel sorry that it took days. If you want to play around with the tool, you might want to select other search engines as well and see your id rate going up while results aggregate :)
Also, if you have any question on the tool usage, we will be happy to help.
Hope that you are happy with the results!
Marc
Pratik Jagtap
Nov 18, 2014, 1:53:41 PM11/18/14
to Marc Vaudel, harald.barsnes, Galaxy for Proteomics, Candace Guerrero
> Hope that you are happy with the results!
Thanks for your help. I am just testing basic features of the tool right now. I am already excited of its use when in GalaxyP.
More soon...
Thanks again.
Regards,
Pratik
Pratik Jagtap,
Managing Director,
Center for Mass Spectrometry and Proteomics,
43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108
1479 Gortner Avenue
St. Paul, MN 55108
Phone: 612-624-9275
Pratik Jagtap
Nov 19, 2014, 12:18:50 PM11/19/14
to Marc Vaudel, harald.barsnes, Galaxy for Proteomics, Candace Guerrero
Hello Marc and Harald,
With the large database search this is the error that I got with PeptideShaker:
Report:
# ------------------------------------------------------------------ # PeptideShaker 0.35.4 Report File # # Originally saved by: pjagtap @ UMN201557439 # on: 18 Nov 2014, 19:52 # ------------------------------------------------------------------ Tue Nov 18 13:41:32 CST 2014 Unzipping searchgui_out.zip. Tue Nov 18 13:41:32 CST 2014 Import process for test2 (Sample: test2, Replicate: 0) Tue Nov 18 13:41:33 CST 2014 Importing sequences from 3Frame_EnSEMBL_only_Human_UniProt_FASTA_database_04202014_concatenated_target_decoy.fasta. Tue Nov 18 13:41:43 CST 2014 Estimated import time: 11 hours. Tue Nov 18 13:41:43 CST 2014 See http://code.google.com/p/compomics-utilities/wiki/ProteinInference. Tue Nov 18 19:52:01 CST 2014 FASTA file import completed. Tue Nov 18 19:52:01 CST 2014 Establishing local database connection. Tue Nov 18 19:52:02 CST 2014 Reading identification files. Tue Nov 18 19:52:02 CST 2014 No identifications retained. Tue Nov 18 19:52:02 CST 2014 Importing Data Canceled!
Regards,
Pratik
Pratik Jagtap,
Managing Director,
Center for Mass Spectrometry and Proteomics,
43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108
1479 Gortner Avenue
St. Paul, MN 55108
Phone: 612-624-9275
Marc Vaudel
Nov 19, 2014, 12:27:24 PM11/19/14
to Pratik Jagtap, harald.barsnes, Galaxy for Proteomics, Candace Guerrero
Hi Pratik,
The good news is that you were able to index the database without issue, and you need to do that only once. The tool broke when importing the ms-gf+ file, sounds like a parsing error or a memory issue there. Can you send us the log available under "Settings & Help" -> "Bug Report" when starting the tool?
The good news is that you were able to index the database without issue, and you need to do that only once. The tool broke when importing the ms-gf+ file, sounds like a parsing error or a memory issue there. Can you send us the log available under "Settings & Help" -> "Bug Report" when starting the tool?
Best regards,
Marc
Marc
Pratik Jagtap
Nov 19, 2014, 12:31:49 PM11/19/14
to Marc Vaudel, harald.barsnes, Galaxy for Proteomics, Candace Guerrero
Hello Marc,
This is the bug report for PeptideShaker:
Tue Nov 18 12:07:48 CST 2014: PeptideShaker version 0.35.4.
Memory given to the Java virtual machine: 3817865216.
Total amount of memory in the Java virtual machine: 129499136.
Free memory: 114474728.
Java version: 1.7.0_71.
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_71
os.name: Windows 7
memory: 37.3/129.5
processors available: 8
useCommandThread: false
Exception in thread "AWT-EventQueue-0" java.lang.IllegalArgumentException: Cannot format given Object as a Number
at java.text.DecimalFormat.format(Unknown Source)
at java.text.Format.format(Unknown Source)
at javax.swing.plaf.synth.SynthTableUI$SynthTableCellRenderer.configureValue(Unknown Source)
at javax.swing.plaf.synth.SynthTableUI$SynthTableCellRenderer.getTableCellRendererComponent(Unknown Source)
at javax.swing.JTable.prepareRenderer(Unknown Source)
at javax.swing.plaf.synth.SynthTableUI.paintCell(Unknown Source)
at javax.swing.plaf.synth.SynthTableUI.paintCells(Unknown Source)
at javax.swing.plaf.synth.SynthTableUI.paint(Unknown Source)
at javax.swing.plaf.synth.SynthTableUI.update(Unknown Source)
at javax.swing.JComponent.paintComponent(Unknown Source)
at javax.swing.JComponent.paint(Unknown Source)
at javax.swing.JComponent.paintChildren(Unknown Source)
at javax.swing.JComponent.paint(Unknown Source)
at javax.swing.JViewport.paint(Unknown Source)
at javax.swing.JComponent.paintChildren(Unknown Source)
at javax.swing.JComponent.paint(Unknown Source)
at javax.swing.JComponent.paintChildren(Unknown Source)
at javax.swing.JComponent.paint(Unknown Source)
at javax.swing.JComponent.paintChildren(Unknown Source)
at javax.swing.JComponent.paint(Unknown Source)
at javax.swing.JLayeredPane.paint(Unknown Source)
at javax.swing.JComponent.paintChildren(Unknown Source)
at javax.swing.JComponent.paint(Unknown Source)
at javax.swing.JComponent.paintChildren(Unknown Source)
at javax.swing.JSplitPane.paintChildren(Unknown Source)
at javax.swing.JComponent.paint(Unknown Source)
at javax.swing.JComponent.paintChildren(Unknown Source)
at javax.swing.JComponent.paint(Unknown Source)
at javax.swing.JComponent.paintChildren(Unknown Source)
at javax.swing.JComponent.paint(Unknown Source)
at javax.swing.JLayeredPane.paint(Unknown Source)
at javax.swing.JComponent.paintChildren(Unknown Source)
at javax.swing.JComponent.paint(Unknown Source)
at javax.swing.JComponent.paintToOffscreen(Unknown Source)
at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(Unknown Source)
at javax.swing.RepaintManager$PaintManager.paint(Unknown Source)
at javax.swing.RepaintManager.paint(Unknown Source)
at javax.swing.JComponent._paintImmediately(Unknown Source)
at javax.swing.JComponent.paintImmediately(Unknown Source)
at javax.swing.RepaintManager$3.run(Unknown Source)
at javax.swing.RepaintManager$3.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source)
at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source)
at javax.swing.RepaintManager.prePaintDirtyRegions(Unknown Source)
at javax.swing.RepaintManager.access$1100(Unknown Source)
at javax.swing.RepaintManager$ProcessingRunnable.run(Unknown Source)
at java.awt.event.InvocationEvent.dispatch(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$200(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.WaitDispatchSupport$2.run(Unknown Source)
at java.awt.event.InvocationEvent.dispatch(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$200(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
Tue Nov 18 13:05:05 CST 2014: PeptideShaker version 0.35.4.
Memory given to the Java virtual machine: 3817865216.
Total amount of memory in the Java virtual machine: 129499136.
Free memory: 114462096.
Java version: 1.7.0_71.
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_71
os.name: Windows 7
memory: 36.8/129.5
processors available: 8
useCommandThread: false
Tue Nov 18 13:41:32 CST 2014: PeptideShaker version 0.35.4.
Memory given to the Java virtual machine: 3817865216.
Total amount of memory in the Java virtual machine: 129499136.
Free memory: 105165200.
Java version: 1.7.0_71.
Wed Nov 19 11:29:52 CST 2014: PeptideShaker version 0.35.4.
Memory given to the Java virtual machine: 3817865216.
Total amount of memory in the Java virtual machine: 129499136.
Free memory: 115152552.
Java version: 1.7.0_71.
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_71
os.name: Windows 7
memory: 37.0/129.5
processors available: 8
useCommandThread: false
Pratik Jagtap,
Managing Director,
Center for Mass Spectrometry and Proteomics,
43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108
1479 Gortner Avenue
St. Paul, MN 55108
Phone: 612-624-9275
Marc Vaudel
Nov 19, 2014, 1:05:23 PM11/19/14
to Pratik Jagtap, harald.barsnes, Galaxy for Proteomics, Candace Guerrero
Hi again,
This is really strange, there is nothing wrong as far as I can tell from the log file. In fact, it seems that there is no identification file at all - so no identification to load. Did the ms-gf+ search complete properly? Can you send me searchgui_out.zip located in your search result folder?
Thank you,
Marc
Pratik Jagtap
Nov 19, 2014, 1:12:24 PM11/19/14
to Marc Vaudel, harald.barsnes, Galaxy for Proteomics, Candace Guerrero
Please see below MS-GF+ report. Also this was a large db search. See attached .out report.
Tue Nov 18 13:37:00 CST 2014 Processing tgriffin_koore004_040511_patient4_control_CA_Fr1.mgf with MS-GF+.
MS-GF+ Beta (v10024) (5/9/2014) Loading database files... Creating the suffix array indexed file... Size: 349247901 AlphabetSize: 28 Suffix creation: 0.00% complete. Suffix creation: 2.86% complete. Suffix creation: 5.73% complete. Suffix creation: 8.59% complete. Suffix creation: 11.45% complete. Suffix creation: 14.32% complete. Exception in thread "main" java.lang.OutOfMemoryError: Java heap space at java.util.Arrays.copyOf(Unknown Source) at edu.ucsd.msjava.msdbsearch.CompactSuffixArray$1Bucket.add(CompactSuffixArray.java:238) at edu.ucsd.msjava.msdbsearch.CompactSuffixArray.createSuffixArrayFiles(CompactSuffixArray.java:300) at edu.ucsd.msjava.msdbsearch.CompactSuffixArray.(CompactSuffixArray.java:68) at edu.ucsd.msjava.msdbsearch.CompactSuffixArray.(CompactSuffixArray.java:87) at edu.ucsd.msjava.ui.MSGFPlus.runMSGFPlus(MSGFPlus.java:246) at edu.ucsd.msjava.ui.MSGFPlus.runMSGFPlus(MSGFPlus.java:140) at edu.ucsd.msjava.ui.MSGFPlus.main(MSGFPlus.java:78) Tue Nov 18 13:39:15 CST 2014 MS-GF+ Process Finished. Tue Nov 18 13:39:15 CST 2014 Could not find MSGF result file for tgriffin_koore004_040511_patient4_control_CA_Fr1.mgf. Tue Nov 18 13:39:15 CST 2014 Processing tgriffin_koore004_040511_patient4_control_CA_Fr2.mgf with MS-GF+. MS-GF+ Beta (v10024) (5/9/2014) Loading database files... Creating the suffix array indexed file... Size: 349247901 AlphabetSize: 28 Suffix creation: 0.00% complete. Suffix creation: 2.86% complete. Suffix creation: 5.73% complete. Suffix creation: 8.59% complete. Suffix creation: 11.45% complete. Suffix creation: 14.32% complete. Exception in thread "main" java.lang.OutOfMemoryError: Java heap space at java.util.Arrays.copyOf(Unknown Source) at edu.ucsd.msjava.msdbsearch.CompactSuffixArray$1Bucket.add(CompactSuffixArray.java:238) at edu.ucsd.msjava.msdbsearch.CompactSuffixArray.createSuffixArrayFiles(CompactSuffixArray.java:300) at edu.ucsd.msjava.msdbsearch.CompactSuffixArray.(CompactSuffixArray.java:68) at edu.ucsd.msjava.msdbsearch.CompactSuffixArray.(CompactSuffixArray.java:87) at edu.ucsd.msjava.ui.MSGFPlus.runMSGFPlus(MSGFPlus.java:246) at edu.ucsd.msjava.ui.MSGFPlus.runMSGFPlus(MSGFPlus.java:140) at edu.ucsd.msjava.ui.MSGFPlus.main(MSGFPlus.java:78) Tue Nov 18 13:41:32 CST 2014 MS-GF+ Process Finished. Tue Nov 18 13:41:32 CST 2014 Could not find MSGF result file for tgriffin_koore004_040511_patient4_control_CA_Fr2.mgf. Tue Nov 18 13:41:32 CST 2014 Zipping output files. Tue Nov 18 13:41:32 CST 2014 Processing identification files with PeptideShaker. Tue Nov 18 19:52:03 CST 2014 PeptideShaker processing canceled. See the PeptideShaker log for details. Tue Nov 18 19:52:03 CST 2014 Search Canceled! Tue Nov 18 19:52:03 CST 2014 The search or post-processing did not finish properly!
Pratik Jagtap,
Managing Director,
Center for Mass Spectrometry and Proteomics,
43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108
1479 Gortner Avenue
St. Paul, MN 55108
Phone: 612-624-9275
Marc Vaudel
Nov 19, 2014, 1:28:14 PM11/19/14
to Pratik Jagtap, harald.barsnes, Galaxy for Proteomics, Candace Guerrero
Hi again,
Indeed, ms-gf+ runs out of memory and crashes. We will contact the developer and hopefully come up with a solution. In the meantime, you might want to try other search engines. X!Tandem and Myrimatch for example are very robust and also provide higher identification rate than ms-gf+ according to our users.
Best regards,
Marc
Indeed, ms-gf+ runs out of memory and crashes. We will contact the developer and hopefully come up with a solution. In the meantime, you might want to try other search engines. X!Tandem and Myrimatch for example are very robust and also provide higher identification rate than ms-gf+ according to our users.
Best regards,
Marc
Pratik Jagtap
Nov 19, 2014, 2:31:33 PM11/19/14
to Marc Vaudel, harald.barsnes, Galaxy for Proteomics, Candace Guerrero
Thanks - I will give X!tandem and Myrimatch a try for large databases.
Regards,
Pratik
Pratik Jagtap,
Managing Director,
Center for Mass Spectrometry and Proteomics,
43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108
1479 Gortner Avenue
St. Paul, MN 55108
Phone: 612-624-9275
harald.barsnes
Nov 19, 2014, 8:49:39 PM11/19/14
to gal...@umn.edu, mva...@gmail.com, harald....@gmail.com, cgue...@umn.edu
Hi Pratik,
About the memory usage. We give MS-GF+ the same amount of memory as what is given to our tools. From the PeptideShaker log file it seems like you give PeptideShaker (and thus also SearchGUI has both tools use the same memory settings) only 4 GB of memory. For bigger databases or larger spectrum files we'd strongly recommend providing a lot more memory. Our tools should simply take longer in low memory settings, but as you can see MS-GF+ will simply stop working.
As Marc already mentioned you can edit the memory settings at tool startup via "Settings and Help" -> "Settings" -> "Java Settings" in PeptideShaker, or via "Edit" -> "Java Settings" in both SearchGUI and PeptideShaker.
If you still experience memory issues with MS-GF+ after increasing the provided memory, I'd recommend contacting Sangtae to see if there is anything he can do about this. As there is nothing we can do on our side in terms of how MS-GF+ uses the memory.
However, as Marc also mentioned, you can try some of the other search engines as most of them (with the exception of OMSSA) should work fine even when processing large databases and/or spectrum files, and are less dependent on the available memory.
Best regards,
Harald
...
Pratik Jagtap
Nov 19, 2014, 9:15:48 PM11/19/14
to harald.barsnes, Galaxy for Proteomics, Marc Vaudel, Candace Guerrero
Thanks Harald,
> For bigger databases or larger spectrum files we'd strongly recommend providing a lot more memory. As > Marc already mentioned you can edit the memory settings at tool startup via "Settings and Help" ->
> "Settings" -> "Java Settings" in PeptideShaker, or via "Edit" -> "Java Settings" in both SearchGUI and
> PeptideShaker.
How much more should I go? 8 GB ? 16 GB? Or should I try different settings?
> Our tools should simply take longer in low memory settings, but as you can see MS-GF+ will simply stop > working.
i will contact Sangtae and see whether he can help.
I will also try Myrimatch, X!tandem and other search algorithms.
I am going a step at a time - and I very much appreciate your inputs and changes. I am hoping once we have a working version for both Candace and myself - we will request Ira or Bjoern to galaxy-wrap the tool.
Thanks,
Pratik
Pratik Jagtap,
Managing Director,
Center for Mass Spectrometry and Proteomics,
43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108
1479 Gortner Avenue
St. Paul, MN 55108
Phone: 612-624-9275
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harald.barsnes
Nov 19, 2014, 11:14:45 PM11/19/14
to gal...@umn.edu, harald....@gmail.com, mva...@gmail.com, cgue...@umn.edu
Hi Pratik,
Generally, the more memory you give PeptideShaker (and I assume the same is true for MS-GF+) the quicker it will go, as this makes it possible to keep all the information in memory and thus reduces the need to read/write to the disk. So the more memory you can give these tools the better.
We run most of our heavier searches using 60 GB of memory. But most searches should run fine with a lot less memory.
And as you mention, the search settings used also has an impact. Both on the speed and the memory required. The number of variable modifications is usually the setting that has the biggest impact. But this may differ between the search engines.
Best regards,
Harald
...
Pratik Jagtap
Nov 20, 2014, 9:24:06 AM11/20/14
to harald.barsnes, Galaxy for Proteomics, Marc Vaudel, Candace Guerrero
Thanks Harald,
I will give it a try once I am back in the office.
Regards,
Pratik
Pratik Jagtap,
Managing Director,
Center for Mass Spectrometry and Proteomics,
43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108
1479 Gortner Avenue
St. Paul, MN 55108
Phone: 612-624-9275
--
You received this message because you are subscribed to the Google Groups "Galaxy for Proteomics" group.
To post to this group, send email to gal...@umn.edu.
Visit this group at http://groups.google.com/a/umn.edu/group/galaxyp/.
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Pratik Jagtap
Nov 25, 2014, 10:55:10 AM11/25/14
to harald.barsnes, Galaxy for Proteomics, Marc Vaudel, Candace Guerrero
Hello Harald,
Sorry for taking time to get back to you. I was not well last week and hence the delay.
I tried searches with MS-GF+, X!tandem and Myrimatch against a large target-decoy database after increasing the allocated memory to 16 GB on SearchGUI and PeptideShaker and here is the message I got (example of MyriMatch). I am going to try searches with smaller subset databases to see how it works.
Tue Nov 25 09:16:06 CST 2014 Processing tgriffin_koore004_040511_patient4_control_CA_Fr1.mgf with MyriMatch.
Process #0 (UMN201557439) is starting.
MyriMatch 2.2.140 (2014-4-4)
FreiCore 1.6.230 (2014-4-7)
ProteoWizard MSData 3.0.5941 (2014-3-20)
ProteoWizard Proteome 3.0.4080 (2012-11-7)
Vanderbilt University (c) 2012, D.Tabb/M.Chambers/S.Dasari
Licensed under the Apache License, Version 2.0
Could not find the default configuration file (hard-coded defaults in use).
Reading "C:\Users\pjagtap\DATA\Databases\Human_UniProt_06272014_HOMD_dynamic_12252013_Modified_concatenated_target_decoy.fasta"
Read 9760648 proteins; 65.6576 seconds elapsed.
Reading spectra from file "C:\Users\pjagtap\DATA\MGF files\tgriffin_koore004_040511_patient4_control_CA_Fr1.mgf"
Read 331 spectra with 74309 peaks; 0.163324 seconds elapsed.
Preparing 331 spectra.
Trimming spectra with less than 7 peaks.
Trimmed 4 spectra for being too sparse.
Preprocessing 327 spectra.
Finished preprocessing its spectra; 0.0329603 seconds elapsed.
Trimming spectra with less than 7 peaks.
Trimming spectra with precursors too small or large: 0 - 10000
Trimmed 0 spectra.
Finished preparing spectra; 0.0330231 seconds elapsed.
Mean original (filtered) peak count: 227 (88)
Min/max original (filtered) peak count: 7 (7) / 1060 (100)
Original (filtered) peak count at 1st/2nd/3rd quartiles: 115 (98), 226 (98), 315 (99)
Filtered out 61.2335% of peaks.
Monoisotopic mass precursor hypotheses: 1308
Average mass precursor hypotheses: 0
Min. effective peptide mass is 684.85
Max. effective peptide mass is 4832.76
Min. effective peptide length is 6
Max. effective peptide length is 30
Commencing database search on 327 spectra.
Searched 329352 of 9760648 proteins; 16501 per second, 00:00:19 elapsed, 00:09:32 remaining.
Searched 658449 of 9760648 proteins; 16494 per second, 00:00:39 elapsed, 00:09:12 remaining.
Searched 992451 of 9760648 proteins; 16574 per second, 00:00:59 elapsed, 00:08:49 remaining.
Searched 1327906 of 9760648 proteins; 16632 per second, 00:01:19 elapsed, 00:08:27 remaining.
Searched 1664228 of 9760648 proteins; 16676 per second, 00:01:39 elapsed, 00:08:06 remaining.
Searched 2000586 of 9760648 proteins; 16705 per second, 00:01:59 elapsed, 00:07:45 remaining.
Searched 2338319 of 9760648 proteins; 16736 per second, 00:02:19 elapsed, 00:07:24 remaining.
Searched 2506847 of 9760648 proteins; 16741 per second, 00:02:29 elapsed, 00:07:13 remaining.
Searched 2843571 of 9760648 proteins; 16755 per second, 00:02:49 elapsed, 00:06:53 remaining.
Searched 3181400 of 9760648 proteins; 16773 per second, 00:03:09 elapsed, 00:06:32 remaining.
Searched 3518651 of 9760648 proteins; 16784 per second, 00:03:29 elapsed, 00:06:12 remaining.
Searched 3854861 of 9760648 proteins; 16788 per second, 00:03:49 elapsed, 00:05:52 remaining.
Searched 4023003 of 9760648 proteins; 16789 per second, 00:03:59 elapsed, 00:05:42 remaining.
Searched 4359938 of 9760648 proteins; 16793 per second, 00:04:19 elapsed, 00:05:22 remaining.
Searched 4527528 of 9760648 proteins; 16791 per second, 00:04:29 elapsed, 00:05:12 remaining.
Searched 4864665 of 9760648 proteins; 16796 per second, 00:04:49 elapsed, 00:04:51 remaining.
Searched 5200021 of 9760648 proteins; 16794 per second, 00:05:09 elapsed, 00:04:32 remaining.
Searched 5369595 of 9760648 proteins; 16799 per second, 00:05:19 elapsed, 00:04:21 remaining.
Searched 5700341 of 9760648 proteins; 16786 per second, 00:05:39 elapsed, 00:04:02 remaining.
Searched 6037671 of 9760648 proteins; 16789 per second, 00:05:59 elapsed, 00:03:42 remaining.
Searched 6206091 of 9760648 proteins; 16790 per second, 00:06:09 elapsed, 00:03:32 remaining.
Searched 6534539 of 9760648 proteins; 16771 per second, 00:06:29 elapsed, 00:03:12 remaining.
Searched 6867766 of 9760648 proteins; 16766 per second, 00:06:49 elapsed, 00:02:53 remaining.
Searched 7032862 of 9760648 proteins; 16760 per second, 00:06:59 elapsed, 00:02:43 remaining.
Searched 7365703 of 9760648 proteins; 16755 per second, 00:07:19 elapsed, 00:02:23 remaining.
Searched 7699359 of 9760648 proteins; 16752 per second, 00:07:39 elapsed, 00:02:03 remaining.
Searched 7868334 of 9760648 proteins; 16754 per second, 00:07:49 elapsed, 00:01:53 remaining.
Searched 8037315 of 9760648 proteins; 16757 per second, 00:07:59 elapsed, 00:01:43 remaining.
Searched 8206030 of 9760648 proteins; 16759 per second, 00:08:09 elapsed, 00:01:33 remaining.
Searched 8540595 of 9760648 proteins; 16760 per second, 00:08:29 elapsed, 00:01:13 remaining.
Searched 8847716 of 9760648 proteins; 16706 per second, 00:08:49 elapsed, 00:00:55 remaining.
Searched 9006065 of 9760648 proteins; 16690 per second, 00:08:59 elapsed, 00:00:45 remaining.
Searched 9170331 of 9760648 proteins; 16684 per second, 00:09:09 elapsed, 00:00:35 remaining.
Searched 9336019 of 9760648 proteins; 16682 per second, 00:09:19 elapsed, 00:00:25 remaining.
Searched 9670888 of 9760648 proteins; 16684 per second, 00:09:39 elapsed, 00:00:05 remaining.
Finished database search; 586.301 seconds elapsed.
Overall stats: 9760648 proteins; 357285325 peptides; 474713452 variants; 29018772 comparisons
Writing search results to file "tgriffin_koore004_040511_patient4_control_CA_Fr1.mgf.myrimatch.mzid".
Finished file "C:\Users\pjagtap\DATA\MGF files\tgriffin_koore004_040511_patient4_control_CA_Fr1.mgf"; 586.728 seconds elapsed.
Tue Nov 25 09:26:59 CST 2014 MyriMatch Process Finished.
Tue Nov 25 09:26:59 CST 2014 Processing tgriffin_koore004_040511_patient4_control_CA_Fr2.mgf with MyriMatch.
Process #0 (UMN201557439) is starting.
MyriMatch 2.2.140 (2014-4-4)
FreiCore 1.6.230 (2014-4-7)
ProteoWizard MSData 3.0.5941 (2014-3-20)
ProteoWizard Proteome 3.0.4080 (2012-11-7)
Vanderbilt University (c) 2012, D.Tabb/M.Chambers/S.Dasari
Licensed under the Apache License, Version 2.0
Could not find the default configuration file (hard-coded defaults in use).
Reading "C:\Users\pjagtap\DATA\Databases\Human_UniProt_06272014_HOMD_dynamic_12252013_Modified_concatenated_target_decoy.fasta"
Read 9760648 proteins; 0.0326305 seconds elapsed.
Reading spectra from file "C:\Users\pjagtap\DATA\MGF files\tgriffin_koore004_040511_patient4_control_CA_Fr2.mgf"
Read 3187 spectra with 533722 peaks; 0.782982 seconds elapsed.
Preparing 3187 spectra.
Trimming spectra with less than 7 peaks.
Trimmed 11 spectra for being too sparse.
Preprocessing 3176 spectra.
Finished preprocessing its spectra; 0.249652 seconds elapsed.
Trimming spectra with less than 7 peaks.
Trimming spectra with precursors too small or large: 0 - 10000
Trimmed 1 spectra.
Finished preparing spectra; 0.249828 seconds elapsed.
Mean original (filtered) peak count: 168 (88)
Min/max original (filtered) peak count: 7 (7) / 822 (100)
Original (filtered) peak count at 1st/2nd/3rd quartiles: 107 (93), 162 (98), 217 (99)
Filtered out 47.619% of peaks.
Monoisotopic mass precursor hypotheses: 12700
Average mass precursor hypotheses: 0
Min. effective peptide mass is 686.918
Max. effective peptide mass is 6056.36
Min. effective peptide length is 6
Max. effective peptide length is 30
Commencing database search on 3175 spectra.
Searched 104820 of 9760648 proteins; 10475 per second, 00:00:10 elapsed, 00:15:22 remaining.
Searched 210707 of 9760648 proteins; 10527 per second, 00:00:20 elapsed, 00:15:07 remaining.
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Searched 2175875 of 9760648 proteins; 10356 per second, 00:03:30 elapsed, 00:12:12 remaining.
Searched 2278310 of 9760648 proteins; 10351 per second, 00:03:40 elapsed, 00:12:03 remaining.
Searched 2456104 of 9760648 proteins; 10230 per second, 00:04:00 elapsed, 00:11:54 remaining.
Searched 2547871 of 9760648 proteins; 10187 per second, 00:04:10 elapsed, 00:11:48 remaining.
Searched 2644671 of 9760648 proteins; 10167 per second, 00:04:20 elapsed, 00:11:40 remaining.
Searched 2744342 of 9760648 proteins; 10159 per second, 00:04:30 elapsed, 00:11:31 remaining.
Searched 2845401 of 9760648 proteins; 10157 per second, 00:04:40 elapsed, 00:11:21 remaining.
Searched 2942510 of 9760648 proteins; 10142 per second, 00:04:50 elapsed, 00:11:12 remaining.
Searched 3037071 of 9760648 proteins; 10119 per second, 00:05:00 elapsed, 00:11:04 remaining.
Searched 3135665 of 9760648 proteins; 10110 per second, 00:05:10 elapsed, 00:10:55 remaining.
Searched 3234727 of 9760648 proteins; 10104 per second, 00:05:20 elapsed, 00:10:46 remaining.
Searched 3436026 of 9760648 proteins; 10101 per second, 00:05:40 elapsed, 00:10:26 remaining.
Searched 3535834 of 9760648 proteins; 10098 per second, 00:05:50 elapsed, 00:10:16 remaining.
Searched 3634191 of 9760648 proteins; 10090 per second, 00:06:00 elapsed, 00:10:07 remaining.
Searched 3734563 of 9760648 proteins; 10089 per second, 00:06:10 elapsed, 00:09:57 remaining.
Searched 3936091 of 9760648 proteins; 10088 per second, 00:06:30 elapsed, 00:09:37 remaining.
Searched 4137453 of 9760648 proteins; 10087 per second, 00:06:50 elapsed, 00:09:17 remaining.
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Searched 4643630 of 9760648 proteins; 10090 per second, 00:07:40 elapsed, 00:08:27 remaining.
Searched 4743238 of 9760648 proteins; 10087 per second, 00:07:50 elapsed, 00:08:17 remaining.
Searched 4845707 of 9760648 proteins; 10091 per second, 00:08:00 elapsed, 00:08:07 remaining.
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Searched 5049742 of 9760648 proteins; 10095 per second, 00:08:20 elapsed, 00:07:47 remaining.
Searched 5149600 of 9760648 proteins; 10093 per second, 00:08:30 elapsed, 00:07:37 remaining.
Searched 5250979 of 9760648 proteins; 10093 per second, 00:08:40 elapsed, 00:07:27 remaining.
Searched 5350770 of 9760648 proteins; 10091 per second, 00:08:50 elapsed, 00:07:17 remaining.
Searched 5449967 of 9760648 proteins; 10088 per second, 00:09:00 elapsed, 00:07:07 remaining.
Searched 5550203 of 9760648 proteins; 10087 per second, 00:09:10 elapsed, 00:06:57 remaining.
Searched 5652335 of 9760648 proteins; 10089 per second, 00:09:20 elapsed, 00:06:47 remaining.
Searched 5752948 of 9760648 proteins; 10088 per second, 00:09:30 elapsed, 00:06:37 remaining.
Searched 5853553 of 9760648 proteins; 10088 per second, 00:09:40 elapsed, 00:06:27 remaining.
Searched 6049176 of 9760648 proteins; 10077 per second, 00:10:00 elapsed, 00:06:08 remaining.
Searched 6246496 of 9760648 proteins; 10070 per second, 00:10:20 elapsed, 00:05:49 remaining.
Searched 6348688 of 9760648 proteins; 10073 per second, 00:10:30 elapsed, 00:05:39 remaining.
Searched 6448754 of 9760648 proteins; 10071 per second, 00:10:40 elapsed, 00:05:29 remaining.
Searched 6542126 of 9760648 proteins; 10060 per second, 00:10:50 elapsed, 00:05:20 remaining.
Searched 6642884 of 9760648 proteins; 10060 per second, 00:11:00 elapsed, 00:05:10 remaining.
Searched 6744540 of 9760648 proteins; 10062 per second, 00:11:10 elapsed, 00:05:00 remaining.
Searched 6846478 of 9760648 proteins; 10064 per second, 00:11:20 elapsed, 00:04:50 remaining.
Searched 6943808 of 9760648 proteins; 10059 per second, 00:11:30 elapsed, 00:04:40 remaining.
Searched 7044300 of 9760648 proteins; 10059 per second, 00:11:40 elapsed, 00:04:30 remaining.
Searched 7143783 of 9760648 proteins; 10057 per second, 00:11:50 elapsed, 00:04:20 remaining.
Searched 7245438 of 9760648 proteins; 10058 per second, 00:12:00 elapsed, 00:04:10 remaining.
Searched 7344949 of 9760648 proteins; 10057 per second, 00:12:10 elapsed, 00:04:00 remaining.
Searched 7445738 of 9760648 proteins; 10057 per second, 00:12:20 elapsed, 00:03:50 remaining.
Searched 7541682 of 9760648 proteins; 10051 per second, 00:12:30 elapsed, 00:03:41 remaining.
Searched 7642014 of 9760648 proteins; 10051 per second, 00:12:40 elapsed, 00:03:31 remaining.
Searched 7743809 of 9760648 proteins; 10052 per second, 00:12:50 elapsed, 00:03:21 remaining.
Searched 7939027 of 9760648 proteins; 10045 per second, 00:13:10 elapsed, 00:03:01 remaining.
Searched 8029553 of 9760648 proteins; 10032 per second, 00:13:20 elapsed, 00:02:53 remaining.
Searched 8129810 of 9760648 proteins; 10032 per second, 00:13:30 elapsed, 00:02:43 remaining.
Searched 8228268 of 9760648 proteins; 10030 per second, 00:13:40 elapsed, 00:02:33 remaining.
Searched 8422734 of 9760648 proteins; 10022 per second, 00:14:00 elapsed, 00:02:13 remaining.
Searched 8521681 of 9760648 proteins; 10021 per second, 00:14:10 elapsed, 00:02:04 remaining.
Searched 8621841 of 9760648 proteins; 10021 per second, 00:14:20 elapsed, 00:01:54 remaining.
Searched 8820558 of 9760648 proteins; 10019 per second, 00:14:40 elapsed, 00:01:34 remaining.
Searched 8919186 of 9760648 proteins; 10017 per second, 00:14:50 elapsed, 00:01:24 remaining.
Searched 9017653 of 9760648 proteins; 10015 per second, 00:15:00 elapsed, 00:01:14 remaining.
Searched 9203528 of 9760648 proteins; 9999 per second, 00:15:20 elapsed, 00:00:56 remaining.
Searched 9301167 of 9760648 proteins; 9996 per second, 00:15:30 elapsed, 00:00:46 remaining.
Searched 9497002 of 9760648 proteins; 9992 per second, 00:15:50 elapsed, 00:00:26 remaining.
Searched 9594362 of 9760648 proteins; 9989 per second, 00:16:00 elapsed, 00:00:17 remaining.
Searched 9693199 of 9760648 proteins; 9988 per second, 00:16:10 elapsed, 00:00:07 remaining.
Finished database search; 977.919 seconds elapsed.
Overall stats: 9760648 proteins; 357285325 peptides; 474195809 variants; 610251975 comparisons
Writing search results to file "tgriffin_koore004_040511_patient4_control_CA_Fr2.mgf.myrimatch.mzid".
Finished file "C:\Users\pjagtap\DATA\MGF files\tgriffin_koore004_040511_patient4_control_CA_Fr2.mgf"; 981.208 seconds elapsed.
Tue Nov 25 09:43:21 CST 2014 MyriMatch Process Finished.
Tue Nov 25 09:43:21 CST 2014 Zipping output files.
Tue Nov 25 09:43:22 CST 2014 Processing identification files with PeptideShaker.
Tue Nov 25 09:47:03 CST 2014 PeptideShaker processing canceled. See the PeptideShaker log for details.
Tue Nov 25 09:47:04 CST 2014 Search Canceled!
Tue Nov 25 09:47:04 CST 2014 The search or post-processing did not finish properly!
PeptideShaker Log:
Tue Nov 25 09:43:23 CST 2014: PeptideShaker version 0.35.4.
Memory given to the Java virtual machine: 15270936576.
Total amount of memory in the Java virtual machine: 129499136.
Free memory: 105176432.
Tue Nov 25 09:47:29 CST 2014: PeptideShaker version 0.35.4.
Memory given to the Java virtual machine: 15270936576.
Total amount of memory in the Java virtual machine: 129499136.
Free memory: 114446856.
Java version: 1.7.0_71.
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_71
os.name: Windows 7
memory: 37.3/129.5
processors available: 8
useCommandThread: false
Pratik Jagtap,
Managing Director,
Center for Mass Spectrometry and Proteomics,
43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108
1479 Gortner Avenue
St. Paul, MN 55108
Phone: 612-624-9275
harald.barsnes
Nov 25, 2014, 1:09:25 PM11/25/14
to gal...@umn.edu, harald....@gmail.com, mva...@gmail.com, cgue...@umn.edu
Hi Pratik,
It would again seem like you have problems with the connection to the database dropping in between SearchGUI and PeptideShaker. I'm not really sure why this is happening. Could you try loading the search results manually in PeptideShaker? Simply start PeptideShaker and choose New Project, load the zip file as the identification files and try loading the data. This should give as a bit more details on what the problem is.
...
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