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compomics / peptide-shaker

Interpretation of proteomics identification results
http://compomics.github.io/projects/peptide-shaker.html
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ReportCLI : The FASTA file was not found. Please locate it using the GUI #95

Closed cdlawless closed 8 years ago

cdlawless commented 9 years ago

Hi

Trying to get peptide/protein reports out of the PeptideShaker project. I ran a search using SearchCLI with options to zip results, mgfs etc. I then use this zip file for PeptideShaker using PeptideShakerCLI.

When I come to export reports from the PeptideShaker project files, I get the above error about the fasta file. Is there no way of telling PeptideShakerCLI where to locate the fasta file (etc.)

Regards

Craig

mvaudel commented 9 years ago

Hi Craig,

Would it be possible to share with us the different command lines used? I see nothing wrong with your setup so the files should be included in the zip package.

Best regards,

Marc

cdlawless commented 9 years ago

No problem.

SearchCLI command:

java -Xms4096M -Xmx131072m -cp /mnt/fls01-home01/mjfidcl2/scratch/SearchGUI/SearchGUI-2.0.4/SearchGUI-2.0.4.jar eu.isas.searchgui.cmd.SearchCLI -spectrum_files "/mnt/lustre/scratch/mjfidcl2 /DDIP/TimePoints/mgfs_0_2" -output_folder /mnt/lustre/scratch/mjfidcl2/DDIP/TimePoints/output_0_2/ -id_params /mnt/lustre/scratch/mjfidcl2/DDIP/TimePoints/params/GUI-2.0.4_timepoints_nophos ph.par -output_option 0 -output_data 1 -output_date 1 -mgf_splitting 2000 -temp_folder /mnt/lustre/scratch/mjfidcl2/DDIP/TimePoints/temp -xtandem 1 -msgf 1 -omssa 1 -myrimatch 1 -comet 1 -t ide 0 -ms_amanda 0 -andromeda 0 -xtandem_folder /mnt/lustre/scratch/mjfidcl2/DDIP/TimePoints/temp -myrimatch_folder /mnt/lustre/scratch/mjfidcl2/DDIP/TimePoints/temp -comet_folder /mnt/lust re/scratch/mjfidcl2/DDIP/TimePoints/temp -omssa_folder /mnt/lustre/scratch/mjfidcl2/DDIP/TimePoints/temp -msgf_folder /mnt/lustre/scratch/mjfidcl2/DDIP/TimePoints/temp

PeptideShakerCLI command:

java -Xms1024m -Xmx262144m -cp /scratch/mjfidcl2/PeptideShaker-1.0.4/PeptideShaker-1.0.4.jar eu.isas.peptideshaker.cmd.PeptideShakerCLI -experiment TP_0_2 -sample TP_0_2_sample -replicate 1 -identification_files "/scratch/mjfidcl2/DDIP/TimePoints/SearchGUI_results/outputs_0_2/2015-9-16_0.15.5_searchgui_out.zip" -out "./TP_0_2.cpsx" -ptm_score 1

ReportCLI Command: java -Xms1024m -Xmx262144m -cp /scratch/mjfidcl2/PeptideShaker-1.0.4/PeptideShaker-1.0.4.jar eu.isas.peptideshaker.cmd.ReportCLI -in "./TP_0_2.cps" -out_reports "../SearchGUI_results/output _0_2/" -reports "0,3, 4"

Craig Lawless

Postdoctoral Research Associate Faculty of Life Sciences Rm B.1071 Michael-Smith Oxford Road Manchester M13 9PT

TEL:(+44)0161 275 1680

From: Marc Vaudel [notifications@github.com] Sent: 21 October 2015 11:55 To: compomics/peptide-shaker Cc: Craig Lawless Subject: Re: [peptide-shaker] ReportCLI : The FASTA file was not found. Please locate it using the GUI (#95)

Hi Craig,

Would it be possible to share with us the different command lines used? I see nothing wrong with your setup so the files should be included in the zip package.

Best regards,

Marc

— Reply to this email directly or view it on GitHubhttps://github.com/compomics/peptide-shaker/issues/95#issuecomment-149853805.

mvaudel commented 9 years ago

Many thanks, it seems that the mgf and fasta files are not included in the PeptideShaker project. Can you try to add -zip "myPath/myFile.zip" to the PeptideShakerCLI command, and pass this file as -in "myPath/myFile.zip" to the ReportCLI command?

cdlawless commented 9 years ago

Hi Marc

I had just set that running as you replied. I will let you know that outcome.

Many thanks

Craig Lawless

Postdoctoral Research Associate Faculty of Life Sciences Rm B.1071 Michael-Smith Oxford Road Manchester M13 9PT

TEL:(+44)0161 275 1680

From: Marc Vaudel [notifications@github.com] Sent: 21 October 2015 12:23 To: compomics/peptide-shaker Cc: Craig Lawless Subject: Re: [peptide-shaker] ReportCLI : The FASTA file was not found. Please locate it using the GUI (#95)

Many thanks, it seems that the mgf and fasta files are not included in the PeptideShaker project. Can you try to add -zip "myPath/myFile.zip" to the PeptideShakerCLI command, and pass this file as -in "myPath/myFile.zip" to the ReportCLI command?

— Reply to this email directly or view it on GitHubhttps://github.com/compomics/peptide-shaker/issues/95#issuecomment-149859747.

mvaudel commented 9 years ago

Hi again,

Great, eager to know whether it worked. Please note that ReportCLI is essentially made for report generation on existing projects. You can also export the reports upon creation of the projects, for this, append the ReportCLI arguments directly to the PeptideShakerCLI. Something like:

java -Xms1024m -Xmx262144m -cp /scratch/mjfidcl2/PeptideShaker-1.0.4/PeptideShaker-1.0.4.jar eu.isas.peptideshaker.cmd.PeptideShakerCLI -experiment TP_0_2 -sample TP_0_2_sample -replicate 1
 -identification_files "/scratch/mjfidcl2/DDIP/TimePoints/SearchGUI_results/outputs_0_2/2015-9-16_0.15.5_searchgui_out.zip" -out "./TP_0_2.cpsx" -ptm_score 1 -out_reports "../SearchGUI_results/output_0_2/" -reports "0,3, 4"

You will have one less command to maintain and the generation of reports will be faster :)

Best regards,

Marc

cdlawless commented 9 years ago

Hi Marc

No success using the zip option / report output options with PeptideShakerCLI.

First the report indexes are different than those described on the ReportCLI page on github:

Github: 0: Certificate of Analysis, 1: Default Hierarchical Report, 2: Default PSM Report, 3: Default Peptide Report, 4: Default Protein Report, 5-n: Your own custom reports.

Actual: 0: Certificate of Analysis, 1: Default Hierarchical Report, 2: Default PSM Phosphorylation Report, 3: Default PSM Report, 4: Default Peptide Phosphorylation Report, 5: Default Peptide Report, 6: Default Protein Phosphorylation Report, 7: Default Protein Report

Second using the -out_reports & -reports options with PeptideShaker CLI give the following log/error: Command:

java -Xms1024m -Xmx262144m -cp /scratch/mjfidcl2/PeptideShaker-1.0.4/PeptideShaker-1.0.4.jar eu.isas.peptideshaker.cmd.PeptideShakerCLI -experiment TP_14_16 -sample TP_14_16_sample -replica te 1 -identification_files "/scratch/mjfidcl2/DDIP/TimePoints/SearchGUI_results/output_14_16/2015-9-16_14.22.23_searchgui_out.zip" -out "./TP_14_16.cpsx" -ptm_score 1 -out_reports "../Searc hGUI_results/output_14_16/" -reports "0,3, 4" -zip "./TP_14_16.zip"

Report log: Wed Oct 21 14:18:03 BST 2015 Starting report export. Wed Oct 21 14:18:03 BST 2015 Exporting. Please Wait... Wed Oct 21 14:18:03 BST 2015 An error occurred while exporting the Default PSM Report. Wed Oct 21 14:18:03 BST 2015 Exporting. Please Wait... Wed Oct 21 14:18:03 BST 2015 An error occurred while exporting the Default Peptide Phosphorylation Report.

Error log: java.sql.SQLSyntaxErrorException: Table/View '24072015_Stages_14-16h_R4.mgf_psms' does not exist. at org.apache.derby.impl.jdbc.SQLExceptionFactory40.getSQLException(Unknown Source) at org.apache.derby.impl.jdbc.Util.generateCsSQLException(Unknown Source) at org.apache.derby.impl.jdbc.TransactionResourceImpl.wrapInSQLException(Unknown Source) at org.apache.derby.impl.jdbc.TransactionResourceImpl.handleException(Unknown Source) at org.apache.derby.impl.jdbc.EmbedConnection.handleException(Unknown Source) at org.apache.derby.impl.jdbc.ConnectionChild.handleException(Unknown Source) at org.apache.derby.impl.jdbc.EmbedStatement.execute(Unknown Source) at org.apache.derby.impl.jdbc.EmbedStatement.executeQuery(Unknown Source) at com.compomics.util.db.ObjectsDB.loadObjects(ObjectsDB.java:615) at com.compomics.util.experiment.identification.IdentificationDB.loadSpectrumMatches(IdentificationDB.java:841) at com.compomics.util.experiment.identification.Identification.loadSpectrumMatches(Identification.java:241) at com.compomics.util.experiment.identification.matches_iterators.PsmIterator.checkBuffer(PsmIterator.java:262) at com.compomics.util.experiment.identification.matches_iterators.PsmIterator.next(PsmIterator.java:231) at eu.isas.peptideshaker.export.sections.PsPsmSection.writeSection(PsPsmSection.java:179) at eu.isas.peptideshaker.export.PSExportFactory.writeExport(PSExportFactory.java:300) at eu.isas.peptideshaker.cmd.CLIMethods.exportReport(CLIMethods.java:294) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:299) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1026) Caused by: java.sql.SQLException: Table/View '24072015_Stages_14-16h_R4.mgf_psms' does not exist. at org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source) at org.apache.derby.impl.jdbc.SQLExceptionFactory40.wrapArgsForTransportAcrossDRDA(Unknown Source) ... 18 more Caused by: ERROR 42X05: Table/View '24072015_Stages_14-16h_R4.mgf_psms' does not exist. at org.apache.derby.iapi.error.StandardException.newException(Unknown Source) at org.apache.derby.impl.sql.compile.FromBaseTable.bindTableDescriptor(Unknown Source) at org.apache.derby.impl.sql.compile.FromBaseTable.bindNonVTITables(Unknown Source) at org.apache.derby.impl.sql.compile.FromList.bindTables(Unknown Source) at org.apache.derby.impl.sql.compile.SelectNode.bindNonVTITables(Unknown Source) at org.apache.derby.impl.sql.compile.DMLStatementNode.bindTables(Unknown Source) at org.apache.derby.impl.sql.compile.DMLStatementNode.bind(Unknown Source) at org.apache.derby.impl.sql.compile.CursorNode.bindStatement(Unknown Source) at org.apache.derby.impl.sql.GenericStatement.prepMinion(Unknown Source) at org.apache.derby.impl.sql.GenericStatement.prepare(Unknown Source) at org.apache.derby.impl.sql.conn.GenericLanguageConnectionContext.prepareInternalStatement(Unknown Source) ... 12 more java.sql.SQLSyntaxErrorException: Table/View 'PEPTIDES' does not exist. at org.apache.derby.impl.jdbc.SQLExceptionFactory40.getSQLException(Unknown Source) at org.apache.derby.impl.jdbc.Util.generateCsSQLException(Unknown Source) at org.apache.derby.impl.jdbc.TransactionResourceImpl.wrapInSQLException(Unknown Source) at org.apache.derby.impl.jdbc.TransactionResourceImpl.handleException(Unknown Source) at org.apache.derby.impl.jdbc.EmbedConnection.handleException(Unknown Source) at org.apache.derby.impl.jdbc.ConnectionChild.handleException(Unknown Source) at org.apache.derby.impl.jdbc.EmbedStatement.execute(Unknown Source) at org.apache.derby.impl.jdbc.EmbedStatement.executeQuery(Unknown Source) at com.compomics.util.db.ObjectsDB.loadObjects(ObjectsDB.java:615) at com.compomics.util.experiment.identification.IdentificationDB.loadPeptideMatches(IdentificationDB.java:963) at com.compomics.util.experiment.identification.Identification.loadPeptideMatches(Identification.java:312) at com.compomics.util.experiment.identification.matches_iterators.PeptideMatchesIterator.checkBuffer(PeptideMatchesIterator.java:194) at com.compomics.util.experiment.identification.matches_iterators.PeptideMatchesIterator.next(PeptideMatchesIterator.java:163) at eu.isas.peptideshaker.export.sections.PsPeptideSection.writeSection(PsPeptideSection.java:154) at eu.isas.peptideshaker.export.PSExportFactory.writeExport(PSExportFactory.java:291) at eu.isas.peptideshaker.cmd.CLIMethods.exportReport(CLIMethods.java:294) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:299) at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1026) Caused by: java.sql.SQLException: Table/View 'PEPTIDES' does not exist. at org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source) at org.apache.derby.impl.jdbc.SQLExceptionFactory40.wrapArgsForTransportAcrossDRDA(Unknown Source) ... 18 more Caused by: ERROR 42X05: Table/View 'PEPTIDES' does not exist. at org.apache.derby.iapi.error.StandardException.newException(Unknown Source) at org.apache.derby.impl.sql.compile.FromBaseTable.bindTableDescriptor(Unknown Source) at org.apache.derby.impl.sql.compile.FromBaseTable.bindNonVTITables(Unknown Source) at org.apache.derby.impl.sql.compile.FromList.bindTables(Unknown Source) at org.apache.derby.impl.sql.compile.SelectNode.bindNonVTITables(Unknown Source) at org.apache.derby.impl.sql.compile.DMLStatementNode.bindTables(Unknown Source) at org.apache.derby.impl.sql.compile.DMLStatementNode.bind(Unknown Source) at org.apache.derby.impl.sql.compile.CursorNode.bindStatement(Unknown Source) at org.apache.derby.impl.sql.GenericStatement.prepMinion(Unknown Source) at org.apache.derby.impl.sql.GenericStatement.prepare(Unknown Source) at org.apache.derby.impl.sql.conn.GenericLanguageConnectionContext.prepareInternalStatement(Unknown Source)

The same/similar results are observed for all data for all timepoints (TP) 0_2, 2_4 etc etc..

I then tried to use the zipped peptideshaker output with reportCLI to generate the reports:

java -Xms4096M -Xmx8192m -cp ../../PeptideShaker/PeptideShaker-1.0.4/PeptideShaker-1.0.4.jar eu.isas.peptideshaker.cmd.ReportCLI -in "PeptideShaker/TP_14_16.zip" -out_reports "./" -reports "0"

I get this output: Wed Oct 21 19:34:32 BST 2015 Unzipping TP_14_16.zip. Please Wait... 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 10% 90% Wed Oct 21 19:34:44 BST 2015 An error occurred while reading: /mnt/lustre/scratch/mjfidcl2/DDIP/TimePoints/PeptideShaker/TP_14_16.zip. It looks like another instance of PeptideShaker is still connected to the file. Please close all instances of PeptideShaker and try again. java.sql.SQLSyntaxErrorException: Table/View 'PEPTIDESHAKER_EXPERIMENT_SETTINGS' does not exist. at org.apache.derby.impl.jdbc.SQLExceptionFactory40.getSQLException(Unknown Source) at org.apache.derby.impl.jdbc.Util.generateCsSQLException(Unknown Source) at org.apache.derby.impl.jdbc.TransactionResourceImpl.wrapInSQLException(Unknown Source) at org.apache.derby.impl.jdbc.TransactionResourceImpl.handleException(Unknown Source) at org.apache.derby.impl.jdbc.EmbedConnection.handleException(Unknown Source) at org.apache.derby.impl.jdbc.ConnectionChild.handleException(Unknown Source) at org.apache.derby.impl.jdbc.EmbedStatement.execute(Unknown Source) at org.apache.derby.impl.jdbc.EmbedStatement.executeQuery(Unknown Source) at com.compomics.util.db.ObjectsDB.retrieveObjectSynchronized(ObjectsDB.java:797) at com.compomics.util.db.ObjectsDB.retrieveObject(ObjectsDB.java:746) at eu.isas.peptideshaker.fileimport.CpsFileImporter.getPeptideShakerSettings(CpsFileImporter.java:78) at eu.isas.peptideshaker.utils.CpsParent.loadCpsFile(CpsParent.java:234) at eu.isas.peptideshaker.utils.CpsParent.loadCpsFromZipFile(CpsParent.java:167) at eu.isas.peptideshaker.cmd.ReportCLI.call(ReportCLI.java:104) at eu.isas.peptideshaker.cmd.ReportCLI.main(ReportCLI.java:319) Caused by: java.sql.SQLException: Table/View 'PEPTIDESHAKER_EXPERIMENT_SETTINGS' does not exist. at org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source) at org.apache.derby.impl.jdbc.SQLExceptionFactory40.wrapArgsForTransportAcrossDRDA(Unknown Source) ... 15 more Caused by: ERROR 42X05: Table/View 'PEPTIDESHAKER_EXPERIMENT_SETTINGS' does not exist. at org.apache.derby.iapi.error.StandardException.newException(Unknown Source) at org.apache.derby.impl.sql.compile.FromBaseTable.bindTableDescriptor(Unknown Source) at org.apache.derby.impl.sql.compile.FromBaseTable.bindNonVTITables(Unknown Source) at org.apache.derby.impl.sql.compile.FromList.bindTables(Unknown Source) at org.apache.derby.impl.sql.compile.SelectNode.bindNonVTITables(Unknown Source) at org.apache.derby.impl.sql.compile.DMLStatementNode.bindTables(Unknown Source) at org.apache.derby.impl.sql.compile.DMLStatementNode.bind(Unknown Source) at org.apache.derby.impl.sql.compile.CursorNode.bindStatement(Unknown Source) at org.apache.derby.impl.sql.GenericStatement.prepMinion(Unknown Source) at org.apache.derby.impl.sql.GenericStatement.prepare(Unknown Source) at org.apache.derby.impl.sql.conn.GenericLanguageConnectionContext.prepareInternalStatement(Unknown Source) ... 9 more Wed Oct 21 19:34:44 BST 2015 /mnt/lustre/scratch/mjfidcl2/DDIP/TimePoints/PeptideShaker/TP_14_16.zip successfuly loaded. Wed Oct 21 19:34:44 BST 2015 An error occurred while loading the fasta file. java.lang.NullPointerException at eu.isas.peptideshaker.utils.CpsParent.loadFastaFile(CpsParent.java:330) at eu.isas.peptideshaker.utils.CpsParent.loadFastaFile(CpsParent.java:307) at eu.isas.peptideshaker.cmd.ReportCLI.call(ReportCLI.java:133) at eu.isas.peptideshaker.cmd.ReportCLI.main(ReportCLI.java:319)

Checking the contents of TP_14_16.zip:

Archive: TP_14_16.zip Length Date Time Name

20213760 10-21-2015 14:18 TP_14_16.cpsx 0 10-21-2015 14:18 data/ 87080274 10-21-2015 14:18 data/augmented_nr_db_v1_concatenated_target_decoy.fasta 3312980 10-21-2015 14:18 data/augmented_nr_db_v1_concatenated_target_decoy.fasta.cui 30775216 10-21-2015 14:18 data/24072015_Stages_14-16h_R4.mgf 1717174 10-21-2015 14:18 data/24072015_Stages_14-16h_R4.mgf.cui 9171533 10-21-2015 14:18 data/24072015_Stages_14-16h_R2.mgf 344265 10-21-2015 14:18 data/24072015_Stages_14-16h_R2.mgf.cui 11206400 10-21-2015 14:18 data/24072015_Stages_14-16h_R3.mgf 690268 10-21-2015 14:18 data/24072015_Stages_14-16h_R3.mgf.cui 46633149 10-21-2015 14:18 data/24072015_Stages_14-16h_R1.mgf 3104023 10-21-2015 14:18 data/24072015_Stages_14-16h_R1.mgf.cui

214249042 12 files

The contents appear to be correct but the paths do not seem to be pointing to the correct files.

Craig Lawless

Postdoctoral Research Associate Faculty of Life Sciences Rm B.1071 Michael-Smith Oxford Road Manchester M13 9PT

TEL:(+44)0161 275 1680

From: Marc Vaudel [notifications@github.com] Sent: 21 October 2015 12:48 To: compomics/peptide-shaker Cc: Craig Lawless Subject: Re: [peptide-shaker] ReportCLI : The FASTA file was not found. Please locate it using the GUI (#95)

Hi again,

Great, eager to know whether it worked. Please note that ReportCLI is essentially made for report generation on existing projects. You can also export the reports upon creation of the projects, for this, append the ReportCLI arguments directly to the PeptideShakerCLI. Something like:

java -Xms1024m -Xmx262144m -cp /scratch/mjfidcl2/PeptideShaker-1.0.4/PeptideShaker-1.0.4.jar eu.isas.peptideshaker.cmd.PeptideShakerCLI -experiment TP_0_2 -sample TP_0_2_sample -replicate 1 -identification_files "/scratch/mjfidcl2/DDIP/TimePoints/SearchGUI_results/outputs_0_2/2015-9-16_0.15.5_searchgui_out.zip" -out "./TP_0_2.cpsx" -ptm_score 1 -out_reports "../SearchGUI_results/output_0_2/" -reports "0,3, 4"

You will have one less command to maintain and the generation of reports will be faster :)

Best regards,

Marc

— Reply to this email directly or view it on GitHubhttps://github.com/compomics/peptide-shaker/issues/95#issuecomment-149864709.

mvaudel commented 9 years ago

Hi again Craig,

On the report documentation, sorry, just noticed we did not update it, will do that right away.

Concerning the file and packaging, it looks like the file is fine, if you download it to your machine, can you open it using the GUI?

The problem seems to be that the tool somehow lost connection to its back-end database. This can happen (1) when running tools on a different server than the file and the connection drops, (2) if you have IO restrictions on where the tool is located or the user folder, or (3) when running different instances on PeptideShaker in the same time. In order to avoid privileges restrictions we recommend to use the -temp_folder "tempFolder" option in your command lines, with the tempFolder a temporary folder where the tool is allowed to write. The given temporary folder will then be used for all temporary files like indexes and the back-end database.

PeptideShakerCLI with the reports should work then, but please make sure that you are running the latest version as we have recently fixed an issue with the temporary files on some servers which might cause this error. I just noticed that the fix was not included in ReportCLI but it will be in the next release :)

Best regards and apologizes for the inconvenience,

Marc

cdlawless commented 9 years ago

Hi Marc

Have tried opening with GUI but I get error asking if it is still connected by another instance of PeptideShaker and then quits.

I'm not running multiple instances of PeptideShaker (I get errors immediately when I try to do that).

I run SearchGUI on one cluster (high CPU power) output as zip and transfer the zip file to a second cluster (v. high memory and IO speeds). There are no restrictions on IO where I work out of, it's my own high speed IO space directly connected to the cluster.

I tried downloading the lastest version of PeptideShaker, but I get a major.minor version 51.0 error (Exception in thread "main" java.lang.UnsupportedClassVersionError: com/compomics/util/gui/DummyFrame) . The available java on the clusters are 1.6.0, to get 1.7.0 installed is going to be a bit of an ask.

I'll try the tempfolder option and see if that works with the version I am using.

Craig Lawless

Postdoctoral Research Associate Faculty of Life Sciences Rm B.1071 Michael-Smith Oxford Road Manchester M13 9PT

TEL:(+44)0161 275 1680

From: Marc Vaudel [notifications@github.com] Sent: 21 October 2015 20:40 To: compomics/peptide-shaker Cc: Craig Lawless Subject: Re: [peptide-shaker] ReportCLI : The FASTA file was not found. Please locate it using the GUI (#95)

Hi again Craig,

On the report documentation, sorry, just noticed we did not update it, will do that right away.

Concerning the file and packaging, it looks like the file is fine, if you download it to your machine, can you open it using the GUI?

The problem seems to be that the tool somehow lost connection to its back-end database. This can happen (1) when running tools on a different server than the file and the connection drops, (2) if you have IO restrictions on where the tool is located or the user folder, or (3) when running different instances on PeptideShaker in the same time. In order to avoid privileges restrictions we recommend to use the -temp_folder "tempFolder" option in your command lines, with the tempFolder a temporary folder where the tool is allowed to write. The given temporary folder will then be used for all temporary files like indexes and the back-end database.

PeptideShakerCLI with the reports should work then, but please make sure that you are running the latest version as we have recently fixed an issue with the temporary files on some servers which might cause this error. I just noticed that the fix was not included in ReportCLI but it will be in the next release :)

Best regards and apologizes for the inconvenience,

Marc

— Reply to this email directly or view it on GitHubhttps://github.com/compomics/peptide-shaker/issues/95#issuecomment-150003868.

mvaudel commented 9 years ago

Hi again,

The setup of using one cluster with high CPU for SearchGUI and another with high IO/Memory for PeptideShaker is very smart. We are in the process of releasing new versions supporting again java 1.6. If you can wait a couple of days you will have better and more stable versions :)

Best regards,

Marc

2015-10-21 22:29 GMT+02:00 Craig Lawless notifications@github.com:

Hi Marc

Have tried opening with GUI but I get error asking if it is still connected by another instance of PeptideShaker and then quits.

I'm not running multiple instances of PeptideShaker (I get errors immediately when I try to do that).

I run SearchGUI on one cluster (high CPU power) output as zip and transfer the zip file to a second cluster (v. high memory and IO speeds). There are no restrictions on IO where I work out of, it's my own high speed IO space directly connected to the cluster.

I tried downloading the lastest version of PeptideShaker, but I get a major.minor version 51.0 error (Exception in thread "main" java.lang.UnsupportedClassVersionError: com/compomics/util/gui/DummyFrame) . The available java on the clusters are 1.6.0, to get 1.7.0 installed is going to be a bit of an ask.

I'll try the tempfolder option and see if that works with the version I am using.

Craig Lawless

Postdoctoral Research Associate Faculty of Life Sciences Rm B.1071 Michael-Smith Oxford Road Manchester M13 9PT

TEL:(+44)0161 275 1680

From: Marc Vaudel [notifications@github.com] Sent: 21 October 2015 20:40 To: compomics/peptide-shaker Cc: Craig Lawless Subject: Re: [peptide-shaker] ReportCLI : The FASTA file was not found. Please locate it using the GUI (#95)

Hi again Craig,

On the report documentation, sorry, just noticed we did not update it, will do that right away.

Concerning the file and packaging, it looks like the file is fine, if you download it to your machine, can you open it using the GUI?

The problem seems to be that the tool somehow lost connection to its back-end database. This can happen (1) when running tools on a different server than the file and the connection drops, (2) if you have IO restrictions on where the tool is located or the user folder, or (3) when running different instances on PeptideShaker in the same time. In order to avoid privileges restrictions we recommend to use the -temp_folder "tempFolder" option in your command lines, with the tempFolder a temporary folder where the tool is allowed to write. The given temporary folder will then be used for all temporary files like indexes and the back-end database.

PeptideShakerCLI with the reports should work then, but please make sure that you are running the latest version as we have recently fixed an issue with the temporary files on some servers which might cause this error. I just noticed that the fix was not included in ReportCLI but it will be in the next release :)

Best regards and apologizes for the inconvenience,

Marc

— Reply to this email directly or view it on GitHub< https://github.com/compomics/peptide-shaker/issues/95#issuecomment-150003868

.

— Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/95#issuecomment-150015467 .

mvaudel commented 9 years ago

Hi Craig,

A new version was released (https://github.com/compomics/peptide-shaker 1.1.3), it should work on java 1.6, and should be more stable on servers. Can you try to run this new version with the temp_folder option?

Best regards,

Marc

cdlawless commented 9 years ago

Thanks Marc

I'll set this running straight away. I managed to get some of the experiments run on my local machine with v1.1.2, as I had 1.7 installed and it worked with the temp_folder option. I'll use the same option with v1.1.3 on the cluster.

Thanks again

Craig

On 22/10/2015 12:47, Marc Vaudel wrote:

Hi Craig,

A new version was released (https://github.com/compomics/peptide-shaker 1.1.3), it should work on java 1.6, and should be more stable on servers. Can you try to run this new version with the temp_folder option?

Best regards,

Marc

— Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/95#issuecomment-150196378.

Craig Lawless

Post-Doctoral Research Associate Faculty of Life Sciences University of Manchester Manchester M13 9PT

hbarsnes commented 8 years ago

Issue assumed solved by later releases of SearchGUI and PeptideShaker, and as part of the revision of the command lines. If this is not the case, please open a new issue explaining the current problems and we'll take it from there.