Initial testing on PeptideShaker within Galaxy environment.

[Pratik Jagtap]

Hello Everyone,

An update on testing that we have performed using PeptideShaker.

MSI developer team installed the latest build on galaxy test toolshed and JJ had to make a few modifications to make it work (JJ has details on this).

Our first test was with a C. elegans lysate on an Orbitrap Fusion RAW file with default parameters and it worked with MS-GF+, X!tandem and OMSSA. The test worked - however subsequent tests with altered parameters did not. I am currently running a few tests using MS-GF+ and will continue with these tests once Ira visits us in the week of 6/23.

Please see a screenshot of the installed PeptideShaker within Galaxy (it is not yet on usegalaxyp.org).

Bart is working on a draft for a poster which he will be sharing next week before sending it out for printing before ASMS.

Regards,

Pratik

Pratik Jagtap,

Managing Director,

Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108

Phone: 612-624-9275

[Björn Grüning]

Hi Pratik,

if you don't mind please send me all error messages, I will try to fix
it asap.

Thanks for testing!
Bjoern

[Björn Grüning]

Hi James and all,

thanks for your comments. I have added your headless changes to the code.

For the MS-GF+ bug, would it be ok to parse the stdout for
'No identification file found.' and exit with an error code?

<stdio>
<exit_code range="1:" level="fatal" description="Job Failed" />
<regex match="No identification file found." level="fatal"
description="No identification file found!"/>
</stdio>

Do you have any other suggestions?

@all what about the version we want to integrate into our first Tool
Shed version? Should we update the wrappers to the latest version 0.30?
As far as I could see several commandline options changed and a few new
ones are added.

Ciao,
Bjoern


Am 08.06.2014 18:11, schrieb Jim Johnson:
> Björn,
>
> Two things to consider:
>
> 1) I added a command line define param; -Djava.awt.headless=true to
> disable graphics.
>
> gxtest@galaxy-ng
> [/website/galaxy-ng.msi.umn.edu/shed_tools/testtoolshed.g2.bx.psu.edu/repos/bgruening/peptideshaker/7a76958125be/peptideshaker]
> % hg diff peptide_shaker.xml
> diff -r 7a76958125be peptide_shaker.xml
> --- a/peptide_shaker.xml Fri May 09 04:11:23 2014 -0400
> +++ b/peptide_shaker.xml Thu May 29 20:48:49 2014 -0500
> @@ -109,7 +109,7 @@
> ################
> ## Search CLI ##
> ################
> - (java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI
> + (java -Djava.awt.headless=true -cp \$SEARCHGUI_JAR_PATH
> eu.isas.searchgui.cmd.SearchCLI
> -temp_folder `pwd`
> -spectrum_files \$cwd
> -output_folder \$cwd/output
>
> 2) MS-GF+ can exit without producing an output file. Can we have the
> tool_wrapper detect this and report as ERROR state? Should MS-GF+ exit
> with code > 0 on this?
>
> stdout:
>
> ms-gf+ command:
> /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.51.x86_64/jre/bin/java
> -Xms128M -Xmx4096M -jar
> /website/galaxy-ng.msi.umn.edu/NEXTGEN/tool_dependencies/searchgui/1.18.0/iuc/package_searchgui_1_18/0df4db0edb9d/resources/MSGF+/MSGFPlus.jar
> -s
> /galaxy/NEXTGEN/database/job_working_directory/003/3061/Galaxy6-[ProteinPilot_formatted_MGF_of_data_5].mgf
> -d
> /galaxy/NEXTGEN/database/job_working_directory/003/3061/input_database.fasta
> -o
> /galaxy/NEXTGEN/database/job_working_directory/003/3061/output/Galaxy6-[ProteinPilot_formatted_MGF_of_data_5].mzid
> -t 10.0ppm -tda 1 -mod
> /website/galaxy-ng.msi.umn.edu/NEXTGEN/tool_dependencies/searchgui/1.18.0/iuc/package_searchgui_1_18/0df4db0edb9d/resources/MSGF+/Mods.txt
> -minCharge 2 -maxCharge 6 -inst 0 -thread 6 -m 0 -e 1 -protocol 0 -ntt 2
> -minLength 6 -maxLength 30 -n 1 -addFeatures 0 -ti 0,1
>
> Sun Jun 01 09:30:57 CDT 2014 Processing
> Galaxy6-[ProteinPilot_formatted_MGF_of_data_5].mgf with MS-GF+.
>
> Picked up _JAVA_OPTIONS: -Xmx15728640k
> MS-GF+ Beta (v9979) (3/26/2014)
> Loading database files...
> Creating
> /galaxy/NEXTGEN/database/job_working_directory/003/3061/input_database.revCat.fasta.
>
> Error while indexing: input_database.revCat.fasta (too many
> redundant proteins)
> If the database contains forward and reverse proteins, run MS-GF+
> (or BuildSA) again with "-tda 0"
>
>
> Sun Jun 01 09:31:06 CDT 2014 MS-GF+ Process Finished.
>
> Sun Jun 01 09:31:06 CDT 2014 Search Completed.
>
> Search Completed.
>
>
> Identification Parameters file created:
> /galaxy/NEXTGEN/database/job_working_directory/003/3061/PEPTIDESHAKER_IdentificationParameters.parameters
>
>
>
> No identification file found.
>
>
> ==============================
> PeptideShaker - Command Line
> ==============================
>
> The PeptideShaker command line takes identification files from
> X!Tandem, OMSSA and Mascot and generates various types of output files.
>
> For further help see http://peptide-shaker.googlecode.com and
> http://code.google.com/p/peptide-shaker/wiki/PeptideShakerCLI.
>
> Or contact the developers at
> https://groups.google.com/group/peptide-shaker.
>
> ----------------------
> OPTIONS
> ----------------------
>
> Mandatory parameters:
>
> -experiment Specifies the experiment name.
> -sample Specifies the sample name.
> -replicate The replicate number.
> -spectrum_files Spectrum files (mgf format),
> comma separated list or an entire folder.
> -identification_files Identification files (.t.xml,
> .mzid, .cvs, .omx or .dat), comma separated list or an entire folder.

[Marc Vaudel]

Dear all,

Congratulation for the first successful run on the Fusion dataset! Beside the minor changes in the command line options we added a new command line allowing the export of mzidentML files (all documented in "D MzidCLI" of the wiki https://code.google.com/p/peptide-shaker/wiki/PeptideShakerCLI). I guess it would be an interesting option for Galaxy users?

Best regards,

Marc

2014-06-09 3:51 GMT+02:00 Jim Johnson <john...@umn.edu>:

Bjoern,

Catching and searching stdout for MS-GF+ sounds fine to me.

I would say we should try to target the latest versions.

Thanks,

JJ

--
James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota

[Björn Grüning]

Hi Harald,

> As always I'd recommend updating to the latest versions. The changes
> to the command lines are minimal, and the new releases do contain
> some fixes and speedups.

I have updated the dependencies to depend on the newest version.

> Details for the changes in the new versions can be found here:
> https://groups.google.com/forum/#!topic/peptide-shaker/q4rfhLtdZyc
> Let me know if something is unclear or more details are needed.

I'm not sure what that means:

- the e-value search engine filters have been removed
- Improved and extended the Methods Section export.

If have integrated the following:
- protein_index 0 as hardcoded value
- added missing-titles
- added mzidentML as output option with hardcoded emails

Is there anything I missed?

> As for parsing the "No identification file found" as a check for if
> the search went fine, this would only pick up if all of the search
> engines failed. So in the long run we'd need something more advanced
> here.

I'm now grepping for "error" that should find fix that particular issue
and maybe a few more.

I updated the Tool Shed, can be tested :)

Cheers,
Bjoern

> BTW, did anyone contact Sangtae about the MS-GF+ error? As he seem
> to no longer be in the CC of the e-mails, which I think he was at
> some point?
>
> Best regards,
> Harald

[Björn Grüning]

Hi Marc,

I have added that option to the wrapper:

https://bitbucket.org/BjoernGruening/peptideshaker/commits/79b8171779a02c932f2c2918b53e4cc9741b0cbe

As for the parameters ... I don't really care about the email addresses
and names ... would it be possible to make such parameters not
mandatory? For the time being I have added dummy parameters and added
the GalaxyP project.

Thanks,
Bjoern

[Björn Grüning]

Hi JJ,

https://bitbucket.org/BjoernGruening/peptideshaker/commits/bc3360f04e5bee1fb62aa68fc61eb1095b1a5602

That should also fix your error and maybe a few more.

I also updated everything to the latest version.

Cheers,
Bjoern

Am 09.06.2014 03:51, schrieb Jim Johnson:
> Bjoern,
>
> Catching and searching stdout for MS-GF+ sounds fine to me.
>
> I would say we should try to target the latest versions.
>
> Thanks,
>
> JJ
>
>
> On 6/8/14, 5:41 PM, Björn Grüning wrote:

[Pratik Jagtap]

Updates on GalaxyP testing and upgrades.

Pratik Jagtap,

Managing Director,

Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108

Phone: 612-624-9275

On Mon, Jun 9, 2014 at 6:36 AM, <Harald....@biomed.uib.no> wrote:

Quoting Björn Grüning <bjoern....@gmail.com>:

I'm not sure what that means:

- the e-value search engine filters have been removed
- Improved and extended the Methods Section export.

The first is just that before we had options for excluding PSMs based
on the e-values when loading the data in PeptideShaker. But these were
not really used, and we thus removed them from the command lines. There
are some search engines (like X!Tandem) that have these in their own
command lines. But then it's an input to the search and not a filter in
the post-processing. So all you have to do is remove the options from
your PeptideShaker command line, if they were even added in the first
place, as they were not mandatory.

The second is just a feature in the GUI to export a draft of the methods
section for your paper, similar to what Scaffold does. Has no impact on
the command line or the Galaxy wrappers.

Is there anything I missed?

No, I think that should be it.

As for the parameters ... I don't really care about the email addresses and names ... would it be possible to make such parameters not mandatory? For the time being I have added dummy parameters and added the GalaxyP project.

This is included in the mzIdentML files so that you can trace the
files back to the owner. So while perhaps not strictly mandatory,
I'd argue strongly for keeping them as it is not straightforward
to add this information at a later stage, for example when the
user wants to submit the data to PRIDE. It's also a matter of trying
to make the mzIdentML files as MIAPE compliant as possible.

Harald

[Pratik Jagtap]

Details of testing after Ira's visit to Minneapolis.

- Pratik

---------- Forwarded message ----------
From: <Harald....@biomed.uib.no>
Date: Fri, Jun 20, 2014 at 4:40 PM
Subject: Re: Initial testing on PeptideShaker within Galaxy environment.
To: Ira Cooke <I.C...@latrobe.edu.au>
Cc: Marc Vaudel <mva...@gmail.com>, Björn Grüning <bjoern....@gmail.com>, "j...@umn.edu" <j...@umn.edu>, Pratik Jagtap <pja...@umn.edu>, Timothy Griffin <tgri...@umn.edu>, James Johnson <j...@msi.umn.edu>, Bart Gottschalk <bgot...@umn.edu>, "lennart.martens" <lennart...@gmail.com>, Kevin Murray <murr...@umn.edu>, Gerben Menschaert <gerben.m...@gmail.com>

Quoting Ira Cooke <I.C...@latrobe.edu.au>:

Hi Harald,

Thanks for looking into it.

Best wishes
Ira

I made an attempt at a quick fix by simply catching and ignoring the
exception. Which I think should be ok. But I need to debug this in
more detail to see why the exception is thrown in the first place.

The PeptideShaker beta version is found here:
https://www.dropbox.com/s/4nc3lbr4br3apyk/PeptideShaker-0.31.4-beta.zip

And here's a new SearchGUI version to go with it:
https://www.dropbox.com/s/5qfh0dd3pwucfn8/SearchGUI-1.19.5-beta-mac_and_linux.tar.gz

Please use these together and don't mix with the older versions, as
we made some changes to the PTM mapping which we have not test tested
between versions.

Best regards,
Harald

On 20 Jun 2014, at 4:03 pm, Harald....@biomed.uib.no wrote:

Hi Ira,

I'm afraid how you run the steps won't have much of an effect. It is
something we have to fix on our side. As you can see it all happens
when you run PeptideShakerCLI.closePeptideShaker, basically shutting
down PeptideShaker. And as Marc wrote, everything with the search and
processing seems to be ok. So that is good news.

This exception was never a problem for us, as we could just ignore
it. But if it causes issues on your side, we'll do our best to get
rid of it. I'll have a look at it this weekend and release a new
version that should hopefully fix the problem.

Best regards,
Harald





Quoting Ira Cooke <I.C...@latrobe.edu.au>:

Hi Marc,

I’ve updated to search gui version 1.19.4 … and peptide shaker version 0.31.3

Unfortunately I’m still getting the same exception as before.  As
you say, it looks like it’s happening during a cleanup phase … but
Galaxy will generally mark the tool as failed (and not provide
access to the dataset) if this happens.

Tomorrow I’ll try running all the steps separately to see if that
changes things.

Cheers
Ira



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:214)
at com.compomics.util.db.ObjectsDB.saveLongKeys(ObjectsDB.java:983)
at com.compomics.util.db.ObjectsDB.close(ObjectsDB.java:1013)
at
com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory.close(ProteinTreeComponentsFactory.java:153)
at
com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.close(ProteinTree.java:1406)
at
com.compomics.util.experiment.identification.SequenceFactory.closeFile(SequenceFactory.java:706)
at
com.compomics.util.experiment.identification.SequenceFactory.clearFactory(SequenceFactory.java:133)
at
eu.isas.peptideshaker.cmd.PeptideShakerCLI.closePeptideShaker(PeptideShakerCLI.java:501)
at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:315)
at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:734)
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)
... 16 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:214)
at com.compomics.util.db.ObjectsDB.saveLongKeys(ObjectsDB.java:983)
at com.compomics.util.db.ObjectsDB.close(ObjectsDB.java:1013)
at
com.compomics.util.experiment.identification.IdentificationDB.close(IdentificationDB.java:960)
at
com.compomics.util.experiment.identification.Identification.close(Identification.java:1461)
at
eu.isas.peptideshaker.cmd.PeptideShakerCLI.closePeptideShaker(PeptideShakerCLI.java:505)
at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:315)
at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:734)
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)
... 14 more




On 20 Jun 2014, at 12:33 pm, Marc Vaudel
<mva...@gmail.com<mailto:mvaud...@gmail.com>> wrote:

Hi Ira,

As far as I can see the processing went successfully and the SQL
exception only occurs when closing the tool. This happens when the
connection to the database we use to store data is dropped before
closing, since that occurs after saving and exporting the reports it
is nothing alarming. Actually, if you update to the latest version
available online I think we got rid of this error in most cases.

Beside that error trace it looks like everything went perfectly ok.
You should have the results of the four search engines along with
the PeptideShaker .cps file, and some text exports?

Best regards,

Marc


2014-06-20 19:24 GMT+02:00 Ira Cooke
<I.C...@latrobe.edu.au<mailto:I.C...@latrobe.edu.au>>:
Dear All,

I’m planning on spending some time over the next week or so testing
the peptide shaker tool in galaxy.

I’m starting out with the version that is currently on the
testtoolshed.  I found and fixed one easy bug (the peptide shaker
.jar was the wrong name).

But I’m now encountering an SQL exception (see command log
attached).  I’m at MSI this week, and so was able to cross reference
this with jj … he seems to get the same error with a different
dataset.

I must admit I don’t really know where to start with this, so any
advice would be much appreciated.  I’ll keep digging around to see
if I can trace the error to a particular set of commands.

Cheers
Ira





Fatal error: Error encounterd!
Creating decoy database.
Reindexing: input_database.fasta.
Input:
/home/vagrant/galaxy-dist/database/job_working_directory/000/135/input_database.fasta

Name: input_database.fasta
Version: 20.6.2014
Decoy Tag: null
Type: Generic_Header
Last modified: Fri Jun 20 15:33:08 UTC 2014
Size: 12 sequences

Fri Jun 20 15:33:09 UTC 2014 Appending Decoy Sequences. Please Wait...
Reindexing: input_database_concatenated_target_decoy.fasta.
Decoy file successfully created:

Output:
/home/vagrant/galaxy-dist/database/job_working_directory/000/135/input_database_concatenated_target_decoy.fasta

Name: input_database_concatenated_target_decoy.fasta
Version: 20.6.2014
Decoy Tag: REVERSED
Type: Generic_Header
Last modified: Fri Jun 20 15:33:09 UTC 2014
Size: 24 sequences (12 target)


Identification Parameters file created:
/home/vagrant/galaxy-dist/database/job_working_directory/000/135/SEARCHGUI_IdentificationParameters.parameters

Reindexing: input_database.fasta.
Path configuration completed.
Fri Jun 20 15:33:10 UTC 2014 Validating MGF file:
/home/vagrant/galaxy-dist/database/job_working_directory/000/135/tinyspectra.mgf


makeblastdb command:
/home/vagrant/tool_dependencies/searchgui/1.19.1/iuc/package_searchgui_1_19/3b9a00dd3518/resources/makeblastdb/linux/linux_64bit/makeblastdb -in input_database.fasta -dbtype
prot

Fri Jun 20 15:33:10 UTC 2014 Formatting input_database.fasta for OMSSA.



Building a new DB, current time: 06/20/2014 15:33:10
New DB name:   input_database.fasta
New DB title:  input_database.fasta
Sequence type: Protein
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 24 sequences in 0.00118494 seconds.


Fri Jun 20 15:33:10 UTC 2014 Database Formating Process Finished.

Fri Jun 20 15:33:10 UTC 2014 input_database.fasta formatted for OMSSA.



Processing: tinyspectra.mgf (1/1)


omssa command:
/home/vagrant/tool_dependencies/searchgui/1.19.1/iuc/package_searchgui_1_19/3b9a00dd3518/resources/OMSSA/omssa-2.1.9.linux/omssacl -w -to 0.5 -te 10.0 -teppm -e 0 -zl 2 -zh 4 -zt 3 -tex 1446.94 -cl 0.0 -ch 0.2 -ci 5.0E-4 -w1 27 -w2 14 -h1 2 -h2 2 -hl 30 -hm 2 -hs 4 -ht 6 -mm 128 -zoh 2 -z1 0.95 -pc 1 -sb1 0 -sp 100 -scorp 0.5 -is 0.0 -ir 0.0 -ii 0.01 -v 2 -he 100.0 -tez 1 -zcc 2 -cp 0 -no 6 -nox 30 -tom 0 -tem 0 -i 1,4 -mf 1 -mv 3 -d input_database.fasta -fm /home/vagrant/galaxy-dist/database/job_working_directory/000/135/tinyspectra.mgf -ox /home/vagrant/galaxy-dist/database/job_working_directory/000/135/output/tinyspectra.omx -nt
1

Fri Jun 20 15:33:10 UTC 2014 Processing tinyspectra.mgf with OMSSA.

Info: Sequence=0 Percent=0%


Fri Jun 20 15:33:10 UTC 2014 OMSSA Process Finished.



xtandem command:
/home/vagrant/tool_dependencies/searchgui/1.19.1/iuc/package_searchgui_1_19/3b9a00dd3518/resources/XTandem/linux_64bit/tandem
/home/vagrant/tool_dependencies/searchgui/1.19.1/iuc/package_searchgui_1_19/3b9a00dd3518/resources/XTandem/linux_64bit/input_searchGUI.xml

Fri Jun 20 15:33:10 UTC 2014 Processing tinyspectra.mgf with X!Tandem.


X! TANDEM Sledgehammer (2013.09.01.1)

Loading spectra (mgf). loaded.
Spectra matching criteria = 21
Starting threads . started.
Computing models:
       S       sequences modelled = 0 ks
Model refinement:
       partial cleavage ..... done.
       unanticipated cleavage ..... done.
       finishing refinement ... done.
Creating report:
       initial calculations  ..... done.
       sorting  ..... done.
       finding repeats ..... done.
       evaluating results ..... done.
       calculating expectations ..... done.
       writing results ..... done.

Valid models = 21




Fri Jun 20 15:33:10 UTC 2014 X!Tandem Process Finished.



ms-gf+ command:
/usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java
-Djava.awt.headless=true -jar
/home/vagrant/tool_dependencies/searchgui/1.19.1/iuc/package_searchgui_1_19/3b9a00dd3518/resources/MSGF+/MSGFPlus.jar -s /home/vagrant/galaxy-dist/database/job_working_directory/000/135/tinyspectra.mgf -d /home/vagrant/galaxy-dist/database/job_working_directory/000/135/input_database.fasta -o /home/vagrant/galaxy-dist/database/job_working_directory/000/135/output/tinyspectra.mzid -t 10.0ppm -tda 0 -mod /home/vagrant/tool_dependencies/searchgui/1.19.1/iuc/package_searchgui_1_19/3b9a00dd3518/resources/MSGF+/Mods.txt -minCharge 2 -maxCharge 4 -inst 0 -thread 1 -m 0 -e 1 -protocol 0 -ntt 2 -minLength 6 -maxLength 30 -n 1 -addFeatures 0 -ti
0,1

Fri Jun 20 15:33:10 UTC 2014 Processing tinyspectra.mgf with MS-GF+.

MS-GF+ Beta (v10024) (5/9/2014)
Loading database files...
Creating the suffix array indexed file... Size: 9173
AlphabetSize: 28
Suffix creation: 0.00% complete.
Sorting 0.00% complete.
Sorting 5.81% complete.
Sorting 11.62% complete.
Sorting 17.43% complete.
Sorting 23.24% complete.
Sorting 29.05% complete.
Sorting 34.86% complete.
Sorting 40.67% complete.
Sorting 46.48% complete.
Sorting 52.29% complete.
Sorting 58.10% complete.
Sorting 63.91% complete.
Sorting 69.73% complete.
Sorting 75.54% complete.
Sorting 81.35% complete.
Sorting 87.16% complete.
Sorting 92.97% complete.
Sorting 98.78% complete.
Loading database finished (elapsed time: 0.31 sec)
Reading spectra...
Ignoring 0 profile spectra.
Ignoring 0 spectra having less than 10 peaks.
Reading spectra finished (elapsed time: 0.81 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: 1
Spectrum 0-20 (total: 21)
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...
pool-1-thread-1: Database search progress... 0.0% complete
pool-1-thread-1: Database search finished (elapsed time: 0.00 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: 1.18 sec)
MS-GF+ complete (total elapsed time: 5.14 sec)


Fri Jun 20 15:33:16 UTC 2014 MS-GF+ Process Finished.



ms amanda command:
/home/vagrant/tool_dependencies/searchgui/1.19.1/iuc/package_searchgui_1_19/3b9a00dd3518/resources/MsAmanda/MSAmanda.exe /home/vagrant/galaxy-dist/database/job_working_directory/000/135/tinyspectra.mgf /home/vagrant/galaxy-dist/database/job_working_directory/000/135/input_database.fasta /home/vagrant/tool_dependencies/searchgui/1.19.1/iuc/package_searchgui_1_19/3b9a00dd3518/resources/MsAmanda/settings_SearchGUI.xml
/home/vagrant/galaxy-dist/database/job_working_directory/000/135/output/tinyspectra.csv

Fri Jun 20 15:33:16 UTC 2014 Processing tinyspectra.mgf with MS Amanda.

/home/vagrant/tool_dependencies/searchgui/1.19.1/iuc/package_searchgui_1_19/3b9a00dd3518/resources/MsAmanda/MSAmanda.exe: 1: /home/vagrant/tool_dependencies/searchgui/1.19.1/iuc/package_searchgui_1_19/3b9a00dd3518/resources/MsAmanda/MSAmanda.exe: MZ�  ���@�  � �: not
found
/home/vagrant/tool_dependencies/searchgui/1.19.1/iuc/package_searchgui_1_19/3b9a00dd3518/resources/MsAmanda/MSAmanda.exe: 3: /home/vagrant/tool_dependencies/searchgui/1.19.1/iuc/package_searchgui_1_19/3b9a00dd3518/resources/MsAmanda/MSAmanda.exe: Syntax error: "("
unexpected


Fri Jun 20 15:33:16 UTC 2014 MS Amanda Process Finished.

Fri Jun 20 15:33:16 UTC 2014 Search Completed.

Search Completed.


Identification Parameters file created:

/home/vagrant/galaxy-dist/database/job_working_directory/000/135/PEPTIDESHAKER_IdentificationParameters.parameters

Path configuration completed.
Fri Jun 20 15:33:17 UTC 2014 Import process for
Galaxy_Experiment_2014062015331403278388 (Sample:
Sample_2014062015331403278388, Replicate: 1)

Fri Jun 20 15:33:17 UTC 2014 Importing sequences from input_database.fasta.
Fri Jun 20 15:33:19 UTC 2014 Expected import time: 0 seconds. (See
<a
href="https://code.google.com/p/compomics-utilities/wiki/ProteinInference">Protein
Inference</a>.)
Fri Jun 20 15:33:20 UTC 2014 FASTA file import completed.
Fri Jun 20 15:33:20 UTC 2014 Establishing local database connection.
Fri Jun 20 15:33:21 UTC 2014 Reading identification files.
Fri Jun 20 15:33:21 UTC 2014 Parsing tinyspectra.mzid.
Fri Jun 20 15:33:22 UTC 2014 Importing tinyspectra.mgf
Fri Jun 20 15:33:22 UTC 2014 tinyspectra.mgf imported.
Fri Jun 20 15:33:22 UTC 2014 Importing PSMs from tinyspectra.mzid
Fri Jun 20 15:33:22 UTC 2014 Parsing tinyspectra.omx.
Fri Jun 20 15:33:22 UTC 2014 Importing PSMs from tinyspectra.omx
Fri Jun 20 15:33:22 UTC 2014 Parsing tinyspectra.t.xml.
Fri Jun 20 15:33:22 UTC 2014 Importing PSMs from tinyspectra.t.xml
Fri Jun 20 15:33:22 UTC 2014 File import completed. 47 first hits
imported (0 secondary) from 21 spectra.
Fri Jun 20 15:33:22 UTC 2014 [47 first hits passed the initial filtering]
Fri Jun 20 15:33:22 UTC 2014 Computing assumptions probabilities.
Fri Jun 20 15:33:22 UTC 2014 Estimating Probabilities. Please Wait...
Fri Jun 20 15:33:22 UTC 2014 Estimating Probabilities. Please Wait...
Fri Jun 20 15:33:22 UTC 2014 Estimating Probabilities. Please Wait...
Fri Jun 20 15:33:22 UTC 2014 Estimating Probabilities. Please Wait...
Fri Jun 20 15:33:22 UTC 2014 Estimating Probabilities. Please Wait...
Fri Jun 20 15:33:22 UTC 2014 Estimating Probabilities. Please Wait...
Fri Jun 20 15:33:22 UTC 2014 Saving assumptions probabilities.
Fri Jun 20 15:33:22 UTC 2014 Selecting best peptide per spectrum.
Fri Jun 20 15:33:23 UTC 2014 Computing PSM probabilities.
Fri Jun 20 15:33:23 UTC 2014 Estimating Probabilities. Please Wait...
Fri Jun 20 15:33:23 UTC 2014 Scoring PTMs in PSMs (D-score)
Fri Jun 20 15:33:23 UTC 2014 Scoring Peptide PTMs. Please Wait...
Fri Jun 20 15:33:23 UTC 2014 Thresholding PTM localizations.
Fri Jun 20 15:33:23 UTC 2014 Estimating FLR. Please Wait...
Fri Jun 20 15:33:23 UTC 2014 Resolving peptide inference issues.
Fri Jun 20 15:33:23 UTC 2014 Solving Peptide Inference. Please Wait...
Fri Jun 20 15:33:23 UTC 2014 Saving probabilities, building peptides
and proteins.
Fri Jun 20 15:33:23 UTC 2014 Attaching Spectrum Probabilities -
Building Peptides and Proteins. Please Wait...
Fri Jun 20 15:33:23 UTC 2014 Simplifying protein groups.
Fri Jun 20 15:33:23 UTC 2014 Symplifying Protein Groups. Please Wait...
Fri Jun 20 15:33:23 UTC 2014 Generating peptide map.
Fri Jun 20 15:33:23 UTC 2014 Filling Peptide Maps. Please Wait...
Fri Jun 20 15:33:23 UTC 2014 Computing peptide probabilities.
Fri Jun 20 15:33:23 UTC 2014 Estimating Probabilities. Please Wait...
Fri Jun 20 15:33:23 UTC 2014 Estimating Probabilities. Please Wait...
Fri Jun 20 15:33:23 UTC 2014 Saving peptide probabilities.
Fri Jun 20 15:33:23 UTC 2014 Attaching Peptide Probabilities. Please Wait...
Fri Jun 20 15:33:23 UTC 2014 Generating protein map.
Fri Jun 20 15:33:23 UTC 2014 Filling Protein Map. Please Wait...
Fri Jun 20 15:33:23 UTC 2014 Resolving protein inference issues,
inferring peptide and protein PI status.
Fri Jun 20 15:33:23 UTC 2014 Cleaning Protein Groups. Please Wait...
Fri Jun 20 15:33:23 UTC 2014 3 conflicts resolved. 2 protein groups
remaining (0 suspicious).
Fri Jun 20 15:33:23 UTC 2014 Correcting protein probabilities.
Fri Jun 20 15:33:23 UTC 2014 Estimating Probabilities. Please Wait...
Fri Jun 20 15:33:23 UTC 2014 Estimating Probabilities. Please Wait...
Fri Jun 20 15:33:23 UTC 2014 Saving protein probabilities.
Fri Jun 20 15:33:23 UTC 2014 Attaching Protein Probabilities. Please Wait...
Fri Jun 20 15:33:23 UTC 2014 Validating identifications at 1% FDR,
quality control of matches.
Fri Jun 20 15:33:23 UTC 2014 Validating Identifications. Please Wait...
Fri Jun 20 15:33:23 UTC 2014 Scoring PTMs in peptides.
Fri Jun 20 15:33:23 UTC 2014 Scoring Peptide PTMs. Please Wait...
Fri Jun 20 15:33:23 UTC 2014 Scoring PTMs in proteins.
Fri Jun 20 15:33:23 UTC 2014 Scoring Protein PTMs. Please Wait...
Fri Jun 20 15:33:23 UTC 2014 Identification processing completed.


Fri Jun 20 15:33:23 UTC 2014 Project successfully created.
Fri Jun 20 15:33:23 UTC 2014 Saving Results. Please Wait...
Fri Jun 20 15:33:23 UTC 2014 Results saved to
/home/vagrant/galaxy-dist/database/job_working_directory/000/135/peptide_shaker_output.cps.

Fri Jun 20 15:33:23 UTC 2014 PeptideShaker Import Completed.

Fri Jun 20 15:33:23 UTC 2014 End of PeptideShaker processing.
Fri Jun 20 15:33:23 UTC 2014 Processing Completed!
Path configuration completed.
Fri Jun 20 15:33:25 UTC 2014 Protein database input_database.fasta.
Fri Jun 20 15:33:25 UTC 2014 Spectrum file(s) successfully loaded.
Fri Jun 20 15:33:25 UTC 2014 Loading Peptides. Please Wait...
Fri Jun 20 15:33:26 UTC 2014 Loading Peptide Details. Please Wait...
Fri Jun 20 15:33:26 UTC 2014 Exporting. Please Wait...
Fri Jun 20 15:33:26 UTC 2014 Loading Proteins. Please Wait...
Fri Jun 20 15:33:26 UTC 2014 Loading Protein Details. Please Wait...
Fri Jun 20 15:33:26 UTC 2014 Exporting. Please Wait...
Fri Jun 20 15:33:26 UTC 2014 End of PeptideShaker processing.
Fri Jun 20 15:33:26 UTC 2014 Processing Completed!
Reindexing: input_database.fasta. (changes in the file detected)
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in
[jar:file:/home/vagrant/tool_dependencies/peptide_shaker/0.30.1/iuc/package_peptideshaker_0_30/a0574a1dc512/lib/slf4j-log4j12-1.6.1.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in
[jar:file:/home/vagrant/tool_dependencies/peptide_shaker/0.30.1/iuc/package_peptideshaker_0_30/a0574a1dc512/lib/logback-classic-1.0.7.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an
explanation.
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:214)
       at com.compomics.util.db.ObjectsDB.saveLongKeys(ObjectsDB.java:983)
       at com.compomics.util.db.ObjectsDB.close(ObjectsDB.java:1013)
       at
com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory.close(ProteinTreeComponentsFactory.java:153)
       at
com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.close(ProteinTree.java:1406)
       at
com.compomics.util.experiment.identification.SequenceFactory.closeFile(SequenceFactory.java:703)
       at
com.compomics.util.experiment.identification.SequenceFactory.clearFactory(SequenceFactory.java:133)
       at
eu.isas.peptideshaker.cmd.PeptideShakerCLI.closePeptideShaker(PeptideShakerCLI.java:501)
       at
eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:315)
       at
eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:734)
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)
       ... 16 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:214)
       at com.compomics.util.db.ObjectsDB.saveLongKeys(ObjectsDB.java:983)
       at com.compomics.util.db.ObjectsDB.close(ObjectsDB.java:1013)
       at
com.compomics.util.experiment.identification.IdentificationDB.close(IdentificationDB.java:960)
       at
com.compomics.util.experiment.identification.Identification.close(Identification.java:1461)
       at
eu.isas.peptideshaker.cmd.PeptideShakerCLI.closePeptideShaker(PeptideShakerCLI.java:505)
       at
eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:315)
       at
eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:734)
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)
       ... 14 more




On 9 Jun 2014, at 12:21 pm, Björn Grüning

<bjoern....@gmail.com<mailto:bjoern.gruening@gmail.com>> wrote:



As for the parameters ... I don't really care about the email
addresses and names ... would it be possible to make such parameters
not mandatory? For the time being I have added dummy parameters and
added the GalaxyP project.

This is included in the mzIdentML files so that you can trace the
files back to the owner. So while perhaps not strictly mandatory,
I'd argue strongly for keeping them as it is not straightforward
to add this information at a later stage, for example when the
user wants to submit the data to PRIDE. It's also a matter of trying
to make the mzIdentML files as MIAPE compliant as possible.

Oh interesting, than I should expose those to the user, maybe with a
dummy default value. Good to know.

Thanks,
Bjoern