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Mascot error in CPAS

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Mascot error in CPAS susanc  2008-03-07 06:10
Status: Closed
 
I submitted a test Mascot search from CPAS. I could see the search running on our Mascot server, and it completed successfully according to Mascot. I can view the results on the Mascot server, but the CPAS Dashboard reported 'searching' for the duration of the Mascot search, and then reported an error. Here's the CPAS error log file:

-----
07 Mar 2008 08:31:05,112 INFO : Mascot search for MM_clICAT11.mzXML
07 Mar 2008 08:31:05,113 INFO : =======================================
07 Mar 2008 08:31:05,167 INFO : MzXML2Search output
07 Mar 2008 08:31:05,176 INFO : =======================================
07 Mar 2008 08:31:05,694 INFO : running: MzXML2Search -mgf MM_clICAT11.mzXML
07 Mar 2008 08:31:05,768 INFO :
07 Mar 2008 08:31:05,769 INFO : MzXML2Search - Mascot Generic Format
07 Mar 2008 08:31:05,770 INFO :
07 Mar 2008 08:31:05,771 INFO : Reading MM_clICAT11.mzXML
07 Mar 2008 08:31:05,771 INFO : Getting the index offset
07 Mar 2008 08:31:05,772 INFO : Reading the index
07 Mar 2008 08:31:07,173 INFO : scan: 5726 100%
07 Mar 2008 08:31:07,185 INFO : Done.
07 Mar 2008 08:31:07,186 INFO :
07 Mar 2008 08:31:07,186 INFO : mascot client output
07 Mar 2008 08:31:07,187 INFO : =======================================
07 Mar 2008 08:31:07,429 INFO : ../bin/ms-searchcontrol.exe - Version 2.2.03 - Server: Apache/2.2.4 (Unix)
07 Mar 2008 08:31:07,828 INFO : Creating Mascot session...
07 Mar 2008 08:31:07,955 INFO : Mascot session#all_secdisabledsession started.
07 Mar 2008 08:31:07,956 INFO : Creating Mascot search task...
07 Mar 2008 08:31:08,200 INFO : Mascot search task#120489666801 created with 'nph-mascot.exe'.
07 Mar 2008 08:31:08,200 INFO : Submitting search to Mascot server...
07 Mar 2008 08:31:08,234 INFO : Submitting query file, size=6762512
07 Mar 2008 08:40:26,741 INFO : Fail to submit search to Mascot server.
07 Mar 2008 08:40:26,878 INFO : Mascot session ended.
07 Mar 2008 08:40:26,879 ERROR: Failed running Mascot.
---------

and here's the top of the Mascot output showing that it actually completed:
----------
Mascot Search Results

User : LabKey User
Email : susanc@helix.nih.gov
Search title : Conversion of MM_clICAT11.mzXML to mascot generic
MS data file : MM_clICAT11.mgf
Database : Sprot (356194 sequences; 127836513 residues)
Timestamp : 7 Mar 2008 at 13:40:15 GMT
Enzyme : Trypsin
Mass values : Average
Protein Mass : Unrestricted
Peptide Mass Tolerance : ± 2 Da
Fragment Mass Tolerance: ± 0.8 Da
Max Missed Cleavages : 1
Instrument type : Default
Number of queries : 3358
Protein hits :    FOX2_YEAST    (Q02207) Peroxisomal hydratase-dehydrogenase-epimerase (HDE) (Multifunctional
      MDHP_YEAST    (P32419) Malate dehydrogenase, peroxisomal (EC 1.1.1.37).
      FAT2_YEAST    (P38137) Peroxisomal-coenzyme A synthetase (EC 6.-.-.-).
      KCNH7_HUMAN    (Q9NS40) Potassium voltage-gated channel subfamily H member 7 (Voltage-gated
      CO3A1_CHICK    (P12105) Collagen alpha-1(III) chain precursor (Fragments).
      CBLN2_MOUSE    (Q8BGU2) Cerebellin-2.
      PNPH_SCHPO    (Q9UTG1) Putative purine nucleoside phosphorylase (EC 2.4.2.1) (Inosine
      BASS_SALTY    (P36557) Sensor protein basS/pmrB (EC 2.7.13.3).
      DPH5_ARATH    (O81769) Probable diphthine synthase (EC 2.1.1.98) (Diphthamide biosynthesis
      EX5A_HAEIN    (P45158) Exodeoxyribonuclease V alpha chain (EC 3.1.11.5).
      COAA_RHILO    (Q98CS9) Pantothenate kinase (EC 2.7.1.33) (Pantothenic acid kinase).
      CORA1_HUMAN    (Q8IZC6) Collagen alpha-1(XXVII) chain precursor.
      DYSF_HUMAN    (O75923) Dysferlin (Dystrophy-associated fer-1-like protein) (Fer-1-like
      K1305_MOUSE    (Q5DTZ0) Integrase catalytic domain-containing protein KIAA1305 (Pol-like
      TITIN_MOUSE    (A2ASS6) Titin (EC 2.7.11.1) (Connectin).
      LRP1_HUMAN    (Q07954) Prolow-density lipoprotein receptor-related protein 1 precursor (LRP)
      ZFHX3_MOUSE    (Q61329) Zinc finger homeobox protein 3 (Zinc finger homeodomain protein 3)
      TITIN_HUMAN    (Q8WZ42) Titin (EC 2.7.11.1) (Connectin) (Rhabdomyosarcoma antigen MU-RMS-
      OVOS2_HUMAN    (Q6IE36) Ovostatin homolog 2 precursor.
      GRP1_DAUCA    (Q03878) Glycine-rich RNA-binding protein.
-------------
 
 
susanc responded:  2008-03-07 06:49
One more bit of information which may be useful. The Mascot server reported:

Results for your search : Conversion of MM_clICAT12.mzXML to mascot generic
On database: Sprot
You disconnected your browser before the results of your
Mascot search were available. You can see the results at
http://.....
 
wongch responded:  2008-03-07 08:14
Hi Susan,

Could you post the file labkey-errors.log from the logs directory?

Please try out a search using a smaller mzXML file? (E.g. SmallICAT.mzXML in ExampleFiles-win.zip) Let's confirm that whether this is just a simple time out issue or interaction with new Mascot version.

Cheers,
Chee-Hong
 
susanc responded:  2008-03-07 12:13
I'm getting the same error with SmallICAT.mzXML.

Also, the Mascot log file shows the error:
Error [M00267 - Job -1 - X00875:ms_fileutil] - Fri Mar 7 15:05:45 2008
   - Failed to lock file - error Bad file descriptor

But there are many jobs on our Mascot server so I cannot be sure that this error corresponds to my job.

We're running Mascot v2.2.
 
susanc responded:  2008-03-10 06:20
labkey-errors.log
 
rwf responded:  2008-03-11 19:49
My CPAS log shows the same problem:

ERROR PipelineJob 2008-03-11 16:03:13,761 JobThread-4.1 : Failed running Mascot.
 
wongch responded:  2008-03-11 20:47
Hi rwf,

Sorry to hear that it Mascot search support (in CPAS) did not work out for you.

I have located the issue in the Susan's installation and am working on a fix. Could you tell me the version of your Mascot? (See Susan's first posting... e.g. ../bin/ms-searchcontrol.exe - Version 2.2.03 - Server: Apache/2.2.4 (Unix)) Which CPAS version are you using?

Cheers,
Chee-Hong.
 
wongch responded:  2008-03-12 07:13
Hi Susan,

IMPORTANT: The attached file is only meant for LabKey Server version 2.3-7806, released January 11, 2008.

Please install the attached file ms2.module.
1. stop your Tomcat server
2. backup your original copy of <labkey_home>/modules/ms2.module
3. place the downloaded ms2.module into <labkey_home>/modules/
4. start your Tomcat server

It has been tested on Windows and Linux system, and Mascot v2.0, v2.1 and v2.2.

Please let us know if this resolve the issue.

*Chee-Hong.
 
wongch responded:  2008-03-12 07:30
Hi rwf,

I just sieved thru' your log file and found that you have already upgraded to LabKey v2.3.

The attached ms2.module in the previous post should address the issue your installation is experiencing.

*Chee-Hong.
 
susanc responded:  2008-03-12 10:49
I installed the new ms2.module file as described. The job ran on
the Mascot server as before while my CPAS window said 'Searching'.
Then the job completed in Mascot, and the CPAS window then said 'Synchronizing' (so it progressed beyond the previous errors).

At that point I got a different error, not sure what it indicates.
I append the SmallCAT.log file.

Susan.
 
wongch responded:  2008-03-12 16:20
Hi Susan,

From SmallCAT.log, your Mascot search has completed successfully and the result file F470854.dat has been downloaded successfully to LabKey server for further processing.

"Synchronizing" is the state where LabKey server attempts to download a copy of the fasta sequence database used in the Mascot search is not already on LabKey server.

The .dat file is then converted to pepXML, followed by running peptideProphet to compute peptide identification probability. Next, proteinProphet is used to inference the protein identification with a probability score.

Finally, all these files together with .xar (your (wet and dry) experiments descriptions and protocols) are then loaded into your database. While doing this, Labkey Server needs to load the copy of the freshly downloaded fasta sequence so that you can view many other related information when inspecting the peptide and protein identification via LabKey server. It is at this point the process failed.

Based on your log file, please check that you have the following file:
<labkey_home>/labkeywebapp/MS2/externalData/ProtSprotOrgMap.txt

If you do not have it, a copy can be retrieve from ms2.module as follow (assuming that <labkey_home> is "/labkeyserver"):
1) copy ms2.module to a temp directory, e.g. /tmp
2) expand the content in ms2.module [command: cd /tmp ; unzip ms2.module]
3) create the directory <labkey_home>/labkeywebapp/MS2/externalData/ if it is not already present [command: mkdir /labkeyserver/labkeywebapp/MS2/externalData/]
3) copy the file ProtSprotOrgMap.txt to <labkey_home>/labkeywebapp/MS2/externalData/ [command: cp MS2/externalData/ProtSprotOrgMap.txt /labkeyserver/labkeywebapp/MS2/externalData/]

*Chee-Hong
 
susanc responded:  2008-03-13 08:33
The file <labkey_home>/labkeywebapp/MS2/externalData/ProtSprotOrgMap.txt
does exist, and is dated 12 March so it was written after I downloaded
the new ms2.module.
 
susanc responded:  2008-03-14 11:52
Dr. Wong's latest ms2.module update fixed the problem, and now my CPAS Mascot jobs complete successfully.
 
wongch responded:  2008-03-14 18:44
There is something specific to Tomcat v5.5.26 as the same exception does not occur on Tomcat v5.5.15 and v5.5.20.

In case someone out there is experiencing similar issue with their SwissProt Organisms mapping loading, please use this updated ms2.module in this specific message. IMPORTANT: The attached file is only meant for LabKey Server version 2.3-7806, released January 11, 2008.
 
adam responded:  2008-03-16 12:02
Thank you Susan & Chee-Hong for researching and reporting the ProtSprotOrgMap.txt import issue. I have tracked this down to a change the Tomcat dev team made to their implementation of ServletContext.getResourceAsStream() in Tomcat 5.5.26. https://issues.apache.org/bugzilla/show_bug.cgi?id=43241

We will address this issue in our next release of CPAS. See https://www.labkey.org/issues/home/Developer/issues/details.view?issueId=5449