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Showing: limited to 100 messages
LCMS data for skyline
(1 response) viviana greco82 2014-12-01 01:40
dear all
I've performed a shotgun experiment (DDA) on a nanoACQUITY UPLC MS system (waters) and processed raw data with PLGS software (waters). We found some proteins differentially expressed in two conditions and now a validation of these is required. I was thinking of building a library (fasta from uniprot) only with these proteins and use this as my database. Then I think to compare the retention times of the peptides found. is that correct? do you have any suggestions for me?
Thanks in advance.
best regards,
Viviana
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"ERROR: Unsupported search enzyme" for searches with Chymotrypsin
(3 responses) t s loo 2014-11-10 18:17
Hi everyone,

I'm a relatively new user of Labkey and encountered an error during a search using chymotrypsin as the digesting enzyme. I've noticed Labkey automatically set <note label="protein, cleavage site" type="input">[YWFM]|{P}</note>. The error log said to use [FLMWY]|{P} for chymotrypsin which I did but then it said "The enzyme [FLMWY]|{P} was not found". Please see attached files and check if I set the parameters wrong. Any help is much appreciated.

Cheers,
Trevor
 TL_PME2_aChymo20min.log  tandem.xml  enzyme was not found.JPG 
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Importing excel files
(1 response) jacoffer 2014-09-29 16:25
My lab uses Gen5 plate reader software for the BioTek Synergy plate reader. After exporting all the data into an excel file, LabKey doesn't recognize the file for upload. The error message says "XXX.xls does not appear to be a valid data file: unable to locate cell values."

The data was exported using the standard excel export option. We are using Windows 7 Enterprise and Google Chrome browser.
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Combining results from two or more search engines
(1 response) vidya 2014-08-06 15:43
Hi,

I have recently started using Labkey server 14.1 version on a stand alone windows machine.
I also have a independent sequest license.

I was wondering if it is possible to combine xtandem and sequest search results on labkey server or run xtandem and sequest searches independently and then use TPP pipeline on Labkey server to merge the results?

Thanks
Vidya
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Xtandem crashed when processing the big mzXML files.
(1 response) andyzcq 2014-06-12 05:58
I used the command line to search mzXML file with Xtandem, and Xtandem works fine when processing rather little mzXML (<800MB).
Xandem always crashed when processing big mzXML file (>1GB), and the screenshot of error is in the attachment.

I do not know how to fix this problem.

Best,
 Xtandem_error.png 
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Panorama Server
(4 responses) jannis schulte 2014-03-17 09:32
Dear all,

I am having an issue with the Panorama server that should be included in the LabKey installation, doesn't it?
When I try to publish data from Skyline to our labkey server, I get an error message saying "The server ourServer is not a Panorama server.".

Everything else works fine with our LabKey 14.1 server running on Ubuntu 12.04 LTS server.

Is there any module that I have to activate to use the Panorama feature?
Or do I need to use a specific version of Skyline? I tried 2.1 and 2.5.

Thank you for your help.
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error with: pk_runisotopemodification. what does it mean?
(3 responses) fabian bindel 2014-03-10 05:26
Dear all,

our systems administrator were kind to install LabKey for me in order to use the possibility with Skyline (Panorama).
But we run into a problem when searching for this error message I haven't found anything.

I see our LabKey-Server/Panorama in Skyline and when "publishing" to it I get the following error message:

20140305 Different Gradients Unscheduled_2014-03-10_12-28-51.sky.log    
Show summary

10 Mar 2014 12:28:57,598 INFO : Starting to import Skyline document from 20140305 Different Gradients Unscheduled_2014-03-10_12-28-51.sky.zip

10 Mar 2014 12:28:57,599 INFO : Expanding 20140305 Different Gradients Unscheduled.skyd

10 Mar 2014 12:28:57,648 INFO : Expanding 20140305 Different Gradients Unscheduled.sky.view

10 Mar 2014 12:28:57,649 INFO : Expanding 20140305 Different Gradients Unscheduled.sky

10 Mar 2014 12:28:57,724 ERROR: Skyline document import failed



Thus nothing gets uploaded to the server.
What could be the reason for this? User rights management?

Thank you very much for any help

Fabian Bindel
 Untitled.png 
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Problems importing Peptide Prophet results from TPP 4.6.2
(7 responses) e.k.lowe 2014-01-06 15:36
I have having a very odd issue with importing PepProphet results from the TPP. Sometimes when I go to select the file and click 'Import Data' I only get the msInspect potion NOT Import Search Results!

It seems to be project dependent and so far I have been unable to determine what is different between the projects I have created. All projects are MS2 projects.
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Rlabkey error in getting "Names" from "MS2SearchRuns"
(1 response) ashoka 2013-08-19 15:24
Hi guys,

I am issuing the following command after loading the Rlabkey package in R:

labkey.selectRows(baseUrl="http://myserver:8080/labkey/",folderPath="/myProject", schemaName="ms2",queryName="MS2SearchRuns")

I am getting the following error:
Error in if (mod == "date") { : missing value where TRUE/FALSE needed
In addition: Warning message:
In d[is.na(d)] <- as.Date(s[is.na(d)], "%d %b %Y %H:%M:%S") :
  number of items to replace is not a multiple of replacement length
---
My connection to the server seems to be fine and other commands from Rlabkey work as expected. In "Query Schema Browser" I can see the data when I press "VIEW DATA".
Any idea why this happens?
Thanks.
Ashoka.
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LabKey does not support mgf or pkl searches?
(1 response) dwang7 2013-08-09 09:24
Hi there,
I just have some mgf files from waters machine. when I try tpp tandem through command line, it goes through tandem search successfully; but the web interface for labkey cpas denies this type of format. Is only mzXML supported so far? What is the reason not supporting other format?

Thanks.

Best,
Dong
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FASTA parsing and Gene name
(8 responses) richard wilson 2013-07-10 22:32
Dear Labkey,
I'm using the mouse Complete Proteome Set as my FASTA, which contains a mixture of SwissProt and TrEMBL entries. It would be a massive help if the FASTA file is parsed to reconise GN= as the text that specifies the gene name which can then be viewed in MS dashboard. As the system is currently set up very few entries appear under the Heading 'Best gene name'
Can this be achieved?
Thanks
Richard
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Libra setup for cys-TMT labeling
(3 responses) dwang7 2013-07-06 22:45
Hi there,
I am pretty new to TMT quantitation. Apologies if my questions are too naive.

I am recently tackling iodoTMT6plex labeling on Cys. Libra algorithm, originally designed for itraq labelled at N term and Lys, is claimed to be also suitable for TMT on TPP wiki page. So I assume that labkey would also be capable of handling my situation. However, there is limited introduction to the Libra, and the main one:
http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/src/Quantitation/Libra/docs/libra_info.html
is pretty out of date. I generated the condition.xml file as attached file pretty much as indicated this page. My questions are:

1. can anybody help me look into the condition.xml file to see if there is any problem?
2. the default condition.xml is for itraq quantitation. So even I intended for TMT purpose, the labkey still displays something like:

iTRAQ Quantitation
Normalized 1    1.000    Absolute Intensity 1    666731.188
Normalized 2    2.782    Absolute Intensity 2    1854681.250
Normalized 3    6.175    Absolute Intensity 3    4116809.000
Normalized 4    12.833    Absolute Intensity 4    8556433.000
Normalized 5    25.960    Absolute Intensity 5    17308480.000
Normalized 6    51.994    Absolute Intensity 6    34665692.000

This is confusing since it still says "iTRAQ Quantitation", which lead me think whether Libra is working properly for my TMT.

3. TPP wiki pages says:
"If you would like to generate a condition.xml file, please use http://db.systemsbiology.net/webapps/conditionFileApp/". But the link is dead already. Can anybody update the link possibly?

4. Our TMT is labeled on Cys; so for a lot of identified peptides, if they don't have a cys, then it shouldn't display the quant information for that peptide. I guess I have to program to get rid of these fake quant information and re-assemble the protein quantitation. With that being said, Is there automatic way in labkey to automate this process? Is Libra @ TPP 4.5 suitable for my case?

5. I built TPP 4.5 rev2 in my redhat el6 linux box, together with labkey 13.1 binaries, tomcat 6, postgresql 9.2, and proteowizard 3.0. When it runs ms2, it automatically assign "tandem.exe input.xml" for searches, and of course it stops by complaining "cannot find tandm.exe". So I did the dirty change by "tandem" -> "tandem.exe", now everything works just fine. Maybe you wanna fix it in next release.

Thanks for any input in this thread! You guys are awesome to make beautiful stuff happening.

-Dong Wang
 tmt.xml 
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Q-Exactive files can not pass through labkey CPAS
(1 response) dwang7 2013-05-15 09:31
Hi there,
I have a very strange problem. I have 12 Q-exactive raw data; I converted using two versions of msconvert (pwiz version 3.0.3398, which is shipped with labkey 13.1), msconvert (pwiz version 3.0.4472, which I download myself). Here is my testing:
1. msconvert (old) --mzXML --zlib: can not be completed. Error message:
processing file: IPAS_0512_HCD_TCE_SG78to84.raw
[ThermoRawFile] [RawFile::ctor] Unable to initialize XRawfile; is MSFileReader installed? Reading Thermo RAW files requires MSFileReader to be installed. It is available for download at:
http://sjsupport.thermofinnigan.com/public/detail.asp?id=703
Error processing file IPAS_0512_HCD_TCE_SG78to84.raw

2. msconvert (new) --mzXML --zlib: can not be recognized by labkey xtandem (2009 version)
3. msconvert (new) --mzXML: can not be recognized by labkey xtandem (2009 version)
4. msconvert (new) --mzXML --zlib: can not be recognized by xtandem (2013 version, zlib not recognized)
5. msconvert (new) --mzXML --zlib: successfully recognized by xtandem (2013 version)

The error log file on which the xtandem (2009 version) failed were attached below.

Can anyone here give me hits of how to deal with Q-E data with our current labkey CPAS 13.1? I tried to replace it with xtandem 2013, but this does not support k_score. In my previous communication with labkey support, they said they used 2009 version because this is what TPP has; but I checked with TPP, their current release version is 4.6.2, which contains 2011 version of xandem. Question is: how this will affect the future release of labkey?

Any efforts to solve my Q-Exactive searches will be greatly appreciated. Thanks.

Best,
Dong Wang
 IPAS_0512_HCD_TCE_SG78to84.log 
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MS1 peak areas/msInspect support
(1 response) ashoka 2013-05-09 08:47
Apologies if this question has been answered already. I have also not checked the changelogs to see if this feature is dropped.

Is msinspect for MS1 peak area integration available in LabKey? I remember using this feature in the past but with the new version I didn't see the option. If its not available, are there any other methods to obtain the MS1 peak areas in LabKey?

Thanks!
Ashoka.
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Best Protein Name vs. Name from FASTA mixup
(2 responses) tvaisar 2013-05-07 06:57
I ran into an issue when I started to use Uniprot database for my database searches - although searching against Uniprot FASTA I was getting back a mix of different IDs (UniprotID and IPI IDs) when I uploaded and looked at the data in Labkey server. I changed the "Best name" to "Name from FASTA file" and things got better, but I was getting lot of UniprotIDs which I could not find online in Uniprot database either because they were updated or because they were removed. I thought it was because my database was not the current one so I uploaded and did my search against a current version of the Uniprot database. When uploaded to Labkey server I am now getting correct UniprotIDs when I look at individual samples, but when I use "Compare" for multiple samples it reverts to reporting the "outdated" protein IDs.
I can see that when I look up that particular protein ID the header contains both the ID from FASTA file but after it in parentheses is the "old" incorrect ID.
I tried to use the Sequences schema in the Query, but I do not see a field/variable which would correspond to the "Name from FASTA". I can only see "First Name" or "Best Name".

Any suggestions?

Tomas Vaisar
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rlabkey projects not showing
(4 responses) ashoka 2013-04-11 14:41
Hi,

I have a fresh Rlabkey (v12.3 on Win7) installed and am trying to connect via R. _netrc seem to work and connects to the server but when I do >lsProjects("http://mylabkeyserver:8080/labkey/") it only lists "/home" as the only project. But I do have two other projects. I tried with the admin console checking the permissions etc but all seem good and permitted. Why am i not seeing the projects? Am I missing something here in the folder path?

Thanks.
Ashoka.
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The number of unique peptides is more than the number of total peptides
(1 response) smisra1 2013-03-08 08:43
Hello all,

    I am new to CPAS and trying to understand the system. I have few questions-

1- When I exported the table of ProteinProphet (legacy) view, I notice that for many of the proteins the number of unique peptides is more than the number of total peptides. Why?

2- I am using large dataset and My exported table (excel) is limited by 65,536 rows. I am using excel 2007, so this should not be the case. ow to export so that I have the full list of the proteins/peptides.

3- What is the difference exactly in "protein group" and "proteinProphet(legacy)" under grouping section.

It would be great if somebody can provide me answers to these questions.

Thanks

Sandeep Misra
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urgent: bug in 12.2 excel export does not work
(1 response) anette.karle 2012-10-22 00:09
Dear Peter,

In Version 12.2 there is a bug in the compare peptides grid. When exporting the data in excel 97 only the first 100 rows are exported. The excel 2007 export does not work at all and comes back with an error.

We need to have this bug solved very quickly, since most of our data analysis is based on exported data.

Best
Anette
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Seq Hits in compare peptides grid?
(1 response) anette.karle 2012-10-10 04:46
Dear Peter,

I am looking for an option to include the Seq Hits in the compare peptides grid but I couldn't find it in the customize view. I can only select it if on the run details page. Does it require additional adjustments in our ms2 extensions module to be able to select the Seq Hits from the compare peptides grid?

Thanks in advance and best regards
Anette
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Filters are gone
(1 response) anette.karle 2012-09-10 04:28
Dear Peter,

By accident suddenly the Novstdfilter is not working for the compare peptides view anymore – obviously we did a mistake.
At the beginning it just didn’t work for one folder of a project but for the others it was fine. So I checked the view on the project level and there it said: there is no filter named Novstdfilters. So I tried a couple of things:
- I klicked on a run and selected Novstdfilters – customize – and just saved the view under the same name since it seemed to be correct. I also made it available for childfolders and other users. As a result the Novstdfilters was nowhere to be found in the compare peptides view of any folder anymore!
- So I tried to set the filter directly on this compare page on the project level (and made it available for childfolders and other users) – this worked to some extent: on the project level the peptide numbers are correct, but for all other subfolders there still is no Novstdfilters available to be selected for the peptide comparison.

I really don’t know what to do now – can you help me out here? This is really urgent!

Thanks and best regards
Anette
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Peptide counts don't match the number of peptides in the peptide sequence alignment view
(1 response) anette.karle 2012-08-13 03:42
For some new projects I realized the following: when doing the compare peptide functionality for a protein sequence the view for the aligned blue sequences does not match the distinct peptide counts given below the alignment view. The counts are in many cases higher than the ones shown in the "bluemap" on top. If I check the peptide list below, the list matches the bluemap but not the distinct peptide count value.
This is now really cumbersome since we have to count the peptides now manually since the count value is not reliable.

Do you have an idea why this count value is now suddenly wrong? Maybe some wrong properties of the project folder?

Best regards
Anette
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Spectral Counting / Redundant Protein Identification
(1 response) dennisorton 2012-08-02 13:25
Hello,

I am new to LabKey, and just as new to label-free Quantitative Proteomics (i.e. Spectral Counting) and I am having a problem removing redundant protein identifications prior to statistical analysis. I searched the UniProt database using X! Tandem and obtained the results, and after opening them in the "Spectra Count" view, the first thing I see is a large number of proteins identified by the same peptide(s). I am aware this is normal, however I am having a hard time determining how to eliminate the redundancy in the results without reducing the sensitivity of my statistical analysis.

Any help on how to accomplish this would be greatly appreciated.

Thanks.
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Conversion of LabKey results (X!Tandem/Prophet) to PRIDE XML
robert.winkler 2012-03-22 16:15
Hi, I would like to upload LabKey 11.3 results (X!Tandem/Prophet) to the PRIDE repository.

When starting the conversion with the PRIDE converter v. 2.5.5., the following error occurs:

Found a spectrum query at line 704 which references run '100517_BSA_COOM.mzXML' while it is contained in run element '100517_BSA_COOM'!

Ideas?

Thanks, Robert
 ErrorLog.txt 
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Fixed C13 modifications for Mascot
(2 responses) sanja.trajkovic 2012-02-01 12:59
Hi,

I have a C13 labeled sample, R+6 and K+6 (SILAC), and would like to search through Mascot with those modifications fixed. However, they are not offered in the list. Would you, please, help me write the script? Thank you!

Sincerely,
Sanja
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Stalled sequest data upload
(4 responses) tvaisar 2012-01-31 16:39
I am running into a problem trying to upload sequest/TPP results into CPAS. Nothing obvious changed since the last time (about 10 days ago) I uploaded data. Now I go to Process and import data, point to the directory with data and select prot.xml file - click Import results, and the process stalls - e.g. nothing happens only the webpage activity indicator spins as if trying to reload the page. When I go to the Pipeline page it indicates the given file as Waiting and there is nothing in the log file (blank page). I find no related errors in the Admin console site errors.

I am puzzled and would appreciate any suggestions and help.

Tomas

I would add that there is large number of current threads (guesstimate is ~50) of following type:
http-8080-processorX (WAITING) (or RUNNABLE)
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X!Tandem search
(2 responses) jbas222 2012-01-26 17:45
Hello,

I am getting error for the x!tandem search, in the log file it reads " ERROR: Fault received from Globus on "submit" command". I will appreciate some suggestions, please see attached the log file.
Thanks

Jennifer.
 beiRa.log 
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MudPit analysis problem
(4 responses) sanja.trajkovic 2012-01-25 13:39
Hello,

I am attempting to run a MudPit analysis through CPAS using Mascot. However, I keep getting an error report with this message:
command "PeptideProphetParser 'all.pep.xml' EXTRAITRS=20" exited with non-zero exit code: 256
Would you, please, be so kind to suggest how can I resolve this. Thank you very much!

With regards,
Sanja Trajkovic
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Annotation of large protein databases
(15 responses) weiclav 2012-01-03 23:16
Dear all,

I encountered problems with annotation of the large databases in LabKey server (the whole NCBInr database - FASTA format, about 8 GB; UniRef100 - FASTA and XML format, about 8GB and 22GB, respectively). In the case of processing database in FASTA format the LabKey server reports at least error with small Java heap space ("java.lang.OutOfMemoryError: Java heap space"). When I want to annotate database in XML format I did not get any error report (labkey.log, labkey-errors.log) and the database processing just stopped (CPU usage by tomcat5.exe droped down and the RAM utilization by the process went also down). (I was able to repeat this problem on several computers)

I tried increasing the Java heap space and "MaxPermSize" up to 1400 MB and 256 MB, respectively, but without any luck - the behaviour was the same. Recently I moved to 64-bit Java and tried to increase heap space even more. 3GB were not satisfactory (UniRef100.fasta; I get the same Java heap space error as with 32-bit Java). 6GB Java heap space proved to be "sifficient" without any other changes e.g. in "MaxPermSize" (at least for the UniRef100.fasta, I did not try other large databases yet).

From the labkey.log file I found out that in the case of UniRef100.fasta the LabKey server is trying to processe 20,000 sequences per batch. On the other hand when I annotated smaller databases (e.g. UniProt.fasta(.xml)) the annotation algorithm took 5,000 sequences per batch...

Here are my questions:
1) is it possible to modify the number of sequences processed within the single batch?
2) is the number of sequences per batch connected somehow to the total number of sequences in the database or is it connected with something else?
3) is it possible to get to the state where e.g. 2GB of Java heap space would by ok for 8GB database by modifying any other parameter of JVM or LabKey server?
4) is there any othe place where I would be able to find any log entry for the problems occured while annotating large database in XML format? (I am not sure whether the problem was also in the Java heap size...).

Thanks in advance for your kind responces!

Regards,
David

PS: now, during the continuing annotation, the tomcat5.exe process uses about 2.6GB of RAM; for the first batch to finish it needed more, about 4GB. So maybe the number of annotating sequences does not matter and there is another initial step in database annotation that causes the problem? However, about 4.4 GB is still used by Java heap based on info at "Memory usage" page...
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Uploading data from a sorcerer to CPAS
(12 responses) levb 2011-11-17 12:11
I have CPAS loaded on my primary computer and am trying to import and process files from a Sagen Sorcerer sever that is also in my office. I have mapped the Sorcerer as a network drive and have tried to setup a pipeline override to point CPAS to the folder with the .xml files but I cannot get the files loaded. Does anyone have any suggestions?

Thanks

Lev
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Searching Target-decoy database in CPAS
(1 response) anavare 2011-11-03 10:01
Hello,

I wanted to how can I search mzXML files against a concatenated target-decoy database (created using COMPASS)in CPAS? The way I did it was by adding the following command line in the X!Tandem XML window: <note label="pipeline prophet, decoy tag" type="input">d</note>

The search was completed successfully without any errors, but I am not sure if having the decoy sequence really made any difference.
Any help is appreciated.

Thanks
Arti
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Peptide Search buttons greyed-out??
(3 responses) goodman 2011-10-13 05:46
What would cause the "Sequest Peptide Search" "Mascot Peptide Search" and "X!Tandem Peptide Search" buttons to be greyed-out/non-functional for some folders (but not all)?

MS2 Dashboard > Pipeline > Process and Import Data, or Manage Files.

Logged in as an Administrator; LabKey Server 10.1


Thanks in advance,

Jack Goodman
University of Kentucky
goodman@uky.edu
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Labkey Server 11.2 TPP version
(1 response) rwf 2011-09-19 11:48

Hello,

I am upgrading from 10.3 to 11.2 and would like to know if the TPP version remains the same (4.3.1) ?

thanks

Ron
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Error importing protein prophet prot.xml files
(2 responses) rob_ewing50 2011-09-19 11:46
Hello:
I get the following errors from time to time in importing protein prophet prot.xml files:
It seems to be something to do with the xml itself - but I cannot find the place in the file it refers to. Anyone seen this or know how to find the referenced line in the xml file?
I have attached the guilty prot.xml file.
I am using version 11 of labkey and TPP v4.3 JETSTREAM rev 1, Build 201101131447 to run peptide and protein prophet.

thanks.


18 Feb 2011 21:19:48,550 INFO : Importing MS/MS results is 93% complete
18 Feb 2011 21:19:48,860 INFO : Importing MS/MS results is 94% complete
18 Feb 2011 21:19:48,953 INFO : Importing MS/MS results is 95% complete
18 Feb 2011 21:19:51,080 INFO : Importing MS/MS results is 96% complete
18 Feb 2011 21:19:51,829 INFO : Importing MS/MS results is 97% complete
18 Feb 2011 21:19:51,937 INFO : Importing MS/MS results is 98% complete
18 Feb 2011 21:19:52,048 INFO : Importing MS/MS results is 99% complete
18 Feb 2011 21:19:53,324 INFO : Importing MS/MS results is 100% complete
18 Feb 2011 21:19:55,803 INFO : 25.02 seconds to import spectra from /mnt/rewing/cpas/labkey10/IP_CTNNB1/./bCat_IP_APCKI_HCT116_20Apr2010.tgz
18 Feb 2011 21:19:55,854 INFO : Starting to update SeqId column
18 Feb 2011 21:20:07,242 INFO : 11.39 seconds to update SeqId column
18 Feb 2011 21:20:07,299 INFO : Starting to update SequencePosition column
18 Feb 2011 21:20:10,759 INFO : 3.46 seconds to update SequencePosition column
18 Feb 2011 21:20:10,815 INFO : Starting to update peptide and spectrum counts
18 Feb 2011 21:20:10,934 INFO : 0.12 seconds to update peptide and spectrum counts
18 Feb 2011 21:20:10,981 INFO : ========================================
18 Feb 2011 21:20:11,023 INFO : Summary of all timed tasks:
18 Feb 2011 21:20:11,073 INFO :
18 Feb 2011 21:20:11,115 INFO : 0.20 seconds to clear out any previously imported data
18 Feb 2011 21:20:11,156 INFO : 5.23 seconds to import FASTA file
18 Feb 2011 21:20:11,199 INFO : 14.40 seconds to import peptide search results
18 Feb 2011 21:20:11,265 INFO : 25.02 seconds to import spectra
18 Feb 2011 21:20:11,316 INFO : 11.39 seconds to update SeqId column
18 Feb 2011 21:20:11,366 INFO : 3.46 seconds to update SequencePosition column
18 Feb 2011 21:20:11,416 INFO : 0.12 seconds to update peptide and spectrum counts
18 Feb 2011 21:20:11,466 INFO :
18 Feb 2011 21:20:11,516 INFO : 59.82 seconds to import "interact-bCat_IP_APCKI_HCT116_20Apr2010.pep.xml" and import spectra
18 Feb 2011 21:20:11,566 INFO : ========================================
18 Feb 2011 21:20:23,990 INFO : Starting to move data into ms2.PeptidesMemberships
18 Feb 2011 21:20:26,599 INFO : Finished with moving data into ms2.PeptidesMemberships after 2609 ms
18 Feb 2011 21:20:26,652 INFO : Starting to move data into ms2.ProteinGroupMemberships
18 Feb 2011 21:20:32,075 INFO : Finished with moving data into ms2.ProteinGroupMemberships after 5422 ms
18 Feb 2011 21:20:32,449 INFO : ProteinProphet file import finished successfully, 5110 protein groups loaded
18 Feb 2011 21:20:32,506 INFO : ProteinProphet import took 81 seconds.
23 May 2011 19:23:46,352 INFO : Starting to load ProteinProphet file /mnt/rewing/cpas/labkey10/IP_CTNNB1/./interact-bCat_IP_APCKI_HCT116_20Apr2010.prot.xml
23 May 2011 19:23:46,636 INFO : Resolved referenced PepXML file to /mnt/rewing/cpas/labkey10/IP_CTNNB1/./interact-bCat_IP_APCKI_HCT116_20Apr2010.pep.xml
23 May 2011 19:23:46,687 INFO : Starting import from interact-bCat_IP_APCKI_HCT116_20Apr2010.pep.xml
23 May 2011 19:23:46,825 INFO : Starting to clear out any previously imported data for interact-bCat_IP_APCKI_HCT116_20Apr2010.pep.xml
23 May 2011 19:23:47,142 INFO : 0.32 seconds to clear out any previously imported data for interact-bCat_IP_APCKI_HCT116_20Apr2010.pep.xml
23 May 2011 19:23:47,194 INFO : Starting to import FASTA file /data/public/sequence/ipi.HUMAN.v3.49.mod.fasta
23 May 2011 19:23:52,627 INFO : FASTA file "/data/public/sequence/ipi.HUMAN.v3.49.mod.fasta" has already been imported
23 May 2011 19:23:52,774 INFO : 5.58 seconds to import FASTA file /data/public/sequence/ipi.HUMAN.v3.49.mod.fasta
23 May 2011 19:23:52,826 INFO : Starting to import peptide search results for fraction 1, analysis of file null
23 May 2011 19:23:52,876 INFO : Importing MS/MS results is 0% complete
23 May 2011 19:23:53,158 INFO : Importing MS/MS results is 1% complete
23 May 2011 19:23:54,051 INFO : Importing MS/MS results is 2% complete
23 May 2011 19:23:54,436 INFO : Importing MS/MS results is 3% complete
23 May 2011 19:23:54,711 INFO : Importing MS/MS results is 4% complete
23 May 2011 19:23:55,430 INFO : Importing MS/MS results is 5% complete
23 May 2011 19:23:55,840 INFO : Importing MS/MS results is 6% complete
23 May 2011 19:23:56,232 INFO : Importing MS/MS results is 7% complete
23 May 2011 19:23:56,621 INFO : Importing MS/MS results is 8% complete
23 May 2011 19:23:56,837 INFO : Importing MS/MS results is 9% complete
23 May 2011 19:23:57,150 INFO : Importing MS/MS results is 10% complete
23 May 2011 19:23:57,446 INFO : Importing MS/MS results is 11% complete
23 May 2011 19:23:58,059 INFO : Importing MS/MS results is 12% complete
23 May 2011 19:23:58,638 INFO : Importing MS/MS results is 13% complete
23 May 2011 19:23:59,157 INFO : Importing MS/MS results is 14% complete
23 May 2011 19:23:59,988 INFO : Importing MS/MS results is 15% complete
23 May 2011 19:24:00,511 INFO : Importing MS/MS results is 16% complete
23 May 2011 19:24:01,020 INFO : Importing MS/MS results is 17% complete
23 May 2011 19:24:01,504 INFO : Importing MS/MS results is 18% complete
23 May 2011 19:24:02,129 INFO : Importing MS/MS results is 19% complete
23 May 2011 19:24:02,790 INFO : Importing MS/MS results is 20% complete
23 May 2011 19:24:03,612 INFO : Importing MS/MS results is 21% complete
23 May 2011 19:24:04,149 INFO : Importing MS/MS results is 22% complete
23 May 2011 19:24:04,761 INFO : Importing MS/MS results is 23% complete
23 May 2011 19:24:11,239 INFO : Importing MS/MS results is 24% complete
23 May 2011 19:24:12,084 INFO : Importing MS/MS results is 25% complete
23 May 2011 19:24:12,831 INFO : Importing MS/MS results is 26% complete
23 May 2011 19:24:13,363 INFO : Importing MS/MS results is 27% complete
23 May 2011 19:24:14,282 INFO : Importing MS/MS results is 28% complete
23 May 2011 19:24:14,860 INFO : Importing MS/MS results is 29% complete
23 May 2011 19:24:15,342 INFO : Importing MS/MS results is 30% complete
23 May 2011 19:24:21,546 INFO : Importing MS/MS results is 31% complete
23 May 2011 19:24:30,748 INFO : Importing MS/MS results is 32% complete
23 May 2011 19:24:31,149 INFO : Importing MS/MS results is 33% complete
23 May 2011 19:24:32,181 INFO : Importing MS/MS results is 34% complete
23 May 2011 19:24:34,221 INFO : Importing MS/MS results is 35% complete
23 May 2011 19:24:34,653 INFO : Importing MS/MS results is 36% complete
23 May 2011 19:24:35,257 INFO : 42.43 seconds to import peptide search results for fraction 1, analysis of file null
23 May 2011 19:24:35,298 INFO : Starting to import spectra from /mnt/rewing/cpas/labkey10/IP_CTNNB1/./bCat_IP_APCKI_HCT116_20Apr2010.tgz
23 May 2011 19:24:35,349 INFO : Importing MS/MS results is 37% complete
23 May 2011 19:24:35,570 INFO : Importing MS/MS results is 38% complete
23 May 2011 19:24:36,762 INFO : Importing MS/MS results is 39% complete
23 May 2011 19:24:37,084 INFO : Importing MS/MS results is 40% complete
23 May 2011 19:24:37,458 INFO : Importing MS/MS results is 41% complete
23 May 2011 19:24:38,080 INFO : Importing MS/MS results is 42% complete
23 May 2011 19:24:38,240 INFO : Importing MS/MS results is 43% complete
23 May 2011 19:24:38,609 INFO : Importing MS/MS results is 44% complete
23 May 2011 19:24:38,891 INFO : Importing MS/MS results is 45% complete
23 May 2011 19:24:41,572 INFO : Importing MS/MS results is 46% complete
23 May 2011 19:24:41,908 INFO : Importing MS/MS results is 47% complete
23 May 2011 19:24:42,726 INFO : Importing MS/MS results is 48% complete
23 May 2011 19:24:43,193 INFO : Importing MS/MS results is 49% complete
23 May 2011 19:24:43,738 INFO : Importing MS/MS results is 50% complete
23 May 2011 19:24:47,157 INFO : Importing MS/MS results is 51% complete
23 May 2011 19:24:48,118 INFO : Importing MS/MS results is 52% complete
23 May 2011 19:24:48,700 INFO : Importing MS/MS results is 53% complete
23 May 2011 19:24:49,137 INFO : Importing MS/MS results is 54% complete
23 May 2011 19:24:50,454 INFO : Importing MS/MS results is 55% complete
23 May 2011 19:24:52,374 INFO : Importing MS/MS results is 56% complete
23 May 2011 19:24:52,736 INFO : Importing MS/MS results is 57% complete
23 May 2011 19:24:52,959 INFO : Importing MS/MS results is 58% complete
23 May 2011 19:24:53,321 INFO : Importing MS/MS results is 59% complete
23 May 2011 19:24:53,547 INFO : Importing MS/MS results is 60% complete
23 May 2011 19:24:53,737 INFO : Importing MS/MS results is 61% complete
23 May 2011 19:24:54,088 INFO : Importing MS/MS results is 62% complete
23 May 2011 19:24:54,319 INFO : Importing MS/MS results is 63% complete
23 May 2011 19:24:54,522 INFO : Importing MS/MS results is 64% complete
23 May 2011 19:24:54,802 INFO : Importing MS/MS results is 65% complete
23 May 2011 19:24:56,054 INFO : Importing MS/MS results is 66% complete
23 May 2011 19:24:58,991 INFO : Importing MS/MS results is 67% complete
23 May 2011 19:25:08,471 INFO : Importing MS/MS results is 68% complete
23 May 2011 19:25:10,722 INFO : Importing MS/MS results is 69% complete
23 May 2011 19:25:11,014 INFO : Importing MS/MS results is 70% complete
23 May 2011 19:25:11,232 INFO : Importing MS/MS results is 71% complete
23 May 2011 19:25:11,410 INFO : Importing MS/MS results is 72% complete
23 May 2011 19:25:11,601 INFO : Importing MS/MS results is 73% complete
23 May 2011 19:25:13,334 ERROR: XMLStreamException in hasNext()
javax.xml.stream.XMLStreamException: ParseError at [row,col]:[123448,141]
Message: Element type "analysis_result" must be followed by either attribute specifications, ">" or "/>".
    at com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:588)
    at org.labkey.api.reader.XMLStreamReaderWrapper.next(XMLStreamReaderWrapper.java:246)
    at org.labkey.api.reader.SimpleXMLStreamReader.skipTo(SimpleXMLStreamReader.java:81)
    at org.labkey.api.reader.SimpleXMLStreamReader.skipToStart(SimpleXMLStreamReader.java:67)
    at org.labkey.ms2.reader.PepXmlLoader$FractionIterator.hasNext(PepXmlLoader.java:104)
    at org.labkey.ms2.PepXmlImporter.importRun(PepXmlImporter.java:86)
    at org.labkey.ms2.MS2Importer.upload(MS2Importer.java:199)
    at org.labkey.ms2.MS2Manager.importRun(MS2Manager.java:585)
    at org.labkey.ms2.MS2Manager.addRun(MS2Manager.java:570)
    at org.labkey.ms2.ProteinProphetImporter.importRun(ProteinProphetImporter.java:349)
    at org.labkey.ms2.ProteinProphetImporter.importFile(ProteinProphetImporter.java:78)
    at org.labkey.ms2.pipeline.ProteinProphetPipelineJob.run(ProteinProphetPipelineJob.java:69)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
    at java.util.concurrent.FutureTask.run(FutureTask.java:138)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:98)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:207)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
    at java.lang.Thread.run(Thread.java:619)
23 May 2011 19:25:13,401 ERROR: MS2 import failed
java.lang.RuntimeException: XMLStreamException in hasNext()
    at org.labkey.ms2.reader.PepXmlLoader$FractionIterator.hasNext(PepXmlLoader.java:109)
    at org.labkey.ms2.PepXmlImporter.importRun(PepXmlImporter.java:86)
    at org.labkey.ms2.MS2Importer.upload(MS2Importer.java:199)
    at org.labkey.ms2.MS2Manager.importRun(MS2Manager.java:585)
    at org.labkey.ms2.MS2Manager.addRun(MS2Manager.java:570)
    at org.labkey.ms2.ProteinProphetImporter.importRun(ProteinProphetImporter.java:349)
    at org.labkey.ms2.ProteinProphetImporter.importFile(ProteinProphetImporter.java:78)
    at org.labkey.ms2.pipeline.ProteinProphetPipelineJob.run(ProteinProphetPipelineJob.java:69)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
    at java.util.concurrent.FutureTask.run(FutureTask.java:138)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:98)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:207)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
    at java.lang.Thread.run(Thread.java:619)
Caused by: javax.xml.stream.XMLStreamException: ParseError at [row,col]:[123448,141]
Message: Element type "analysis_result" must be followed by either attribute specifications, ">" or "/>".
    at com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:588)
    at org.labkey.api.reader.XMLStreamReaderWrapper.next(XMLStreamReaderWrapper.java:246)
    at org.labkey.api.reader.SimpleXMLStreamReader.skipTo(SimpleXMLStreamReader.java:81)
    at org.labkey.api.reader.SimpleXMLStreamReader.skipToStart(SimpleXMLStreamReader.java:67)
    at org.labkey.ms2.reader.PepXmlLoader$FractionIterator.hasNext(PepXmlLoader.java:104)
    ... 15 more
23 May 2011 19:25:13,484 ERROR: ProteinProphet load failed
java.lang.RuntimeException: XMLStreamException in hasNext()
    at org.labkey.ms2.reader.PepXmlLoader$FractionIterator.hasNext(PepXmlLoader.java:109)
    at org.labkey.ms2.PepXmlImporter.importRun(PepXmlImporter.java:86)
    at org.labkey.ms2.MS2Importer.upload(MS2Importer.java:199)
    at org.labkey.ms2.MS2Manager.importRun(MS2Manager.java:585)
    at org.labkey.ms2.MS2Manager.addRun(MS2Manager.java:570)
    at org.labkey.ms2.ProteinProphetImporter.importRun(ProteinProphetImporter.java:349)
    at org.labkey.ms2.ProteinProphetImporter.importFile(ProteinProphetImporter.java:78)
    at org.labkey.ms2.pipeline.ProteinProphetPipelineJob.run(ProteinProphetPipelineJob.java:69)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
    at java.util.concurrent.FutureTask.run(FutureTask.java:138)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:98)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:207)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
    at java.lang.Thread.run(Thread.java:619)
Caused by: javax.xml.stream.XMLStreamException: ParseError at [row,col]:[123448,141]
Message: Element type "analysis_result" must be followed by either attribute specifications, ">" or "/>".
    at com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:588)
    at org.labkey.api.reader.XMLStreamReaderWrapper.next(XMLStreamReaderWrapper.java:246)
    at org.labkey.api.reader.SimpleXMLStreamReader.skipTo(SimpleXMLStreamReader.java:81)
    at org.labkey.api.reader.SimpleXMLStreamReader.skipToStart(SimpleXMLStreamReader.java:67)
    at org.labkey.ms2.reader.PepXmlLoader$FractionIterator.hasNext(PepXmlLoader.java:104)
    ... 15 more
 interact-bCat_IP_APCKI_HCT116_20Apr2010.prot.xml 
view message
Libra ratios visible?
(1 response) mboehmer 2011-08-29 08:30
I just installed Labkey 11.2 and I am quite excited about the new features. I tested Libra quantification for some iTRAQ data that we did and it seems to be working, after depositing a condition file and using the following commands in the X!Tandem search:

    <note label="pipeline quantitation, libra config name" type="input">libra</note>
    <note label="pipeline quantitation, libra normalization channel" type="input">1</note>

Now I am wondering whether these quantification results can be displayed in the standard view in Labkey? So far I see them only in the generated Excel file.

Thanks
view message
multiple variable modifications in SEQUEST search
(2 responses) anette.karle 2011-06-07 07:29
I would like to run SEQUEST searches with a lot of different PTMs (even if it slows down the search). How many different variable mods can be handled by SEQUEST - I would need to enter several variable mods for one single amino acid. Could you tell me how to do this in the params file?

I would be glad for your help

Best
Anette
view message
Fasta database entries changes and cleanup
(1 response) anette.karle 2011-06-06 04:20
Hi Peter,
I had a wrong sequence in our fasta file, so I deleted this entry, added the new sequence under a new name to be on the safe side and saved the whole fasta file under a new name. I also did the SEQUEST search on the raw files again with the new fasta file. When I search for the old sequence name in these newly analyzed runs I still can find the entry of the wrong sequence. Is there a way to do to a clean-up?
Is it also possible to change a sequence and keep the same protein name?

Best regards
Anette
view message
mzML support in Labkey
(3 responses) mboehmer 2011-05-31 07:18
Hi,

I tried to activate the mzML support in Labkey 11.1. I could not localize the pwiz-swigbindings library on the server. I installed TPP 4.4.1 via repository on an Ubuntu server, not from source. Any suggestions where to look?

Thanks!
view message
CPAS MS2 "Describe data"
(4 responses) marco.falda 2011-04-26 02:30
Hello,

   I have installed Labkey 11.1 both on a Win7 64bit, base version, and on a Linux Debian 64bit, Enterprise Pipeline. I ask your help about three problems I have met:

1. The button "Describe data" cited in point 4 of the CPAS demo (URL: https://www.labkey.org/wiki/home/Documentation/page.view?name=describeAndSearch) and its simplified dialog for describing the MS2 protocol used does not appear in any setup. Could you give me suggestions?

2. I am writing a Prolog application for easing the creation and the management of custom protocols in XAR format, but I am not able to perform a simple search (e.g. protocol n. 5 at https://www.labkey.org/wiki/home/Documentation/page.view?name=tutorial4) because, apparently, a mzXML data handler is missing. Is there a simple example XAR describing a Mascot search? Are there perhaps special predefined "hard-wired" protocols in LabKey?

3. I tried to create SASPECT R views without success (URL: https://www.labkey.org/wiki/home/Documentation/page.view?name=labelFree&_docid=wiki%3A6ba067ef-e8bb-102a-a8c1-d104f9cdbb53). In particular, some custom columns are missing, for example "protein_customannotations_pepperspikedpr3" and also a part of a script "SASPECT_v81_f1_Pei.R". I think that these strange names could be dynamic names, since they are never mentioned in the tutorial (I will re-check all steps).

   Finally, is there a way to recover the "emPAI" parameter from Mascot searches?

   Thank you very much for the replies you will be able to provide me.


        Marco
view message
Mascot 2.3.02 not sending expected end of upload string
heckend 2011-04-14 09:49
Running searches on LabKey 10.3 with our 2.2.1 and 2.2.03 servers work fine. When we attempt to use 2.3.02, Mascot runs the search but never returns the expected "Finished uploading search details and file..." line. Is it possible this is just a configuration problem on our Mascot 2.3.02 server?
Attached are my patch for MascotClientImpl.java to get it working with the 2.3.02 server and the logs for the 2.2.1 and 2.3.02 runs with the server response logging line uncommented.
 mascot-2.3.02.txt  patch.txt  mascot-2.2.1.txt 
view message
Error while Importing Existing Analysis Results
(3 responses) christian.pfaff 2011-04-06 02:34
Hello

I tried to import Existing CPAS Analysis Results from an other server.
Unfortunately I am always running into a null pointer exception (see below).
I tried to import a pep file and I have both, the pep and prot file available in the import folder.
The source server is a windows, the server where I try the import is a linux, don't know if this is relevant.

Additional question: How can I get rid of the jobs in the data pipeline section, which actually failed, but are now in waiting state?

Any ideas?

Best regards, Christian

java.lang.NullPointerException
        at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:160)
        at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)
        at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)
        at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)
        at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)
        at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)
        at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)
        at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)
        at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)
        at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)
        at org.labkey.pipeline.analysis.FileAnalysisJob.findFileInAlternateDirectory(FileAnalysisJob.java:165)
        at org.labkey.pipeline.analysis.FileAnalysisJob.findFile(FileAnalysisJob.java:134)
        at org.labkey.pipeline.analysis.FileAnalysisJob.findInputFile(FileAnalysisJob.java:81)
        at org.labkey.pipeline.api.AbstractWorkDirectory.getDir(AbstractWorkDirectory.java:157)
        at org.labkey.pipeline.api.AbstractWorkDirectory.newFile(AbstractWorkDirectory.java:180)
        at org.labkey.pipeline.analysis.CommandTaskImpl.newWorkFile(CommandTaskImpl.java:306)
        at org.labkey.pipeline.analysis.CommandTaskImpl.getWorkFiles(CommandTaskImpl.java:295)
        at org.labkey.pipeline.analysis.CommandTaskImpl.getProcessPaths(CommandTaskImpl.java:277)
        at org.labkey.api.pipeline.cmd.TaskPathToCommandArgs.getPaths(TaskPathToCommandArgs.java:57)
        at org.labkey.api.pipeline.cmd.PathToCommandArgs.toArgsInner(PathToCommandArgs.java:28)
        at org.labkey.api.pipeline.cmd.TaskToCommandArgs.toArgs(TaskToCommandArgs.java:61)
        at org.labkey.api.pipeline.cmd.ListToCommandArgs.toArgsInner(ListToCommandArgs.java:70)
        at org.labkey.api.pipeline.cmd.TaskToCommandArgs.toArgs(TaskToCommandArgs.java:61)
        at org.labkey.api.pipeline.cmd.EnumToCommandArgs.toArgsInner(EnumToCommandArgs.java:67)
        at org.labkey.api.pipeline.cmd.TaskToCommandArgs.toArgs(TaskToCommandArgs.java:61)
        at org.labkey.pipeline.analysis.CommandTaskImpl$Factory.isParticipant(CommandTaskImpl.java:189)
        at org.labkey.api.pipeline.PipelineJob.findRunnableTask(PipelineJob.java:716)
        at org.labkey.api.pipeline.PipelineJob.runStateMachine(PipelineJob.java:659)
        at org.labkey.api.pipeline.PipelineJob.setQueue(PipelineJob.java:473)
        at org.labkey.pipeline.api.PipelineQueueImpl.addJob(PipelineQueueImpl.java:83)
        at org.labkey.pipeline.api.PipelineServiceImpl.queueJob(PipelineServiceImpl.java:290)
        at org.labkey.pipeline.analysis.AnalysisController$StartAnalysisAction.execute(AnalysisController.java:211)
        at org.labkey.pipeline.analysis.AnalysisController$AbstractAnalysisApiAction.execute(AnalysisController.java:271)
        at org.labkey.pipeline.analysis.AnalysisController$AbstractAnalysisApiAction.execute(AnalysisController.java:251)
        at org.labkey.api.action.ApiAction.handlePost(ApiAction.java:144)
        at org.labkey.api.action.ApiAction.handleRequest(ApiAction.java:95)
        at org.labkey.api.action.BaseViewAction.handleRequestInternal(BaseViewAction.java:167)
        at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153)
        at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:349)
        at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:756)
        at org.labkey.api.view.ViewServlet.service(ViewServlet.java:166)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:36)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:118)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:603)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:138)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:210)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:174)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:151)
        at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:870)
        at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665)
        at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528)
        at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81)
        at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:685)
        at java.lang.Thread.run(Thread.java:619)
view message
Xinteract being called with -d"..\..\.." errors out during XPressPeptideParser TPP xinteract ver 4.3.1
(2 responses) donw 2011-02-25 10:46
Hi, we are still running a SILAC mzXML of Orbitrap data through Mascot pipeline using TPP toolset Ver 4.3.1 except for Mascot2XML which if Ver 4.4.1

**********************************************************
When trying to run Xpress for quantitation we are seeing the following being passed to xinteract:

25 Feb 2011 11:46:19,781 INFO : running: D:\LabKey Server\bin\xinteract -x20 -Opt -nR -X-nK,6.020129 -nR,10.0083 -m0.01 -d"..\..\.." -No261_08mar17_02_sec9.pep.xml ..\o261_08mar17_02_sec9_raw.pep.xml
*********************************************************

Is there a parameter I am using or failing to use which is causing the -d"..\..\.." to be sent?
It seems this trips of the parser when it is trying to find the mzXML file.

Here are the Pipeline Quantitation parameters I am passing. (Full mascot.xml commands attached)

<note label="pipeline quantitation, residue label mass" type="input">6.020129@K,10.0083@R</note>
<note label="pipeline quantitation, algorithm" type="input">xpress</note>
<note label="pipeline quantitation, mass tolerance" type="input">0.01</note>
<note label="pipeline quantitation, max fractional delta mass" type="input">20</note>
<note label="pipeline quantitation, min peptide prophet" type="input">0.90</note>

Thanks
Don


Part of Log file where error first occurs below. Parameters used to kick off run in file attached mascot.xml. Log file is attached.
25 Feb 2011 11:46:19,781 INFO : =======================================
25 Feb 2011 11:46:19,781 INFO : Working directory is D:\LabKey Server\files\Kolla MS2\@files\.\mascot\MascotSearchTest2SilacQuantTry2\o261_08mar17_02_sec9.work
25 Feb 2011 11:46:19,781 INFO : running: D:\LabKey Server\bin\xinteract -x20 -Opt -nR -X-nK,6.020129 -nR,10.0083 -m0.01 -d"..\..\.." -No261_08mar17_02_sec9.pep.xml ..\o261_08mar17_02_sec9_raw.pep.xml
25 Feb 2011 11:46:19,781 INFO :
25 Feb 2011 11:46:19,781 INFO : D:\LabKey Server\bin\xinteract (TPP v4.3 JETSTREAM rev 1, Build 200909211148 (MSVC))
25 Feb 2011 11:46:19,781 INFO :
25 Feb 2011 11:46:19,781 INFO : running: "InteractParser "o261_08mar17_02_sec9.pep.xml" "..\o261_08mar17_02_sec9_raw.pep.xml" -L"7""
25 Feb 2011 11:46:20,046 INFO : file 1: ..\o261_08mar17_02_sec9_raw.pep.xml
25 Feb 2011 11:46:21,203 INFO : processed altogether 4417 results
25 Feb 2011 11:46:22,109 INFO : command completed in 3 sec
25 Feb 2011 11:46:22,109 INFO :
25 Feb 2011 11:46:22,109 INFO : running: "PeptideProphetParser "o261_08mar17_02_sec9.pep.xml" EXTRAITRS=20"
25 Feb 2011 11:46:22,125 INFO : (MASCOT)
25 Feb 2011 11:46:22,250 INFO : results for charge 1: 0 id tot and 0 adj scores
25 Feb 2011 11:46:22,468 INFO : results for charge 2: 3167 id tot and 1086 adj scores
25 Feb 2011 11:46:22,468 INFO : results for charge 2: 12.384 adj_ion_mean and 18.6871 adj_ion_hom mean 35.0093id mean0.941093 correlation (r)
25 Feb 2011 11:46:22,468 INFO : 2+ ion - id = 1.06625*(ion - hom) + -7.54113 with error = 5.81113
25 Feb 2011 11:46:22,468 INFO : mean ion - id: 12.384, mean ion - hom: 18.6871
25 Feb 2011 11:46:22,625 INFO : results for charge 3: 1250 id tot and 149 adj scores
25 Feb 2011 11:46:22,625 INFO : results for charge 3: 4.80601 adj_ion_mean and 11.5607 adj_ion_hom mean 33.7552id mean0.951477 correlation (r)
25 Feb 2011 11:46:22,625 INFO : 3+ ion - id = 1.10366*(ion - hom) + -7.953 with error = 4.20348
25 Feb 2011 11:46:22,625 INFO : mean ion - id: 4.80601, mean ion - hom: 11.5607
25 Feb 2011 11:46:22,750 INFO : results for charge 4: 0 id tot and 0 adj scores
25 Feb 2011 11:46:22,875 INFO : results for charge 5: 0 id tot and 0 adj scores
25 Feb 2011 11:46:22,984 INFO : results for charge 6: 0 id tot and 0 adj scores
25 Feb 2011 11:46:22,984 INFO : results for charge 6: -0 adj_ion_mean and -0 adj_ion_hom mean 0id mean-1.#IND correlation (r)
25 Feb 2011 11:46:23,109 INFO : results for charge 7: 0 id tot and 0 adj scores
25 Feb 2011 11:46:23,109 INFO : init with MASCOT trypsin
25 Feb 2011 11:46:23,406 INFO : MS Instrument info: Manufacturer: Thermo Scientific, Model: LTQ Orbitrap, Ionization: NSI, Analyzer: FTMS, Detector: unknown
25 Feb 2011 11:46:23,406 INFO :
25 Feb 2011 11:46:23,406 INFO : PeptideProphet (TPP v4.3 JETSTREAM rev 1, Build 200909211148 (MSVC)) AKeller@ISB
25 Feb 2011 11:46:23,406 INFO : read in 0 1+, 3082 2+, 1227 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra.
25 Feb 2011 11:46:23,406 INFO : Initialising statistical models ...
25 Feb 2011 11:46:23,531 INFO : Iterations: .........10.........20...
25 Feb 2011 11:46:23,546 INFO : model complete after 24 iterations
25 Feb 2011 11:46:24,125 INFO : command completed in 2 sec
25 Feb 2011 11:46:24,125 INFO :
25 Feb 2011 11:46:24,125 INFO : running: "XPressPeptideParser "o261_08mar17_02_sec9.pep.xml" -nK,6.020129 -nR,10.0083 -m0.01 -d..\..\.."
25 Feb 2011 11:46:24,343 INFO : XPRESS error - cannot open file from basename d:/LabKey Server/files/Kolla MS2/@files/mascot/MascotSearchTest2SilacQuantTry2/o261_08mar17_02_sec9.work/o261_08mar17_02_sec9, will try to derive from scan names
25 Feb 2011 11:46:24,343 INFO : scan-derived scan file d:/LabKey Server/files/Kolla MS2/@files/mascot/MascotSearchTest2SilacQuantTry2/o261_08mar17_02_sec9.mzXML (from ) not found, cannot proceed...
25 Feb 2011 11:46:24,343 INFO :
25 Feb 2011 11:46:24,343 INFO : command "XPressPeptideParser "o261_08mar17_02_sec9.pep.xml" -nK,6.020129 -nR,10.0083 -m0.01 -d..\..\.." failed: Operation not permitted
25 Feb 2011 11:46:24,343 INFO :
25 Feb 2011 11:46:24,343 INFO : command "XPressPeptideParser "o261_08mar17_02_sec9.pep.xml" -nK,6.020129 -nR,10.0083 -m0.01 -d..\..\.." exited with non-zero exit code: 1
25 Feb 2011 11:46:24,343 INFO : QUIT - the job is incomplete
25 Feb 2011 11:46:24,343 INFO : Failed to complete task 'org.labkey.ms2.pipeline.TPPTask'
25 Feb 2011 11:46:24,343 ERROR: Failed to remove work directory D:\LabKey Server\files\Kolla MS2\@files\.\mascot\MascotSearchTest2SilacQuantTry2\o261_08mar17_02_sec9.work unexpected files found:
o261_08mar17_02_sec9.pep.xml
o261_08mar17_02_sec9.pep.xml.tmp.a01468
25 Feb 2011 11:46:25,296 ERROR: Failed running D:\LabKey Server\bin\xinteract, exit code 1
org.labkey.api.pipeline.PipelineJobException: Failed running D:\LabKey Server\bin\xinteract, exit code 1
    at org.labkey.api.pipeline.PipelineJob.runSubProcess(PipelineJob.java:1075)
    at org.labkey.api.pipeline.PipelineJob.runSubProcess(PipelineJob.java:935)
    at org.labkey.ms2.pipeline.TPPTask.run(TPPTask.java:410)
    at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:585)
    at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:813)
    at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
    at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(Unknown Source)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
 o261_08mar17_02_sec9.log  mascot.xml 
view message
Peptide list does not show all peptides derived from protein of interest
(2 responses) anette.karle 2011-02-25 10:15
Dear Labkey team

I have a case where a peptide can match several sequences in the database - however since I put it into the sample I am sure which one is the correct one. If I use the search function in Labkey and enter the protein name I will get a list of all runs in which peps of this protein were found. If I click on one of the blue numbers in the "group" column I get a list with all proteins which contain this peptide and also at the end of the page there is the full list of peptides. However in this list there is no possibility to filter for XCorr and DCn.

As an alternative, if I start from the dashboard instead, click on a run, filter for the protein of interest in the protein name column, I only get a very short list of peptides - those where I only have 1 Sequence hit.
Where have all the others gone? I assuem that it only shows the peps where the score for "my protein" was higher than for other proteins. Since I know that only my protein can be the tue one, I don't care if one other protein with the identical sequence stretch scored higher for whatever reason - I just need all peptides shown.

How can I have a list of all peptides from this protein (regardless of the rank) and at the same time filter for DCn and for charge dependend XCorr values?

I would be glad if you could help me with this as soon as possible.

Best regards
Anette
view message
Mascot 2.3 Pipeline Error with CPAS 10.3
(2 responses) donw 2011-02-21 09:11
Hi,

We recently upgraded our mascot server from 2.2 to 2.3 and our CPAS server from 9.0 to 10.30. I was testing out the searches before we bring it live and noticed some TPP pipeline errors when kicking off a Mascot server search.

Attached is the Log file and our mascot.xml params file

Basically It searches fine, downloads the *.dat and *.fasta fine, but fails to generate a *.pep.xml from the *.dat file with Mascot2XML which then causes Xinteract to fail with exit code 1 due to not having anything in the *.pep.xml file to process.

running: D:\LabKey Server\bin\Mascot2XML 110111_E2_TiO2Elu_neulossMS3.dat -DD:\LabKey Server\files\Don_Test\@files\databases\mascot\SwissProt\SwissProt_2011_01.fasta -xml -notgz -desc

10 Feb 2011 22:18:36,812 INFO : D:\LabKey Server\bin\xinteract (TPP v4.3 JETSTREAM rev 1, Build 200909211148 (MSVC))
10 Feb 2011 22:18:36,812 INFO :
10 Feb 2011 22:18:36,812 INFO : running: "InteractParser "110111_E2_TiO2Elu_neulossMS3.pep.xml" "..\110111_E2_TiO2Elu_neulossMS3_raw.pep.xml" -L"7""
10 Feb 2011 22:18:36,828 INFO : file 1: ..\110111_E2_TiO2Elu_neulossMS3_raw.pep.xml
10 Feb 2011 22:18:36,828 INFO : processed altogether 0 results
10 Feb 2011 22:18:36,828 INFO : ERROR: output file created, d:/LabKey Server/files/Don_Test/@files/mascot/110210_MascotSearch_Test3/110111_E2_TiO2Elu_neulossMS3.work/110111_E2_TiO2Elu_neulossMS3.pep.xml, appears incomplete. Please check the input files for completeness.
10 Feb 2011 22:18:36,828 INFO : command completed in 0 sec

Any thoughts what to troubleshoot next?
Thanks
Don Wolfgeher donw@uchicago.edu
 110111_E2_TiO2Elu_neulossMS3.log  mascot.xml 
view message
Peptide Search
(1 response) lnader 2011-02-08 15:55
I'm trying to search for peptide sequences containing specific modifications using the peptide search feature but it doesn't appear to be working. I've tried *'* and some of the returned peptides don't have this character at all.

https://proteomics.fhcrc.org/CPAS/ms1/ProteomicsLab/skenedy/pepSearch.view?runIds=&pepSeq=*%27*
view message
change organism of FASTA database
(2 responses) mboehmer 2011-01-24 17:27
I searched a huge number of mZXML files against a particular FASTA file using X!Tandem before realizing that Labkey associated no organism with this database. I have an uniprot file from this organism loaded on the same server and was hoping that Labkey can show me information from both, the original FASTA as well as the uniprot file. Is there a way to change the organism from currently unknown unknown to the correct organism?
view message
MS2 runs file export
(4 responses) mboehmer 2011-01-24 17:12
It seems the Issue 9777: Can't see export button on MS2 files export panel is still not resolved or reappeared in Labkey 10.3. Is there an easy workaround until the export panel is updated?
view message
show hierarchy does not show all runs of all project folders
(1 response) anette.karle 2011-01-05 03:57
Hi everyone,

I would like to see all runs I have in all my project folders. However, when I click on "show hierarchy" I just get the list of the files in this folder and not of all runs. Is there a way to see all runs in all project folders?

Best
Anette
view message
Processsing Errors preclude access to valid search results
(6 responses) markeys 2010-12-22 14:13
Occasionally CPAS files are flagged as Errors, apparently due to data failing to meet Peptide Prophet and/or Protein Prophet score requirements. However, examination of Mascot reports for the offending datasets reveal at least some valid and high scoring peptide assignments, not null or obviously flawed data. The fact that the models may not have sufficient information for quality scoring should not kick them out of the processing stream. Ability to post process and review ALL valid result runs is required.
 Mascot Results09March16_OT_3.docx  MarkeyLog09Mar16_OT_03.txt 
view message
truncated view in export file window
(1 response) markeys 2010-12-21 13:16
We are using 10.3 and regardless of the browser (IE on PC, Safari or Firefox on Mac) the Export window is truncated so that selected files cannot be sent to a zip file (action button is not visible, precluding export - see attachment) - any suggestions?
 CPAS_ViewCutoff.tiff 
view message
NCBI database - annotations problem?
(7 responses) weiclav 2010-12-20 01:05
Hi everyone,

we succesfully use Labkey server for searching MS/MS spectra against UniProt (SwissProt) and also against our local database using in house Mascot server. However there is a problem when I try to search against NCBInr database (when searching against the whole database and also in the case of taxonomy restrected search; please see attached log file).

The search itself proceeds without problem on Mascot side (I can go through the results of the search manualy) and the database is correctly downloaded by Labkey server if necessary. The problem is when the server is going to replace proteins IDs by parsing through the database. The mentioned error is "Fail to get line from sequence database".

The database is about 6GB big and is mentioned only in "Fasta File" table on the "Protein Database" site inside admin console. The database is not mentioned in the "Protein Annotations Loaded" table.

I tried to manualy load annotations for the database but without any luck. After submission of the database to annotations load, searver starts to read the database (I hope se, HDD diod blinks :) ) and after a couple of minutes (about 10-20 minutes) HDD stops and only CPU is probably processing the database (tomcat5.exe process is using one CPU core). But even after the weekend the database did not show up in the "Protein Annotations Loaded" table (tomcat5.exe process do not show any activity but it has allocated about 1024MB). When I observed the problem first time I increased Max Heap Size to 1024 MB but it has no effect on annotations load or MS/MS search problem.

Could be the problem with MS/MS search against NCBI database connected with missing annotations?

Thanks in advance for any help.

Best regards,
David

PC specs (Mascot server is running on the same PC):
WinXP-Prof, 64-bit
2 CPUs
4 cores/CPU
16GB RAM
Labkey server version 10.20
 logfile-error.txt 
view message
Apply filter in protein search function
(1 response) anette.karle 2010-12-13 04:55
Hi LabKey team,

I need to look for specific proteins using the protein search function. However the output is unfiltered. How can I specify a filter for XCorr values for different charge states and a DCn filter when using the search function. Is there a way to link it to the filter I already have in place when I use the "compare" function?

Best regards
Anette
view message
Message titles are overlapping with poster's email address at top of message
(2 responses) lamon 2010-12-03 17:32
My message titles are overlapping with my email address that appears at the top of each message I post. I don't remember this happening before.
view message
Mascot search
(4 responses) dwu8 2010-12-01 13:21
Hi,
I try to set up Mascot search. We have CPAS server 9.10 and Mascot server is 2.2.
I had a SILAC experiment. However, on the drop-down list, I cannot find
modification for K and R.
I also try to run without these modifications, still Mascot peptide search gave me
error. I am wondering if we miss something for Mascot set up. Would appreciate
any suggestions and advice.

Ding
view message
How to set DCn filter with "none grouping" setting?
(1 response) anette.karle 2010-11-12 00:17
After a new installation of labkey on the server I don't have my views anymore. I want to have a XCorr filter plus DCn filter. I can find the XCorr filter option for +1, +2 and +2 charged ions but I need to set a DCn filter as well. I wanted to do this by going to customize views but I cannot even see a "view" option next to the "export all" option. The view option only appears if I set the grouping to "query peptides" but since there is a bug in this grouping giving totally wrong values for DCn and XCorr really want to use this option.
What do I have to do to get the DCn filter in place without having any grouping?

Anette
view message
Changing the Default Search Properties on Project Creation
(2 responses) edwin.lowe 2010-11-11 22:02
I've been looking for a way of changing the default X!Tandem search parameters that appear whenever you create a new project. The values that are defined there are suitable for a lo-res instrument and I was wondering if I could simply modify a file somewhere that this is based off. A quick search didn't show up anything for me :(

Edwin
view message
Authors cannot delete files they have uploaded
(3 responses) lamon 2010-11-10 14:00
As a project administrator, I have add a "Files" web part to a project. Users designated as "authors" can upload files here but they cannot delete them. One has to be an "editor" to be able to delete his own file but then he can delete other files as well. Is this a feature or a bug?
view message
mascot default XML parameters
(1 response) hooverdm 2010-11-10 13:29
Is there a way for a normal, non-Site Administrator user to see the mascot default XML parameters? A user can override the default parameters in the Mascot XML section of a Search MS2 Data view, but how are they supposed to know what the XML tags are without being able to view the default XML?
view message
Java Heap Memory Errors
(6 responses) rwf 2010-11-04 09:39
We are running 10.2 with the Enterprise pipeline. I have already modified the Max Memory Pool from 512 to 1024 but I am still getting the same error:

03 Nov 2010 17:35:05,838 ERROR: Java heap space
org.mule.umo.ComponentException: Failed to invoke org.labkey.pipeline.mule.PipelineJobRunner. Component that caused exception is: PipelineJobRunnerUMO. Message payload is of type: ActiveMQTextMessage
    at org.mule.impl.DefaultLifecycleAdapter.intercept(DefaultLifecycleAdapter.java:199)
    at org.mule.impl.InterceptorsInvoker.execute(InterceptorsInvoker.java:47)
    at org.mule.impl.model.DefaultMuleProxy.run(DefaultMuleProxy.java:470)
    at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310)
    at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$CallerRunsPolicy.rejectedExecution(ThreadPoolExecutor.java:1895)
    at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor.reject(ThreadPoolExecutor.java:765)
    at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor.execute(ThreadPoolExecutor.java:1288)
    at org.mule.impl.work.ScheduleWorkExecutor.doExecute(ScheduleWorkExecutor.java:39)
    at org.mule.impl.work.MuleWorkManager.executeWork(MuleWorkManager.java:277)
    at org.mule.impl.work.MuleWorkManager.scheduleWork(MuleWorkManager.java:244)
    at org.mule.impl.model.seda.SedaComponent.run(SedaComponent.java:483)
    at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310)
    at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1061)
    at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:575)
    at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.OutOfMemoryError: Java heap space


I am attaching the complete labkey log for further details.

Any recommendations would be appreciated.

Ron
 09feb02_ot_57.pep.xml  09FEB02_OT_57.prot.xml  labkey-errors.log  labkey.log  09FEB02_OT_57_raw.pep.xml  tomcat.log  09FEB02_OT_57.dat  09FEB02_OT_57.log 
view message
Documentation of the <pipeline prophet> options
(5 responses) edwin.lowe 2010-10-14 21:25
I've been trying to find some documentation on setting the different peptide prophet options. Unfortunately the help section on the web site only shows up setting the min probability value. However in the forum a reply noted thaty accurate mass binning is also supported.

Is there somewhere where all the pipeline prophet commands are documented? I'm particularly interested in doing decoy database searchs and would like to define what the decoy is annotaed as.

Edwin
view message
error in output
(1 response) ljy241 2010-09-17 09:49
Hi,
 
I got the pepXML and protXML files with TPP software (V.4.3), and wanted to use CPAS (v.8.1) for comparing the results from different groups. However, I found many obvious errors that the number of unique peptides of a protein is more than that of total peptides. There were many proteins identified with even zero total peptide and without AAcoverage information, although might the unique peptide number is much larger. I checked the TPP output and didn't find these errors. Is this due to the incompatible of the two softwares?
view message
more options and flexiblility in the filter and result column in the Runs Overview web part
(3 responses) syliang 2010-09-15 19:52
Dear all,

Thanks LavKey developer team for adding Runs Overview web part in CPAS. The tool is very handy for consolidating information across projects. However, it would be nice to provide more options and flexibility in the filter as well as the results column. Thanks again.


Suhyuen
view message
Creation of database service user failed
(5 responses) greener 2010-08-29 13:27
Hey everyone, had an older windows installation that I wanted to upgrade (9.3) . I decided to uninstall it and install a fresh 10.2 copy. While I'm going through the steps it stops at the creation of labkey_postgres user. "Creation database user failed" I am using a sufficient password and have sufficient permissions . Not sure what I could be doing wrong here. Any suggestions? Thanks -Rich
view message
Mascot Default Parameters file
(14 responses) rwf 2010-08-25 11:58
Hello,

I am running the CPAS 10.2 Enterprise Pipleline and I would like to customize the default parameters as defined in the file mascot_default_input.xml at the pipeline root but I am unable to find it. Is this a file that you need to create manually when you are configuring CPAS to process Mascot searches?

thanks

Ron
view message
Out of Memory Errors
(2 responses) rwf 2010-08-10 06:08
When a search is submitted we are getting memory errors.

For example:

ERROR WritableIndex 2010-08-10 08:39:08,213 SearchService:index : Indexing error deleting dav:/_webdav/Jim/Savas25Q/@files/mascot/Savas25Q/20060728_HH_590_25Q_NE_repeat_11.pep.xml
java.lang.IllegalStateException: this writer hit an OutOfMemoryError; cannot flush
    at org.apache.lucene.index.IndexWriter.doFlushInternal(IndexWriter.java:3521)
    at org.apache.lucene.index.IndexWriter.doFlush(IndexWriter.java:3509)
    at org.apache.lucene.index.IndexWriter.flush(IndexWriter.java:3500)
    at org.apache.lucene.index.IndexWriter.deleteDocuments(IndexWriter.java:1974)
    at org.labkey.search.model.WritableIndex.deleteDocument(WritableIndex.java:81)
    at org.labkey.search.model.WritableIndex.index(WritableIndex.java:68)
    at org.labkey.search.model.LuceneSearchServiceImpl.index(LuceneSearchServiceImpl.java:724)
    at org.labkey.search.model.AbstractSearchService$7.run(AbstractSearchService.java:978)
    at java.lang.Thread.run(Unknown Source)
ERROR LuceneSearchServiceImpl 2010-08-10 08:39:08,213 SearchService:index : Indexing error with dav:/_webdav/Jim/Savas25Q/@files/mascot/Savas25Q/20060728_HH_590_25Q_NE_repeat_11.pep.xml
java.lang.IllegalStateException: this writer hit an OutOfMemoryError; cannot flush
    at org.apache.lucene.index.IndexWriter.doFlushInternal(IndexWriter.java:3521)
    at org.apache.lucene.index.IndexWriter.doFlush(IndexWriter.java:3509)
    at org.apache.lucene.index.IndexWriter.flush(IndexWriter.java:3500)
    at org.apache.lucene.index.IndexWriter.addDocument(IndexWriter.java:1952)
    at org.apache.lucene.index.IndexWriter.addDocument(IndexWriter.java:1906)
    at org.labkey.search.model.WritableIndex.index(WritableIndex.java:69)
    at org.labkey.search.model.LuceneSearchServiceImpl.index(LuceneSearchServiceImpl.java:724)
    at org.labkey.search.model.AbstractSearchService$7.run(AbstractSearchService.java:978)
    at java.lang.Thread.run(Unknown Source)
ERROR DavCrawler 2010-08-10 08:39:41,933 DavCrawler : Unexpected error
java.lang.OutOfMemoryError: Java heap space
ERROR LuceneSearchServiceImpl 2010-08-10 08:39:52,850 SearchService:index : Indexing error with dav:/_webdav/Jim/Savas25Q/@files/mascot/Savas25Q/20060728_HH_590_25Q_NE_repeat_13.dat
java.lang.OutOfMemoryError: Java heap space

Is there some way to avoid this problem?

thanks

Ron
 labkey.log 
view message
'ERROR - No matching proteins found' when exporting multiple MS2
(4 responses) btitz 2010-08-05 11:33
We recently upgraded to 10.20 (Windows with MS SQL Server) and now always encounter a strange problem when exporting multiple MS2 runs to an Excel file. The data of the first exported MS2 run (pep.xml) looks perfectly fine. However, the "protein", "SequenceMass", "BestName", and "Description" columns for ALL proteins of ALL other exported MS2 runs show "ERROR - No matching proteins found". This error does not occur, when these MS2 runs are exported individually. This error also does not seem to be affected by the selected export format or protein filter settings.

Thanks a lot in advance for your help!

Bjoern
view message
PEP_ISOTOPE_ERROR in mascot
(1 response) mmetod 2010-08-03 04:33
Hi guys,
How do you set the isotope error in mascot.xml? I am trying to search orbitrap data on Labkey 10.2 using mascot. It gives me very large errors. The data is with low to sub ppm accuracy for peptide precursors and X!Tandem searches show this correctly. Mascot does not. I tried to include various lines with PEP_ISOTOPE_ERROR in the xml but it doesn't work.
Thanks,
Metodi
view message
LDAP Authentication
(10 responses) rwf 2010-07-22 14:14
We are using 10.1 and are having problems with the LDAP authorization. The configuration within CPAS is completed and both connection and authorization tests within CPAS report successful. However, when a new user is created; CPAS is not authenticating the user against the active directory. This was indicated by several tests where the new user purposely selected a password different from their domain password. The new user was allowed to log in using this new password. Also, on another test; a new user selected a password which matched their AD domain login password but after changing their password out on the domain; they were not able to log in to CPAS with the new password. They could only log in to CPAS using the originally created password.

So, my question to the forum is how can you troubleshoot the LDAP authorization when the CPAS application reports back that connection and authorization are working?

thanks

Ron
view message
@files directory not created in some places
(4 responses) dompealer 2010-07-08 07:55
Hello,

  We recently upgraded to labkey 10.1, and are having problems uploading files. I have noticed that the new '@files' directory has only appeared in some of our folders, and I would like to know the significance of that.

  The error is this: I just created a project in a sub directory, and I want to upload all of my related raw data files (mzXML files) into this project. When I tried to add the "Files" as Web Part from the "Select Part" list, I got an error message "The file root for this folder is invalid. It may not exist or may have been configured incorrectly. File roots can be configured from the project settings view."
  
  The new project inherits its settings from its parent, and I know the parent's root exists. Could someone please explain what may be wrong? Thanks in advance.
view message
Protein Prophet Compare
(2 responses) wnels2 2010-06-23 09:14
I am have two questions about the protein prophet compare report.
1. The Venn diagram reports the number of proteins in each category. There can be multiple proteins in a protein group so the report is counting a lot of redundant information. Is there a way for it to count only the groups.

2. On the same report, if you click on the run group link it goes to a 404 error run not found. The links URL is missing the the run and the groupNumber.
view message
Express quantitsation of 15N labeled peptides
(2 responses) mboehmer 2010-05-07 11:41
Hi,

I am trying to use CPAS and Xpress for the analysis of a metabolically labeled sample. The sample is a mix between 14N-labeled peptides and 15N-labeled peptides. The parameters I use for the search of 15N-labeled peptides are:

<?xml version="1.0" encoding="UTF-8"?>
<bioml>
    <note label="protein, cleavage site" type="input">[KR]|{P}</note>
    <note label="protein, modified residue mass file" type="input">C:\Inetpub\wwwroot\ISB\data\parameters\n15.xml</note>
    <note label="pipeline quantitation, algorithm" type="input">xpress</note>
    <note label="pipeline quantitation, metabolic search type" type="input">heavy</note>
    <!-- Override default parameters here. -->
    <note label="pipeline, database" type="input">TAIR9_pep_20090619.fasta</note>
</bioml>

I then repeat the search for the same sample changing the parameters to consider 14N-labeled peptides that are picked up by the mass spec. Is there a way to combine these two searches and to get one final protXML file. Or does this have to be done outside of CPAS using interprophet?

Thanks,

Maik
view message
Grap fragment ion intensity from search results
(2 responses) pyan 2010-05-03 15:05
Hi,

I run x!Tandem through CPAS. I would like to export the intensity value for each matched fragment ion.

I know if I click the peptide, it will open a new window showing the detailed info with spectral graph. But is there an easy way for me just to download the intensity values?

Thanks,

Ping
view message
multi plot R view
wnels2 2010-04-18 09:38
I have an R script to plot q-values using the R view of a peptide query report. I would like to overlay multiple runs on the same plot. Is that possible?

Also, I loaded a database with a decoy database appended marked with rev_. This turned on the fval score field. Does it do anything else?

Thanks,
Bill
view message
@files
(1 response) wnels2 2010-04-15 11:20
I've been using 10.1 and there is this @files directory that is doing things that I don't expect. Is there any documentation that explains it's behavior or how to set the pipeline root properly?

Thanks,
Bill
view message
X! Tandem fails to run
(5 responses) rwf 2010-04-08 08:34
The X! Tandem fails to run with the following entry in the labkey-errors.log

org.labkey.api.pipeline.PipelineJobException: Failed running C:\Program Files (x86)\LabKey Server\bin\tandem.exe, exit code 1
    at org.labkey.api.pipeline.PipelineJob.runSubProcess(PipelineJob.java:1098)
    at org.labkey.api.pipeline.PipelineJob.runSubProcess(PipelineJob.java:962)
    at org.labkey.ms2.pipeline.tandem.XTandemSearchTask.run(XTandemSearchTask.java:161)
    at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:624)
    at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:847)
    at org.labkey.pipeline.mule.PipelineJobRunner.run(PipelineJobRunner.java:31)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    at org.mule.impl.model.resolvers.DynamicEntryPoint.invokeMethod(DynamicEntryPoint.java:312)
    at org.mule.impl.model.resolvers.DynamicEntryPoint.invoke(DynamicEntryPoint.java:259)
    at org.mule.impl.DefaultLifecycleAdapter.intercept(DefaultLifecycleAdapter.java:193)
    at org.mule.impl.InterceptorsInvoker.execute(InterceptorsInvoker.java:47)
    at org.mule.impl.model.DefaultMuleProxy.run(DefaultMuleProxy.java:470)
    at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310)
    at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$CallerRunsPolicy.rejectedExecution(ThreadPoolExecutor.java:1895)
    at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor.reject(ThreadPoolExecutor.java:765)
    at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor.execute(ThreadPoolExecutor.java:1288)
    at org.mule.impl.work.ScheduleWorkExecutor.doExecute(ScheduleWorkExecutor.java:39)
    at org.mule.impl.work.MuleWorkManager.executeWork(MuleWorkManager.java:277)
    at org.mule.impl.work.MuleWorkManager.scheduleWork(MuleWorkManager.java:244)
    at org.mule.impl.model.seda.SedaComponent.run(SedaComponent.java:483)
    at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310)
    at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1061)
    at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:575)
    at java.lang.Thread.run(Unknown Source)


Any assistance would be greatly appreciated.

Ron
view message
Show Libra results as proteinprophet columns
(3 responses) mboehmer 2010-03-29 16:18
When running the TPP outside of CPAS, it is possible to quantify iTRAQ labeled proteins using Libra. After import of the resulting Proteinprophet files, is there a way to display the libra output in CPAS ( e.g. as a Proteinprophet column)?
view message
insert or update on table "statusfiles" violates foreign key constraint
(2 responses) wnels2 2010-03-05 10:05
We just started getting this error on all of our runs on a 9.3 server. This causes the pipeline to hang at IMPORT RESULTS WAITING.

ERROR Table 2010-03-05 11:05:37,253 AnnotLoader45 : SQL [31007]
    INSERT INTO pipeline.statusfiles
        (_ts, createdby, created, modifiedby, modified, container, entityid, status, info, filepath, email, description, dataurl, job, provider, haderror, jobparent, jobstore, activetaskid)
        VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, NULL, ?, ?, ?, ?, NULL, NULL);
    SELECT CURRVAL('pipeline.statusfiles_rowid_seq')
    ?[1] 2010-03-05 11:05:37.252
    ?[2] 1018
    ?[3] Fri Mar 05 11:05:37 EST 2010
    ?[4] 1018
    ?[5] 2010-03-05 11:05:37.252
    ?[6] 5033a93a-07f4-102d-a5ac-8f9e9bccb7ce
    ?[7] 5033aa18-07f4-102d-a5ac-8f9e9bccb7ce
    ?[8] ERROR
    ?[9] ERROR: insert or update on table "statusfiles" violates foreign key constraint "fk_statusfiles_jobparent"
  Detail: Key (jobparent)=(5033a949-07f4-102d-a5ac-8f9e9bccb7ce) is not present in table "statusfiles".
    ?[10] /home/massspec/cpas/pipeline/projects/LynnGroup/Jackson/sequest/HNE_Farm_FR_ARP/LabelFree_2.0ug_wIS_v0022_i01_5074.log
    ?[11] lcjack3@uky.edu
    ?[12] Jackson/LabelFree_2.0ug_wIS_v0022_i01_5074 (HNE_Farm_FR_ARP)
    ?[13] 5033a95c-07f4-102d-a5ac-8f9e9bccb7ce
    ?[14] Sequest
    ?[15] true
    ?[16] 5033a949-07f4-102d-a5ac-8f9e9bccb7ce
view message
Can't execute MzXML2Search binary on Mac OSX
(1 response) i.cooke 2010-02-22 19:18
I've just installed labkey server 9.3 by compiling from source on MacOSX. When I go to run a Mascot search I get a weird error though. I've pasted the full error log below .. it fails when trying to run the MzXML2Search binary with the line.

/Users/iracooke/Sources/labkey/build/deploy/bin/MzXML2Search: cannot execute binary file

I've verified that MzXML2Search can be run using a relative path from the bin directory, but it always fails when I run it with an absolute path.

OK, this was a simple case of having another copy of the file (that does work) in my path. I've deleted the remainder of the question because it's no longer relevant.
view message
escaping special characters in FASTA for XML - pep.xml
(2 responses) ksdoctor 2010-02-12 11:04
Hi,

We are using LabKey 9.3 on a linux system.

In trying to run Mascot (2.1.03) remotely, some data uploads fail due to finding proteins with special characters in their fasta header files.

I have installed cgi/labkeydbmgmt.pl on our Mascot server as per you instructions.

[BTW, there is no Mascot 2.1.3 that I know of, instead the current linux version is 2.1.03 and the current Win is 2.2.x -- please correct your "mascot setup" documentation.. I wasted 1/2hr on that alone.]

LabKey runs the Mascot queries very well -- thanks! But sometimes fails in loading the results and gives this error:

11 Feb 2010 22:15:27,918 INFO : Starting to import spectra from /home/labkey/Masc_Larry/Sample3746_SCXf14_IMACe_lcmsms_1.mzXML
11 Feb 2010 22:15:28,024 INFO : Importing MS/MS results is 32% complete
11 Feb 2010 22:15:28,380 INFO : Importing MS/MS results is 33% complete
11 Feb 2010 22:15:28,889 INFO : Importing MS/MS results is 34% complete
11 Feb 2010 22:15:29,178 ERROR: XMLStreamException in hasNext()
com.ctc.wstx.exc.WstxParsingException: Unexpected close tag </search_hit>; expected </psi>.
 at [row,col {unknown-source}]: [258980,12]
        at com.ctc.wstx.sr.StreamScanner.constructWfcException(StreamScanner.java:605)
        at com.ctc.wstx.sr.StreamScanner.throwParseError(StreamScanner.java:461)
        at com.ctc.wstx.sr.BasicStreamReader.reportWrongEndElem(BasicStreamReader.java:3256)

(and stops after a few of these error lines).

I have found this to be solely due to special characters in the FASTA files, replacing those characters immediately fixes the problem.

Here are the cases where I LabKey is failing to put import into XML properly:
IPI human:
>IPI:IPI00431197.3| .... intron 4&9 variant
>IPI:IPI00465120.3|TREMBL:P78550;Q6I955 Tax_Id=9606 Gene_Symbol=- 3<beta>-HSD <psi>1 protein
>IPI:IPI00816409.1|TREMBL:A0N5T0 Tax_Id=9606 Gene_Symbol=- V<gamma>1 protein (Fragment)
>IPI:IPI00816761.1|TREMBL:Q16366 Tax_Id=9606 Gene_Symbol=CREB1 <alpha>CREB-1 protein (Fragment)

It fails the first due to ampersand and then a number.
It fails the second (and I expect others also) due to the <psi> (unmatched XML end-tag).

They are unusual characters in the FASTA files, so I expect you just missed them when testing the otherwise excellent app.

Can you fix this?

thanks,
Kutbuddin
view message
Error when connecting to Mascot server .. trouble receving enzyme lists?
(1 response) edwin.lowe 2010-02-10 21:53
I've just set up a connection to a mascot server hosted elsewhere from my Labkey Server. However, when I try and send a search to it i get the following error message popping up.

"Trouble retrieving enzyme list: Could not find any enzymes, perhaps labkeydbmgmt.pl is out of date?"

I'm running Labkey Server 9.3 and the Mascot server i'm trying to search is 2.2

Cheers
Edwin
view message
T2D extraction tool for 4700/4800 TOF/TOF
(4 responses) vensel 2010-02-10 13:00
I am trying to find the T2D extraction tool for the ABI 4800 TOF/TOF. I have a copy of version T2DE_EXE_04-12-2007, but wondered if there was a later version available. I am running windows XP.

Thanks,

Bill
view message
Sitewide emailing to all users
(1 response) ashoka 2010-02-05 12:28
Hi,
Is there a way to send email notifications to all users on a LabKey server, for example, about an upcoming maintenance etc.?
Thanks.
-Ashoka
view message
Creating a New Globus GRAM user certificate fails
(3 responses) greener 2010-02-01 16:49
Since our certificate expired on our enterprise pipeline, I have been trying to request a new certificate, I tripled checked the password that was used during install, but openssl continues to fails. Any suggestions folks have is muchly appreciated. Thanks -Rich

[root@oscarproto1 .globus]# /usr/cpas/gt4.0.6/bin/grid-ca-sign -in ~labkey/.globus/usercert_request.pem -out ~labkey/.globus/usercert.pem

To sign the request
please enter the password for the CA key:

ERROR running command:

 /usr/cpas/gt4.0.6/bin/openssl ca -passin stdin \
    -batch -config /root/.globus/simpleCA//grid-ca-ssl.conf \
    -in /tmp/tmp_cert_req.pem.1791 -out /tmp/tmp_cert.pem.1791

========== ERROR MESSAGES FROM OPENSSL ==========
Using configuration from /root/.globus/simpleCA//grid-ca-ssl.conf
unable to load CA private key
1826:error:0E06D06C:configuration file routines:NCONF_get_string:no value:conf_lib.c:329:group=CA_default name=unique_subject
1826:error:06065064:digital envelope routines:EVP_DecryptFinal:bad decrypt:evp_enc.c:450:
1826:error:0906A065:PEM routines:PEM_do_header:bad decrypt:pem_lib.c:423:
=================================================

ERROR: The CA private key could not be loaded.
Possibly an incorrect password for the CA key was used.
view message
Sitewide user-defined queries
(2 responses) ashoka 2010-01-27 16:43
Hi,

I want a query (ex. in ms2) that I created in one project be available in another. So far I have been copying the source from one project to another. Is there a way to make these queries to appear in all projects?

Thanks.
-Ashoka
view message
Experience with uploading LabKey Server Results to PRIDE
edwin.lowe 2010-01-26 19:54
This is just a general query .. but has anyone had any experience uploading their results generated by the LabKey Server into PRIDE Proteomics Data Repository? I'm just at the early stages of looking at this.

BTW .. if this was automated in some way it would make a very nice feature *hint hint*

cheers
Edwin
view message
XTandem, decoy searching, and FDR
(1 response) ashoka 2010-01-25 09:32
Hi,

I have a question about running a decoy search in labkey. Is there a way to do this automatically or should we generate our own decoy fasta file? Once the search is done, is there a way to filter the results through the web interface based on a FDR cutoff using decoy hits?

Thanks,
-Ashoka @ TGen
view message
Peptide Prophet Details > Prophet FVal
(3 responses) wnels2 2010-01-14 08:41
I'd like to include the peptide prophet fval score in a report. From the Query - Peptides> Views> Customize views, I am able to expand Peptide Prophet Details and select Prophet FVal.
The column appears on the report but it is blank.
Thanks,
Bill
view message
TPP patch
(9 responses) wnels2 2010-01-07 12:41
I'm upgrading to 9.3 on a CentOS 5 server. I checked out https://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-3-1 with svn and downloaded your patch.
From the ~/release_4-3-1/trans_proteomic_pipeline directory I ran patch -p0 -i ~/TPP4_3_1.patch. The TPP patches worked but not the xtandem patches.

Thanks,
Bill

[labkey@berkelium trans_proteomic_pipeline]# patch -p0 -i /root/Desktop/TPP4_3_1.patch
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/mpmods.cpp
Hunk #1 FAILED at 170.
Hunk #2 FAILED at 189.
Hunk #3 FAILED at 203.
Hunk #4 FAILED at 247.
Hunk #5 FAILED at 283.
Hunk #6 FAILED at 318.
6 out of 6 hunks FAILED -- saving rejects to file extern/xtandem/src/mpmods.cpp.rej
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/mprocess.cpp
Hunk #1 FAILED at 161.
Hunk #2 FAILED at 256.
Hunk #3 FAILED at 283.
Hunk #4 FAILED at 881.
Hunk #5 FAILED at 1203.
Hunk #6 FAILED at 1285.
Hunk #7 FAILED at 1508.
Hunk #8 FAILED at 1836.
Hunk #9 FAILED at 1852.
Hunk #10 FAILED at 2118.
Hunk #11 FAILED at 2638.
Hunk #12 FAILED at 2948.
Hunk #13 FAILED at 2990.
Hunk #14 FAILED at 3161.
Hunk #15 FAILED at 3333.
Hunk #16 FAILED at 3537.
Hunk #17 FAILED at 3762.
Hunk #18 FAILED at 3898.
18 out of 18 hunks FAILED -- saving rejects to file extern/xtandem/src/mprocess.cpp.rej
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/mprocess.h
Hunk #1 FAILED at 282.
Hunk #2 FAILED at 302.
Hunk #3 FAILED at 318.
Hunk #4 FAILED at 331.
Hunk #5 FAILED at 401.
5 out of 5 hunks FAILED -- saving rejects to file extern/xtandem/src/mprocess.h.rej
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/mscore.cpp
Hunk #1 FAILED at 153.
Hunk #2 FAILED at 206.
Hunk #3 FAILED at 527.
Hunk #4 FAILED at 703.
Hunk #5 FAILED at 1357.
Hunk #6 FAILED at 1570.
Hunk #7 FAILED at 1692.
7 out of 7 hunks FAILED -- saving rejects to file extern/xtandem/src/mscore.cpp.rej
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/mscore.h
Hunk #1 FAILED at 381.
Hunk #2 FAILED at 468.
2 out of 2 hunks FAILED -- saving rejects to file extern/xtandem/src/mscore.h.rej
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/mscore_s.cpp
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/mscore_s.h
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/mscorepam.h
Hunk #1 FAILED at 283.
Hunk #2 FAILED at 322.
2 out of 2 hunks FAILED -- saving rejects to file extern/xtandem/src/mscorepam.h.rej
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/msequenceserver.h
Hunk #1 FAILED at 161.
1 out of 1 hunk FAILED -- saving rejects to file extern/xtandem/src/msequenceserver.h.rej
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/msequtilities.cpp
Hunk #1 FAILED at 389.
Hunk #2 FAILED at 419.
2 out of 2 hunks FAILED -- saving rejects to file extern/xtandem/src/msequtilities.cpp.rej
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/msequtilities.h
Hunk #1 FAILED at 192.
Hunk #2 FAILED at 238.
2 out of 2 hunks FAILED -- saving rejects to file extern/xtandem/src/msequtilities.h.rej
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/p3.cpp
Hunk #1 FAILED at 175.
Hunk #2 FAILED at 187.
Hunk #3 FAILED at 258.
Hunk #4 FAILED at 271.
Hunk #5 FAILED at 607.
5 out of 5 hunks FAILED -- saving rejects to file extern/xtandem/src/p3.cpp.rej
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/resource1.h
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/stdafx.h
Hunk #1 FAILED at 1.
Hunk #2 FAILED at 10.
Hunk #3 FAILED at 186.
Hunk #4 FAILED at 261.
4 out of 4 hunks FAILED -- saving rejects to file extern/xtandem/src/stdafx.h.rej
(Stripping trailing CRs from patch.)
patching file extern/xtandem/src/tandem.cpp
Hunk #1 FAILED at 175.
Hunk #2 FAILED at 187.
Hunk #3 FAILED at 258.
Hunk #4 FAILED at 271.
4 out of 4 hunks FAILED -- saving rejects to file extern/xtandem/src/tandem.cpp.rej
(Stripping trailing CRs from patch.)
patching file src/Validation/ProteinProphet/ProteinProphet.cpp
(Stripping trailing CRs from patch.)
patching file src/Visualization/xinteract/xinteract.cxx
view message
tpp 4.3.1 and cpas 9.3
(1 response) greener 2010-01-06 10:09
We are running CPAS 9.2 and haven't upgraded yet to 9.3. Is it o.k. to import sequest/tpp data from tpp4.3.1 into the 9.2 build? any issues? let me know thanks -Rich
view message
64 bit xtandem download location
(1 response) greener 2009-12-21 22:44
is this the correct location to btain the 64 bit xtandem to be used on the enterprise pipeline?

https://www.labkey.org/wiki/home/Documentation/page.view?name=thirdPartyCode

thanks

-Rich
view message
Pipeline failing at the TPP step with LabKey Server 9.3
(2 responses) edwin.lowe 2009-12-13 15:01
I've just installed LabKey Server 9.3 on a new PC and am getting this error message when I perform a search. Have I forgotten to set some configuration variable? The PC is running Windows 7 64bit.

11 Dec 2009 16:50:14,093 INFO : Tandem2XML output
11 Dec 2009 16:50:14,093 INFO : =======================================
11 Dec 2009 16:50:14,093 INFO : Working directory is E:\Pipeline\Data\FoodSafety\RolfMUDPIT\data_aug09\xtandem\SemiTryp_Lmono_EGDe\3697.work
11 Dec 2009 16:50:14,093 INFO : running: Tandem2XML 3697.xtan.xml 3697_raw.pep.xml
11 Dec 2009 16:50:14,389 INFO : Moving E:\Pipeline\Data\FoodSafety\RolfMUDPIT\data_aug09\xtandem\SemiTryp_Lmono_EGDe\3697.work\3697.xtan.xml to E:\Pipeline\Data\FoodSafety\RolfMUDPIT\data_aug09\xtandem\SemiTryp_Lmono_EGDe\3697.xtan.xml
11 Dec 2009 16:50:14,389 INFO : Moving E:\Pipeline\Data\FoodSafety\RolfMUDPIT\data_aug09\xtandem\SemiTryp_Lmono_EGDe\3697.work\3697_raw.pep.xml to E:\Pipeline\Data\FoodSafety\RolfMUDPIT\data_aug09\xtandem\SemiTryp_Lmono_EGDe\3697_raw.pep.xml
11 Dec 2009 16:50:14,389 INFO : Completed task 'org.labkey.ms2.pipeline.tandem.XTandemSearchTask'
11 Dec 2009 16:50:14,389 INFO : Starting to run task 'org.labkey.ms2.pipeline.TPPTask' at location 'webserver'
11 Dec 2009 16:50:14,389 ERROR: Uncaught exception in PiplineJob: (DONE) data_aug09/3697 (SemiTryp_Lmono_EGDe)
java.lang.NullPointerException
    at org.labkey.ms2.pipeline.TPPTask.run(TPPTask.java:393)
    at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:622)
    at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:846)
    at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
    at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(Unknown Source)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
view message
job retry
(1 response) wnels2 2009-12-13 08:23
After finishing a search with a lot of fractions there were a couple that errored out at the TppTask.
When I hit the retry button it starts at the tpp task but it needs to go back and redo the search.
In the status files table I changed the activeTaskId to XtandemSearchTask and I deleted all of the old files for that fraction from the protocol directory but it still starts at the tpp task. To get it to start over again from the beginning do I have to manually edit the jobStore in the statusfiles table or is there an easier way?

Thanks,
Bill
view message
xinteract
(1 response) wnels2 2009-12-09 12:12
I know I'll be ashamed when I find out the answer but I am not able to get xinteract to run manually via command line on my windows dev server.
C:\tmp\ms2sandbox\2_32_48_64_72_79\xtandem\singleMod_both>C:\CPAS\build\deploy\bin\xinteract -x20 -Opt -nR -p0.0 010511_f32a_raw.pep.xml 010515_f02_raw.pep.xml

C:\CPAS\build\deploy\bin\xinteract (TPP v4.3 JETSTREAM rev 1, Build 200909211148
 (MSVC))
error: file C:/Inetpub/tpp-bin/InteractParser does not exist

I've set WEBSERVER_ROOT to C:\CPAS\build\deploy\bin\
and confirmed that C:\CPAS\build\deploy\bin\ is on the PATH

The binaries are from the repository trunk. What have I forgotten?
Thanks,
Bill
view message
msinspect: fail to read in mzxml data
charon 2009-12-04 12:16
Dear MSinspect developers,

I installed MSinspect build 540, and was able to read in the sample data files on your website. But I got an error(attached) when trying to open my data file(around 700Mb, mzxml version="1.0").
Any idea what's wrong here?

Thank you,
Charon

P.S. The head of my file is as follows:

<?xml version="1.0" encoding="ISO-8859-1"?>
<mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_2.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_2.1 http://sashimi.sourceforge.net/schema_revision/mzXML_2.1/mzXML_idx_2.1.xsd">
<msRun scanCount="4776">
<parentFile fileName="./analysis.baf" fileType="RAWData" fileSha1="5ba1cce526dde25ba17ead1adfd96926bec72b8f"/>
<msInstrument>
<msManufacturer category="msManufacturer" value="Bruker Daltonics"/>
<msModel category="msModel" value="microTOFLC"/>
<msIonisation category="msIonisation" value="ESI"/>
<msMassAnalyzer category="msMassAnalyzer" value="TOF"/>
<msDetector category="msDetector" value=""/>
<software type="acquisition" name="micrOTOFcontrol" version="2.2.23.0"/>
<operator first="Bruker" last="Customer"/>
</msInstrument>
<dataProcessing>
<software type="conversion" name="CompassXport" version="1.3.5"/>
</dataProcessing>
<scan num="1" retentionTime="PT1.207000S" polarity="+" msLevel="1" peaksCount="1207" lowMz="294.52670428" highMz="3005.38570928" basePeakMz="1092.06675453" basePeakIntensity="140.00000000" totIonCurrent="62168.00000000">
<peaks precision="32" byteOrder="network" pairOrder="m/z-int">Q5UQ1EIwAABDrpGlQkAAAEOu8BRCkAAAQ7P8aUJgAABDvAamQiAAAEO+ijlCIAAAQ772bkJQAABDwJh5QmAAAEPCrl9CIAAAQ8MNREIgAABDxZY8QoAAAEPHBOtCcAAAQ8cgjkIgAABDx4VpQlAAAEPIfRZCUAAAQ8jVOEIgAABDyQl8QhAAAEPJ7M9CYAAAQ8qNYkIQAABDzFflQlAAAEPMgrpCwAAAQ81s9kJQAABDzbP
 MSinspect error.docx 
view message
mzXML2search and mascot server error 26
(5 responses) humramos 2009-11-19 05:35
Please, I need a help with the use of the mascot on LabKey server.
When I sent a search on mascot server, I had the message:
 Mascot search status: error=26

I verified that the mgf file that was generated by MzXML2search contain many peaks and not was performed the processing of the spectrum. In this case was not obtained one peaklist (not was obtained monoisotopic peaks) compatible with the mascot requirements.
When I use the same file generated to performe a search in mascot web, I receive a message that I have many peaks. I realize that the mzXML2search was not configured to processing the spectrum, but only made a conversion from mzXML to mgf. I need process my raw data using a good algorithm to obtain a best peaklist.
How can I configure the MzXML2search.exe? Is there some parameter file to the MzXML2Search? Or Will I need to complile a new executable file MzXML2search?
Someone can help me?
Thanks
Humberto Ramos
view message
Spectra Counts: Peptide sequence, ProteinProphet protein assignment, No peptide filter
(1 response) wnels2 2009-11-09 11:58
We're getting an error when using the spectral counting feature. We just installed R so this is the first time it has been tried. The error message is below. The R console in the study module is working (without graphics).

Thanks,
Bill


Spectra Counts: Peptide sequence, ProteinProphet protein assignment, No peptide filter

An unexpected error occurred

java.lang.NullPointerException
org.labkey.api.util.UnexpectedException: java.lang.NullPointerException:java.lang.NullPointerException
       at org.labkey.api.data.AsyncQueryRequest.waitForResult(AsyncQueryRequest.java:106)
       at org.labkey.api.data.Table.selectForDisplayAsync(Table.java:1332)
       at org.labkey.api.data.RenderContext.selectForDisplay(RenderContext.java:347)
       at org.labkey.api.data.RenderContext.getResultSet(RenderContext.java:228)
       at org.labkey.api.data.DataRegion.getResultSet(DataRegion.java:610)
       at org.labkey.api.data.DataRegion.getResultSet(DataRegion.java:594)
       at org.labkey.api.data.DataRegion._renderTable(DataRegion.java:683)
       at org.labkey.api.data.DataRegion.render(DataRegion.java:1915)
       at org.labkey.api.data.DataRegion.renderTable(DataRegion.java:668)
       at org.labkey.api.view.GridView._renderDataRegion(GridView.java:71)
       at org.labkey.api.view.DataView.renderView(DataView.java:124)
       at org.labkey.api.view.DataView.renderView(DataView.java:31)
       at org.labkey.api.view.WebPartView.renderView(WebPartView.java:569)
       at org.labkey.api.view.WebPartView.renderInternal(WebPartView.java:180)
       at org.labkey.api.view.HttpView.render(HttpView.java:135)
       at org.labkey.api.view.HttpView.render(HttpView.java:117)
       at org.labkey.api.view.HttpView.include(HttpView.java:536)
       at org.labkey.api.query.QueryView.renderDataRegion(QueryView.java:1049)
       at org.labkey.api.query.QueryView.renderView(QueryView.java:885)
       at org.labkey.api.view.WebPartView.renderView(WebPartView.java:569)
       at org.labkey.api.query.QueryView.renderView(QueryView.java:910)
       at org.labkey.api.view.WebPartView.renderInternal(WebPartView.java:180)
       at org.labkey.api.view.HttpView.render(HttpView.java:135)
       at org.labkey.api.view.HttpView.render(HttpView.java:117)
       at org.labkey.api.view.HttpView.include(HttpView.java:536)
       at org.labkey.jsp.compiled.org.labkey.api.view.template.CommonTemplate_jsp._jspService(CommonTemplate_jsp.java:204)
       at org.labkey.api.view.JspView.renderView(JspView.java:119)
       at org.labkey.api.view.WebPartView.renderInternal(WebPartView.java:180)
       at org.labkey.api.view.HttpView.render(HttpView.java:135)
       at org.labkey.api.view.HttpView.render(HttpView.java:117)
       at org.labkey.api.action.SpringActionController.renderInTemplate(SpringActionController.java:420)
       at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:344)
       at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:726)
       at org.labkey.api.view.ViewServlet.service(ViewServlet.java:140)
       at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
       at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:36)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
       at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:124)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
       at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:651)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
       at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:101)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
       at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
       at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172)
       at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
       at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117)
       at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108)
       at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174)
       at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:875)
       at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665)
       at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528)
       at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81)
       at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689)
       at java.lang.Thread.run(Thread.java:619)
Caused by: java.lang.NullPointerException
       at org.labkey.api.query.AliasManager.legalNameFromName(AliasManager.java:70)
       at org.labkey.api.query.AliasManager.makeLegalName(AliasManager.java:96)
       at org.labkey.query.QueryServiceImpl.getSelectSQL(QueryServiceImpl.java:643)
       at org.labkey.api.data.Table.getSelectSQL(Table.java:1164)
       at org.labkey.api.data.Table.selectForDisplay(Table.java:1323)
       at org.labkey.api.data.Table.access$300(Table.java:52)
       at org.labkey.api.data.Table$2.call(Table.java:1336)
       at org.labkey.api.data.Table$2.call(Table.java:1334)
       at org.labkey.api.data.AsyncQueryRequest$1.run(AsyncQueryRequest.java:69)
       ... 1 more
request attributes
LABKEY.StartTime = 1257796367437
LABKEY.action = spectraCount
org.springframework.web.servlet.DispatcherServlet.CONTEXT = org.springframework.web.context.support.XmlWebApplicationContext@5b9a82ee: display name [MS2 WebApplicationContext]; startup date [Mon Nov 09 09:20:25 EST 2009]; parent: org.springframework.web.context.support.XmlWebApplicationContext@46b4be3d
LABKEY.controller = ms2
WebPartView.frame = DIV
LABKEY.container = /LynnGroup/Jackson/ProbeQuantMethodDev/PreAvidin
LABKEY.RequestURL = /labkey/ms2/LynnGroup/Jackson/ProbeQuantMethodDev/PreAvidin/spectraCount.view?runList=73&spectraConfig=SpectraCountPeptideProteinPP&peptideFilterType=none&peptideProphetProbability=
LABKEY.OriginalURL = http://berkelium.gws.uky.edu:8080/labkey/ms2/LynnGroup/Jackson/ProbeQuantMethodDev/PreAvidin/spectraCount.view?runList=73&spectraConfig=SpectraCountPeptideProteinPP&peptideFilterType=none&peptideProphetProbability=

core schema database configuration
Server URL    jdbc:postgresql://localhost/labkey
Product Name    PostgreSQL
Product Version    8.3.7
Driver Name    PostgreSQL Native Driver
Driver Version    PostgreSQL 8.3 JDBC3 with SSL (build 604)
view message
Private Key Section not found
(5 responses) wnels2 2009-10-28 13:12
My globus certificates just expired! I'm trying to install new ones under project setup but I keep getting the error "PRIVATE KEY section not found". I created the userkey.pem and usercert.pem (with a five year expiration date this time) from the procedure at http://www.globus.org/toolkit/docs/4.0/admin/docbook/ch07.html#simpleca-usercert
section 1.4
as the root user.
I created new certificates for the globus and Labkey server and restarted both servers before I tryed making the new user files.
There appears to be a private key section in the userkey.pem.
Thanks in advance for your help.
Bill
view message
'Protein BestName' and gi numbers
(2 responses) edwin.lowe 2009-10-08 23:27
I have an issue that I strike every now and then with the way that LabKey reports Protein names. It may or may not be a LabKey issue (perhaps I should use a different database).

Quite often I have some users who want to do a comparison that uses the 'Protein' name (which with my databases is a gi number) rather than the 'Protein Best' name. However, when I add the 'Protein' name to the comparison view it is actually displaying the 'Protein BestName' not the 'Protein' name that appears in the standard 'ShowRun' MS2 Dashboard view.

EXCEPT, the Spectral Count comparison shows the 'Protein' name, not the ProteinBest name.

The reason why is is an issue is that in a database like NR sometimes the protein name will be a SwisProt name (if its there) and sometimes a gi number. I've tried playing with setting the protein best name for the database but unfortunately that doesn't fix it completely. Any tips on how I can get the system to not use the ProteinBest name on the comparison views would be much appreciated.
view message
Globus timeout
(5 responses) wnels2 2009-10-08 06:46
I'm running a very long X!Tandem search. In my ms2Config.xml the maxWallTIme is set to 1440 (24hrs)and this is working as expected. I'm trying to override this with an input parameter:

<note label="xtandem, globus max cpu-time" type="input">10080</note> (7 days)

but is still times out at 24 hours.

Am I doing this correctly?

Thanks,
Bill
view message
Problems with Spectral Counts Compare in 9.2
(5 responses) edwin.lowe 2009-10-06 20:21
I recently upgraded 9.2 and am having problems with using the Compare tool and Spectral Counts. I was previously running 9.1 with the the data in the older PostgreSQL 8.2 server and dumped and reimported my data into PostgreSQL 8.3 when i updated.

I get the following error

An unexpected error occurred
java.lang.NullPointerException

[Show more details]

org.labkey.api.util.UnexpectedException: java.lang.NullPointerException:java.lang.NullPointerException
       at org.labkey.api.data.AsyncQueryRequest.waitForResult(AsyncQueryRequest.java:106)
       at org.labkey.api.data.Table.selectForDisplayAsync(Table.java:1332)
       at org.labkey.api.data.RenderContext.selectForDisplay(RenderContext.java:347)
       at org.labkey.api.data.RenderContext.getResultSet(RenderContext.java:228)
       at org.labkey.api.data.DataRegion.getResultSet(DataRegion.java:610)
       at org.labkey.api.data.DataRegion.getResultSet(DataRegion.java:594)
       at org.labkey.api.data.DataRegion._renderTable(DataRegion.java:683)
       at org.labkey.api.data.DataRegion.render(DataRegion.java:1915)
       at org.labkey.api.data.DataRegion.renderTable(DataRegion.java:668)
       at org.labkey.api.view.GridView._renderDataRegion(GridView.java:71)
       at org.labkey.api.view.DataView.renderView(DataView.java:124)
       at org.labkey.api.view.DataView.renderView(DataView.java:31)
       at org.labkey.api.view.WebPartView.renderView(WebPartView.java:569)
       at org.labkey.api.view.WebPartView.renderInternal(WebPartView.java:180)
       at org.labkey.api.view.HttpView.render(HttpView.java:135)
       at org.labkey.api.view.HttpView.render(HttpView.java:117)
       at org.labkey.api.view.HttpView.include(HttpView.java:536)
       at org.labkey.api.query.QueryView.renderDataRegion(QueryView.java:1049)
       at org.labkey.api.query.QueryView.renderView(QueryView.java:885)
       at org.labkey.api.view.WebPartView.renderView(WebPartView.java:569)
       at org.labkey.api.query.QueryView.renderView(QueryView.java:910)
       at org.labkey.api.view.WebPartView.renderInternal(WebPartView.java:180)
       at org.labkey.api.view.HttpView.render(HttpView.java:135)
       at org.labkey.api.view.HttpView.render(HttpView.java:117)
       at org.labkey.api.view.HttpView.include(HttpView.java:536)
       at org.labkey.jsp.compiled.org.labkey.api.view.template.CommonTemplate_jsp._jspService(CommonTemplate_jsp.java:204)
       at org.labkey.api.view.JspView.renderView(JspView.java:119)
       at org.labkey.api.view.WebPartView.renderInternal(WebPartView.java:180)
       at org.labkey.api.view.HttpView.render(HttpView.java:135)
       at org.labkey.api.view.HttpView.render(HttpView.java:117)
       at org.labkey.api.action.SpringActionController.renderInTemplate(SpringActionController.java:420)
       at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:344)
       at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:726)
       at org.labkey.api.view.ViewServlet.service(ViewServlet.java:140)
       at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
       at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:36)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
       at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:124)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
       at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:651)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
       at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:101)
       at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
       at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
       at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
       at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178)
       at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126)
       at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)
       at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107)
       at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)
       at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869)
       at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:664)
       at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527)
       at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80)
       at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)
       at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.NullPointerException
       at org.labkey.api.query.AliasManager.legalNameFromName(AliasManager.java:70)
       at org.labkey.api.query.AliasManager.makeLegalName(AliasManager.java:96)
       at org.labkey.query.QueryServiceImpl.getSelectSQL(QueryServiceImpl.java:643)
       at org.labkey.api.data.Table.getSelectSQL(Table.java:1164)
       at org.labkey.api.data.Table.selectForDisplay(Table.java:1323)
       at org.labkey.api.data.Table.access$300(Table.java:52)
       at org.labkey.api.data.Table$2.call(Table.java:1336)
       at org.labkey.api.data.Table$2.call(Table.java:1334)
       at org.labkey.api.data.AsyncQueryRequest$1.run(AsyncQueryRequest.java:69)
       ... 1 more

request attributes
LABKEY.StartTime = 1254885570546
LABKEY.container = /Jay Kocharunchitt/Plasmid Data
LABKEY.OriginalURL = http://proteome.csl.utas.edu.au:8080/labkey/ms2/Jay%20Kocharunchitt/Plasmid%20Data/spectraCount.view?runList=127&spectraConfig=SpectraCountProteinPP&peptideFilterType=peptideProphet&peptideProphetProbability=0.8
LABKEY.action = spectraCount
org.springframework.web.servlet.DispatcherServlet.CONTEXT = org.springframework.web.context.support.XmlWebApplicationContext@5f39b0: display name [MS2 WebApplicationContext]; startup date [Tue Oct 06 16:22:52 EST 2009]; parent: org.springframework.web.context.support.XmlWebApplicationContext@1babddb
LABKEY.controller = ms2
WebPartView.frame = DIV
LABKEY.RequestURL = /labkey/ms2/Jay%20Kocharunchitt/Plasmid%20Data/spectraCount.view?runList=127&spectraConfig=SpectraCountProteinPP&peptideFilterType=peptideProphet&peptideProphetProbability=0.8

core schema database configuration
Server URL    jdbc:postgresql://xxx.yyy.zzz.au:5432/labkey
Product Name    PostgreSQL
Product Version    8.3.8
Driver Name    PostgreSQL Native Driver
Driver Version    PostgreSQL 8.3 JDBC3 with SSL (build 604)
view message
TPP version recommended with 9.2
(1 response) greener 2009-09-17 12:20
Hi there Cpasers, Quick question , We are running labkey server 9.2 and was wondering which version of the TPP you recommend with this, We have not upgraded in a while, we are still running TPP v3.4 SQUALL rev.2, Build 200906181759. Please advise Thanks -Rich
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