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HIV Study Tutorial
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"cpas_log.txt" attached to message "Search MS2 Data Failed"

06 Jan 2006 16:07:43,194 ERROR MS2PipelineProvider: Error writing default input file. java.io.FileNotFoundException: /h1/lyang/default_input.xml (Permission denied) at java.io.FileOutputStream.open(Native Method) at java.io.FileOutputStream.<init>(FileOutputStream.java:179) at java.io.FileOutputStream.<init>(FileOutputStream.java:131) at java.io.FileWriter.<init>(FileWriter.java:73)...

"cpas.addUser.log" attached to message "Uploading MS2 Data"

21 Dec 2005 17:48:26,207 ERROR ViewServlet : error javax.servlet.ServletException: javax/activation/DataSource at org.apache.beehive.netui.pageflow.internal.DefaultExceptionsHandler.handleException(DefaultExceptionsHandler.java:188) at org.apache.beehive.netui.pageflow.FlowController.handleException(FlowController.java:258) at org.apache.beehive.netui.pageflow.FlowController.internalExecute(FlowController.java:442)...

job stuck waiting status

Hi,    a user submit a job but it is stuck in waiting status in the activemq log after it finish the first FAASTA check. 01 Dec 2017 11:40:26,278 INFO : X! Tandem search for all 01 Dec 2017 11:40:26,281 INFO : ======================================= 01 Dec 2017 11:40:26,283 INFO : abac.mzXML 01 Dec 2017 11:40:26,285 INFO : casfdsa.mzXML 01 Dec 2017 11:40:26,287 INFO : cafdsa.mzXML 01 Dec...

MS@ load error

I'm running the Sequest Pipeline just to validate that it is completing the pipeline. So I ran one of the CPASDemo files against a handy database (I think Mouse-Human, not yeast), using default params (not ICAT). I didn't expect good results but I did expect it to complete. I'm getting the error below. I've attached the pep.xml. Thanks, Bill 22 Oct 2007 23:36:52,718 DEBUG: Done creating FASTA...

"labkey.log" attached to message "New Install Fails with "Caused by: java.lang.IllegalStateException: Why am I in a transaction?""

INFO ModuleLoader 2015-04-24 09:04:13,307 localhost-startStop-1 : __ || | _ |_ |/ _ (¯ _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / INFO DbScope 2015-04-24 09:04:17,353 localhost-startStop-1 : Initializing DbScope with the following configuration: DataSource Name:...

drt GWT service failure

Every once in a while I get the exception below returned in the results of a FormSubmitCompleteEvent from a GWT FormHandler.onSubmitComplete(FormSubmitCompleteEvent event). It usually returns a url. I have to restart everything to make it go away. I haven't seen this outside of the drts. Any ideas? Thanks, Bill java.lang.NullPointerException at java.io.Reader.<init>(Reader.java:61) at java.io.InputStreamReader.<init>(InputStreamReader.java:55)...

"human_fasta_upload_failure.txt" attached to message "Error uploading human fasta file"

ERROR: duplicate key violates unique constraint "uq_proteinsequences_databaseid_lookupstring" [Show more details] org.postgresql.util.PSQLException: ERROR: duplicate key violates unique constraint "uq_proteinsequences_databaseid_lookupstring" at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1512) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1297)...

Limits on HTML in WIKI pages?

What are the limits on HTML in WIKI (and I assume, MESSAGE) pages? I tried to place an excel-converted spreadsheet on a wiki page. Initially it crashed the page display service and made the page very hard to delete. After removing external namespace references it displays properly on normal browsers (firefox, ie, safari) but loses all its formatting, color and fonts on the WIKI page. Well there...

"cpas.log" attached to message "CPAS.XML Database setup"

20 Dec 2005 16:50:51,091 DEBUG CoreModule : Connection to cpasDataSource at jdbc:postgresql://otrs.genophobe.org:8090/cpas failed with the following error: 20 Dec 2005 16:50:51,091 DEBUG CoreModule : Message: The connection attempt failed. SQLState: 08001 ErrorCode: 0 20 Dec 2005 16:50:51,091 DEBUG CoreModule : org.postgresql.util.PSQLException: The connection attempt failed. 20 Dec 2005...

"cpas_err" attached to message "ERROR: relation "core.users" does not exist"

500: Unexpected server error Home Back Folder ERROR: relation "core.users" does not exist [Show more details] org.postgresql.util.PSQLException: ERROR: relation "core.users" does not exist at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1592) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1327) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:192)...

Sequest Fractions XAR import failed

Hi, We just did our first Sequest mudpit with 8.2 and are getting the failure below, I have attached the xar file. Thanks, Bill 01 Aug 2008 23:53:59,043 FATAL: Exception during import org.labkey.api.exp.XarFormatException: Could not find Parent protocol with LSID urn:lsid:uky.edu:Protocol.Folder-60:MS2.SequestAnalysis.Fractions:3     at org.labkey.api.exp.XarSource.getProtocol(XarSource.java:204)...

"ShowGraphError.doc" attached to message "Experiment graph error"

Error in generating graph: /usr/local/tomcat/temp/ExperimentRunGraphs/Folder8/run1.map (No such file or directory) java.io.FileNotFoundException: /usr/local/tomcat/temp/ExperimentRunGraphs/Folder8/run1.map (No such file or directory) at java.io.FileInputStream.open(Native Method) at java.io.FileInputStream.(FileInputStream.java:106) at java.io.FileReader.(FileReader.java:55) at Experiment.ExperimentController$GraphView.renderView(ExperimentController.java:1512)...

"unix-ms2admin-exception.txt" attached to message "Error getting "Protein Annotations Loaded" status in showMS2Admin.view"

03 Feb 2006 17:22:38,295 ERROR GroovyView : error executing /_views/HomeTemplate.gm java.io.IOException: java.lang.ClassCastException: java.lang.Thread at MS2.MS2Controller$DisplayThreadStatusColumn.renderGridCellContents(MS2Controller.java:1286) at org.fhcrc.cpas.data.DisplayColumn.renderGridDataCell(DisplayColumn.java:261) at org.fhcrc.cpas.data.DataRegion.renderTableRow(DataRegion.java:663)...

Labkey 14.3 on RHEL 7 - Broken

Following the manual install directions I get error on tomcat start. Labkey doesn't start. Appears to be related to this https://www.labkey.org/announcements/home/Server/Forum/thread.view?rowId=10323. Windows install is not an option. Apache Tomcat/7.0.54 ERROR ModuleLoader 2015-03-05 14:28:43,056 localhost-startStop-1 : Failure occurred during ModuleLoader init. org.labkey.api.util.ConfigurationException:...

Caused by: java.lang.IllegalStateException: Why am I in a transaction?

Hi, I am trying to install labkey on a Ubuntu 14.04 linux. I am using the tomcat7 installation from the distribution. I am using postgres 9.4 installed via the postgres repositories. The connection to the database is made, and the labkey database is created, but stays empty. In the browser I get the following exception: org.labkey.api.util.ConfigurationException: Cannot connect to DataSource...

A database connection is in an unexpected state.

Hi, I'm trying to start Labkey 16.2 on tomcat 7, but I get the following error message: "A database connection is in an unexpected state: auto-commit is false. This indicates a configuration problem with the datasource definition or the database connection pool." I installed Labkey on Ubuntu 14.04 and the database is Postgress 9.5.5. How could I fix this error? Thanks, Romina. Hello...

"labkey.log" attached to message " Help Please"

INFO ModuleLoader 2014-12-24 08:31:58,146 localhost-startStop-1 : __ || | _ |_ |/ _ (¯ _ _ _ _ (__) |_(_||_)|\(/_\/ _)(/_| \/(/_| / INFO DbScope 2014-12-24 08:32:03,395 localhost-startStop-1 : Initializing DbScope with the following configuration: DataSource Name:...

"ListsErrors.log" attached to message "Upgrade version 15.2 to 16.1 (16.2)"

An unexpected error occurred 05_Darce_Serotonin_assay.ID (primary key) has not been provisioned properly. Ensure the domain is established before constructing. java.lang.IllegalStateException: 05_Darce_Serotonin_assay.ID (primary key) has not been provisioned properly. Ensure the domain is established before constructing. at org.labkey.list.model.ListTable.<init>(ListTable.java:105) ...

"labkey-errors.log" attached to message "Compare view?"

ERROR ManagerBase 2007-12-20 15:24:09,279 Thread-1 : IOException while loading persisted sessions: java.io.InvalidClassException: org.labkey.api.data.Container; local class incompatible: stream classdesc serialVersionUID = -4897634681326991901, local class serialVersionUID = 2752793104866219513 java.io.InvalidClassException: org.labkey.api.data.Container; local class incompatible: stream...

Mascot2XML prev_aa

I'm getting an mz/mz results loading error using Mascot with the cluster pipeline. It seems to be related to a Mascot2XML problem that had a fix posted about a year ago on this supprt board. Manually looking in the pep.xml file I cannot find any weird charaters at the peptide_prev_aa attributes. The same search works fine with xtandem. ./Mascot2XML(TPP v3.3 SQUALL rev.1, Build 200711050856)...