Hi Adina,
There was a error in the test even though it said passed at the top.
----Sequest.exe----
Executable = sequest.exe
    Cannot find executable. Check that executable is on server path:
    PATH = C:\Program Files (x86)\LabKey Server\bin;C:\Program Files (x86)\LabKey Server\jre1.5.0_11\bin
    Error message = CreateProcess: sequest.exe error=2

Try including the entire path of the sequest.exe executable in the web.xml.
The SequestQueue hasn't been tested on Bioworks 3.3 yet so please let us know how it goes.
Have a good weekend.

Thanks,
Bill

Hi Bill,

Thanks for the quick response. I tried changing the sequest.exe to "C:\Xcalibur...\sequest.exe". The sequest.exe runs fine in CMD so I'm fairly certain this is the right file for it.

Anytime I check for http://localhost:8080/SequestQueue, I get an error page from TomCat. Is there anything else I can try? I feel like it has to be such an easy fix. Could there be anything else on the 8080 port that is messing things up? The LabKey Server runs fine on as //localhost:8080/labkey. I also have TPP installed on the instrument, though I don't think this would cause anything to be wrong.

Stuck again...same error message from CPAS.

On another note, I tried running the same search with Xtandem and am getting an error there too. Log attached. I'm not sure what is going on. I am wondering if this either...sorry to be such a bother.

Thanks for the help.

Adina

I think I found another forum posting related to my XTandem problem. I will try it and update but will leave the link here for others.

https://www.labkey.org/announcements/home/CPAS/Forum/thread.view?rowId=2692

Hi Adina,
Sorry for your trouble. If you run the sequest test from the admin page is it now able to find the sequest.exe. Can you send that to me again? Also please attach your web.xml file. The http://hostname:8080/SequestQueue was working otherwise you would not have been able to send me the test results so I'm a little confsed about that. There are tomcat log files in the <tomcat home>/logs directory that you might want to look through.

Bill

Hi Bill,

Working on the weekend!!! Thank you. I appreciate it.

The files are attached.

Best,
Adina

Hi Adina,
CPAS is not work ;-)
It looks like you fixed it. The test is now finding the sequest.exe:

----Sequest.exe----
Executable = C:\XCalibur\system\programs\BioworksBrowser\sequest.exe
    The executable is responding.

I think you just have to fix the TPP path and you're set. I'll post a suggestion for the TPP path on your other thread.

Bill,

Thanks for your attentive responses...Still having trouble on this end.

I changed the system path variables to have the labkey directory bin file ahead of the TPP bin file. I'm still getting the same error with XTandem.

With the Sequest search, I'm getting the attached error.
Info: Exception class java.io.FileNotFoundException connect(http://localhost:8080/sequestqueue,)=http://localhost:8080/sequestqueue
It seems to still have trouble communicating with SequestQueue...When I type in the url http://localhost:8080/sequestqueue, I get an http error 404. Is this supposed to happen?

I'm not sure if these two errors are connected. I feel like XTandem searches are at least setting up for a search but failing because of TPP compatibiliy at some junction. The Sequest search doesn't even seem to be even getting to the point where its trying to communicate to TPP. But I have no clue...

Thanks for your support...
Adina

Hi Adina,
From the attached log it looks like sequest is working it just is not done yet. You submitted a pretty large file so a single processor sequest search could take a long time. At the bottom of the log there is a repeated entry:
07 Feb 2009 20:14:45,203 DEBUG: Submitting URL 'http://localhost:8080/SequestQueue//SequestQueue?taskId=1234059041078&cmd=status'.

This is the labkey server checking (every 30 secs) to see if the search is finished. In the log that you sent me the search had only been going for about three minutes.

If you do a Cntl-Alt-Del > task manager > processes and sort by CPU, you shoud see sequest.exe working very hard.

Regarding Xtandem: if you placed the labkey binary path in front of the TPP path and have set the pipeline tools path on the admin page I don't know why it is still using the the TPP path. I did add to the other thread in case you did not see. The Labkey guys may have more info on Monday.
The sequest search won't be able to complete until the path is fixed either.


Bill

Hi Bill,

I just uninstalled TPP on this console and it seems to have fixed the Protein Prophet Errors I was getting. My sequest search for this one file is taking forever though. This file is a dataset I have searched on Bioworks Sequest before and it only took like ten minutes. The size of the .mzmxl file is 43,680 KB...

I've let the search go for about half an hour...Just wondering if you have any advice on how long this should take? It could be that it is significantly longer than the Bioworks Sequest.

Thanks,
Adina

The newer versions of sequest do auto-indexing of the databases. To activate this in CPAS go to the web.xml and add the -I+ to the sequest options. At the command line you if you type sequest.exe -HA you will see this option displayed.
Sorry, we just added this feature recently so it's not in the documentation only mentioned in the web.xml comments. This is working on a 3.2 Sequest Cluster but has not been tested with 3.3 Bioworks so please let me know how it works.
Thanks,
Bill

Hi Bill,

Thanks for bearing with me. I keep convincing myself that all this will be worth it soon.

The dataset I'm searching is one that I have successfully sent through SEQUEST -> TPP.
I can't get it to go through SEQUEST -> CPAS or XTandem -> CPAS and I'm just stumped.

After changing the indexing parameter in the web.xml, restarting TomCat, deleting any old search Sequest files and re-running the search, I'm still feeling like things have gone amuck.

I've attached my error log, it just shows searching going on. During this, I'm not seeing any .out files being generated in my C:\CPAS_Adina\Raw\Test\sequest\sequest_round2\080207-1.work\080207-1 directory. Only DTA files. Now, I'm not sure how this is supposed to work, but I think Sequestqueue is supposed to be generating .OUT files somewhere.

I've also attached the web.xml for your reference.

================

Okay, the search finished. There was an error. I included the log file...I'm going to try searching a different file in case something is wrong with .mzxml as well.

Thanks.
Adina

Originally, I wanted to get all my data through the MS2 pipeline. If this can't work, if I were to just import the protein prophet files that I can successfully get from the TPP, can I still do comparative analysis between runs? As I understood it, that is an option only available to CPAS analyzed runs.

Thanks for all your help.

Also, to note, if you would like to peruse around the install...we have remote access to this computer. I don't know if this would be helpful or not.


Adina

Hi Adina,

There may be a problem with the version of tar that it's trying to run. In the C:\Program Files (x86)\LabKey Server\bin directory you could try copying tar.exe to tar.bak, and then copying bsdtar.exe to tar.exe and retrying the search.

In version 8.3 there are some limitations on the types of comparisons you can do on externally generated MS2 runs, including some of the spectra count reports. Version 9.1, which will be released next month, removes this limitation.

In 8.3 you can do other several other types of comparisions, however, like peptide, search engine protein assignment, and ProteinProphet protein assignment comparisions.

Thanks,
Josh

Hi Josh,

Thanks again for the support.

I changed the bdstar.exe -> tar.exe. I'm getting the following error now. The only other thing I changed because I was having trouble importing the Uniprot-TrEMBL database in a Xtandem run was the java heap size in Tomcat. I don't *think* that would effect this.

Any more advice?

Thanks,
Adina

Hi Adina,

That log file indicates that your Sequest search is running. It initially tried contacting the SequestQueue at the wrong URL but it tried another variation with success.

CPAS checks to see if it's complete every thirty seconds, which is what you're seeing at the end of that log file. All indications from that log file are that it will complete but may take a while.

Thanks,
Josh

Hi Josh,

I'm sorry to be a bother. I'm still getting the same error.

Adina

Hi Adina,
It is not able to find the renamed tar program. If you open the command prompt console and execute
C:\Program Files (x86)\LabKey Server\bin\tar
The program should respond with:
bsdtar: Must specify one of -c, -r, -t, -u, -x
(confirm that it responds with bsdtar at the begining)

The log file indicates that it will respond with:
'tar:' is not recognized as an internal or external command,
operable program or batch file.


Bill