Error: Failed to locate comet/tandem.

General Server Forum (Inactive)
Error: Failed to locate comet/tandem. hyang04  2018-10-11 09:06
Status: Closed
 

Hi LabKey team,
I was trying to use the MS2 module in our internal LabKey server, and was not able to run comet or tandem. The error message I got is posted below.

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2018 23:38:44,413 ERROR: Failed to locate tandem. Use the site pipeline tools settings to specify where it can be found. (Currently 'D:\Program Files\LabKey Server\bin')
Caused by: java.io.FileNotFoundException: Failed to locate tandem. Use the site pipeline tools settings to specify where it can be found. (Currently 'D:\Program Files\LabKey Server\bin')
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The folder D:\Program Files\LabKey Server\bin' does exist on our server computer, but there is no tandem or comet executable file under folder "D:\Program Files\LabKey Server\bin". I attached the screenshot image of that folder. That all the files we can see now.

I wonder if our setting is correct. Could you help us to set up the MS2 module?

Thank you
Best,
Han-Yin

 
 
jeckels responded:  2018-10-11 22:18

Hi Han-Yin,

It sounds like your install didn't include some of optional the proteomics/mass spec third-party tools.

Your easiest approach is likely to download them directly from this URL:

https://www.labkey.org/Documentation/wiki-page.view?name=setupCPASDemo

and extract them to your D:\Program Files\LabKey Server\bin directory.

You can separately download a copy of the Comet executable via this URL:

https://svn.mgt.labkey.host/stedi/binaries/proteomics/comet/comet.exe

Which can be added to the same directory.

Thanks,
Josh

 
hyang04 responded:  2018-10-12 12:32

Hello Josh,
Thank you for your response. We have downloaded the binaries from the svn server and put those binaries into bin folder.
The tandem was done without an issue, but we got an exception from comet (this was checkout from svn as well).
Please see the message below. Could you advice?

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12 Oct 2018 19:18:33,915 INFO : comet output
12 Oct 2018 19:18:33,915 INFO : =======================================
12 Oct 2018 19:18:33,915 INFO : Working directory is D:\Program Files\LabKey Server\files\DAS - Proteomics\2014_CSF_MCP@files\MS2\comet\2014_CSF_MCP_no_glycan\AG_MAP_Plasma_Bound_F1.work
12 Oct 2018 19:18:33,915 INFO : running: D:\Program Files\LabKey Server\bin\comet AG_MAP_Plasma_Bound_F1.mzXML
12 Oct 2018 19:18:34,681 INFO : Failed to complete task 'org.labkey.ms2.pipeline.comet.CometSearchTask'
12 Oct 2018 19:18:34,712 ERROR: Failed running D:\Program Files\LabKey Server\bin\comet, exit code -1073741515
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Another question is about running search starts with raw. In the link you shared. https://www.labkey.org/Documentation/wiki-page.view?name=setupCPASDemo, it seems that we could start with raw if the pwiz was checkout and put into the "D:\Program Files\LabKey Server\bin" folder. we downloaded the pwiz as well, but I am not able to start search with raw. (please see attached figure) I wonder if I miss anything.

The last question is about running job in parallel. I submitted two jobs to the server, and only one job is running at a time. I wonder if LabKey could run multiple search jobs in parallel. or should we change some of our setting to make that happen?

Thank you
Best,
Han-Yin

 
jeckels responded:  2018-10-16 20:55

Hi Han-Yin,

Can you share the full job log file? It may have additional detail on what caused Comet to fail. Please click the "SHOW FULL LOG FILE" link on the job details file to see the full file, and share what it says.

RAW file conversion is possible but not enabled by default, since not all server have the tools installed. You should have the msconvert tool installed per the previous download, so you can enable the conversion by adding a configuration file.

Please create a "config" directory in your LabKey install. It should be in the sample place as the "modules" and "labkeywebapp" directories. Please copy this file into that directory:

https://svn.mgt.labkey.host/stedi/trunk/external/ms2Config.xml

and then restart LabKey Server. It should now be configured to automatically convert RAW files. This doc page has some additional detail:

https://www.labkey.org/Documentation/wiki-page.view?name=configureConversionService

though not all of its steps will be required.

It is possible to configure the LabKey pipeline to run multiple jobs in parallel, but most protein database search tools will use multiple threads so there's no real benefit to running multiple in parallel on a single computer, as it just slows down each individual search. We could discuss this in more detail for what will give the best total performance, but we also don't want to overwhelm the server. It's also possible to share work with other remote computers.

Thanks,
Josh

 
hyang04 responded:  2018-10-17 11:54

Hello Josh,
I attached the log file. The error I mentioned was the error on 12 Oct in the log file. Thank you for your help.
Best,
Han-Yin

 
jeckels responded:  2018-10-18 11:59

Thanks for the full log file. Unfortunately, it doesn't include much additional data. The timestamps on the messages indicate that it's failing immediately after starting the search.

You can try running Comet from the command-line on the server? The generated comet.params file should be available, along with a copy of the mzXML file, in D:\Program Files\LabKey Server\files\DAS - Proteomics\2014_CSF_MCP@files\MS2\comet\2014_CSF_MCP_no_glycan\AG_MAP_Plasma_Bound_F1.work

From that directory, the command-line should be:

D:\Program Files\LabKey Server\bin\comet AG_MAP_Plasma_Bound_F1.mzXML

We could also try out a newer Comet version in case there has been a bug fix. The comet.param file might need updating if there have been changes.

http://comet-ms.sourceforge.net/release/

Thanks,
Josh

 
jeckels responded:  2018-10-19 16:39

I received a separate email on this topic, relaying results from running Comet directly. That yielded a dialog box indicating that MSVCP100.dll could not be found.

This indicates that a Comet dependency, the Microsoft Visual C++ Redistributable Package, is not installed or is somehow incomplete on this computer.

I recommend downloading directly from Microsoft and installing. This should both register the DLL so that it can be found, and also include other DLLs that might be missing or somehow damaged.

https://www.microsoft.com/en-us/download/details.aspx?id=48145

Thanks,
Josh