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Problem running xinteract in Labkey version 2.1

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Problem running xinteract in Labkey version 2.1 pedrioli  2007-06-27 02:32
Status: Closed
 
Hello,
    I have just finished installing LabKey version 2.1-6599 on a machine running Fedora Core 6. To get familiar with the system I was trying to walk through the "Marelli protocol". However, I am getting an error when running xinteract.

It seems like the path passed to xinteract is:

/export/data/braught/LabkeyTest/CPASDemo/Peroxisomal_ICAT/

while in reality the MM_clICAT11-raw.pep.xml file is located at:

/data/braught/LabkeyTest/CPASDemo/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT11.work/

The pipeline root for the demo project is set to:

/export/data/braught/LabkeyTest/CPASDemo

Did I forget to specify some settings for the project?

Let me add that manually running xinteract from the command line into the work directory works fine.

Thank you in advance for your help.

Cheers,

    Patrick


______ Error log _______

27 Jun 2007 05:04:35,508 INFO : X! Tandem search for MM_clICAT11.mzXML
27 Jun 2007 05:04:35,508 INFO : =======================================
27 Jun 2007 05:04:35,573 INFO : tandem.exe output
27 Jun 2007 05:04:35,574 INFO : =======================================
27 Jun 2007 05:04:35,574 INFO : running: tandem.exe input.xml
27 Jun 2007 05:04:35,593 INFO :
27 Jun 2007 05:04:35,594 INFO : X! TANDEM 2 (2007.04.01.1)
27 Jun 2007 05:04:35,594 INFO :
27 Jun 2007 05:04:36,222 INFO : Loading spectra .... loaded.
27 Jun 2007 05:04:36,222 INFO : Spectra matching criteria = 6924
27 Jun 2007 05:04:36,222 INFO : Pluggable scoring enabled.
27 Jun 2007 05:04:36,223 INFO : Starting threads . started.
27 Jun 2007 05:04:36,223 INFO : Computing models:
27 Jun 2007 05:05:42,930 INFO :     Spectrum    sequences modelled = 7 ks
27 Jun 2007 05:05:42,955 INFO : Model refinement:
27 Jun 2007 05:05:42,956 INFO : Creating report:
27 Jun 2007 05:05:42,993 INFO :     initial calculations ..... done.
27 Jun 2007 05:05:42,993 INFO :     sorting ..... done.
27 Jun 2007 05:05:45,732 INFO :     finding repeats ..... done.
27 Jun 2007 05:05:45,737 INFO :     evaluating results ..... done.
27 Jun 2007 05:05:45,753 INFO :     calculating expectations ..... done.
27 Jun 2007 05:05:48,097 INFO :     writing results ..... done.
27 Jun 2007 05:05:48,129 INFO :
27 Jun 2007 05:05:48,129 INFO : Valid models = 72
27 Jun 2007 05:05:48,130 INFO :
27 Jun 2007 05:05:48,130 INFO :
27 Jun 2007 05:05:48,141 INFO : Tandem2XML output
27 Jun 2007 05:05:48,142 INFO : =======================================
27 Jun 2007 05:05:48,142 INFO : running: Tandem2XML MM_clICAT11.xtan.xml MM_clICAT11-raw.pep.xml
27 Jun 2007 05:05:49,403 INFO : xinteract output
27 Jun 2007 05:05:49,403 INFO : =======================================
27 Jun 2007 05:05:49,403 INFO : running: xinteract -Opt -nR -x20 "-X-nC,9.0 -d\"/export/data/braught/LabkeyTest/CPASDemo/Peroxisomal_ICAT\"" -NMM_clICAT11.pep.xml MM_clICAT11-raw.pep.xml
27 Jun 2007 05:05:49,422 INFO :
27 Jun 2007 05:05:49,423 INFO : /usr/local/bin/TPP/bin/xinteract (TPP v3.2 SQUALL rev.1, Build 200706250506)
27 Jun 2007 05:05:49,423 INFO : error, cannot parse input file "-X-nC,9.0 -d\"/export/data/braught/LabkeyTest/CPASDemo/Peroxisomal_ICAT\""
27 Jun 2007 05:05:49,424 ERROR: Failed running xinteract.
 
 
jeckels responded:  2007-07-06 17:30
Patrick,

I ran into what I believe was the same error when doing a search on a SUSE Linux system. The problem, which seems to be dependent on the shell that's being used, is that the arguments to xinteract are being incorrectly quoted, so that it's interpreting the "-X-nC,9.0 -d\"/export/data/braught/LabkeyTest/CPASDemo/Peroxisomal_ICAT\"" as the filename.

I've made a change that will be part of 2.2 that fixed it, at least for my testing. I'm attaching a special build of the 2.1 MS2 module that has the change. Please give it a try:

Back up the existing ms2.module in <labkey_root>/modules to some other directory.
Overwrite the ms2.module in that directory with the one I've attached.
Restart the server.

Then, try doing the search again. You may need to delete the /export/data/braught/LabkeyTest/CPASDemo/Peroxisomal_ICAT/xtandem directory first.

Let me know if that makes any difference, and what shell you're using.

Thanks,
Josh
 
pedrioli responded:  2007-07-09 01:10
Hello Josh,
    replacing the original ms2 module with the one you patched solved the problem. The shell I am using is the bash shell.

Thank you very much for your help.

Cheers,

  Patrick