Is there anything in that directory? The most likely reason for this failing is that there is a file remaining in the directory. There should not be, but if you have an old build of the TPP, or built it incorrectly, there might be.

Did you add the line "XML_ONLY=1" to your Makefile.incl before building the TPP?

Yes, there will be a .shtml and .xsl file. I have modified XTandem pipeline job to clean this up to cater for this. Our environment here is set up in the same way as RunXuan.

This should only be the case if you did not have "XML_ONLY=1" in your Makefile.incl. You should not need to modify XTandemPipelineJob.

There is one file left named 'SmallICAT.pep-prot.shtml_senserr.txt'

I have added the line "XML_ONLY=1" to your Makefile.incl before building the TPP.

There may be one issue relevant. I have installed an old version of TPP on this linux PC long before I installed CPAS. So after install CPAS, i downloaded the TPP using CVS as intructed, built and installed TPP again to the same folder without make clean the older version.Could it be a possible reason?

I delete the folder and re-install TPP again. The same problem still exists. What is this file about? Where is it coming from?

Sorry for the confusion, another Sashimi developer made a change that causes this problem. If you get v1.13 of <tpp root>/perl/ProteinProphet.pl, then you will have a version that does not write this file in XML mode.

I'll get this figured out, and try to post a fix soon.

thanks a lot