I have a bunch of other posts that led to this point. So, I'm going to explain the issues I got resolved. I installed TPP 4.1 revision 1 on my new PC. It has two hard drives, and I needed to install TPP on the secondary hard drive. Since TPP installs to the C: drive by default, I had to use the fixes listed on the forums to getting TPP to save to the D drive.
There were also conflicts because I had IIS and a different version of ActivePerl for the Proteomics Browser Suite, which Thermo Provides to work with SEQUEST. I had to install Apache on a different port than 80 (8888), and I installed ActivePerl on the D: drive. We had to change a bunch of headers in Perl scripts so that they used the right version of ActivePerl because they went to the C: drive by default. There were issues with SEQUEST looking for a params file of the name sequest.params. So, apparently the params file is only found if you change the name to sequest.params. Then, we finally set things so that everything ran from the D: drive and deleted the installation on the C: drive. Then, for some reason we couldn't get pepxmlviewer to work. Before setting up TPP on the D: drive, Pepxmlviewer would froze when we ran it on the C: drive Then, there were issues finding the Pepxmlviewer files after transferring it to the D: drive. It said it couldn't find two files: a log file, and some file for pepxmlviewer. So, finally a graduate student (who has done a lot of work with linux) mapped pepxmlviewer so that it ran from a linux machine. He has to do some work changing locations so that it would work correctly, but his fix seems to work. Finally, my current Issue: Now, I run database search with params files of the name sequest.params. However, I just ran 13 files that were about 20 mb each. After the 11th file, the results said that there were skipping about 2.3 million lines of output. It said the sequest.parms file was out after it called out2xml. And then after the next couple lines of peptide matching, the TPP interface just stopped working. No more matching or SEQUEST output was generated. Any idea why database search stops working after about 2 million lines of output? This seemed to happen before I used params of the name sequest.params also. Should I just run database search until I get to 2 million lines of output, delete the last output file, and rerun on the remaining files? Thanks, Kris --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
