I came across a strange situation that I cannot explain why. I was conducting a Comet search, and I used the xinteract(Analyze Peptides) function to merge all the search results(in pep.xml format). Everything went OK and there is no error message at all. In the data file folder, a new merge.pep.xml was generated as usual as well as .pep.xml.index, and .pep-MODELS.html. However, when I clicked the Refresh and then clicked the resulting merge.pep.xml to view the results, the viewer shown nothing at all. I found out that somehow the merge.pep.xml disappeared at this point.
I used the latest version (4.7.0) for the search. This problem only happens when I try to merge large dataset (>50 individual pep.xml files) into one pep.xml. Searches with smaller size went OK.
This problem is also algorithm/parameter independent, it happens to tandem.pep.XML also.
Any idea why this happen?