Hi, Sorry to bother, but I just setup TPP on a new Windows 10computer where I will be keeping all of my data on D:\. For all searches, I get the error: Error - input file "XXX.mzML" not found. It appears that in Windows, in initial cd command fails if you are trying to both change drives and change directories as the search works if I run it from the command prompt after having switched drives to D:. It is possible to instruct Petunia to prepend the comet commands with a change drive command (simply D:\ && cd D:\xxx).
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