Hi, Congrats on the new instrument, and happy holidays as well! The error seems to indicate that there is no input data for ProteinProphet to work with; can you verify that the input file contains validated search results with probabilities above 0.2 ? Are there any other errors or warnings in the previous steps?
Feel free to directly send me the interact.pep.xml file and I can have a look as well. Cheers, --Luis On Tue, Nov 29, 2022 at 10:31 AM cabarnes...@gmail.com < cabarnescabar...@gmail.com> wrote: > Hi all, > > Happy holidays! I have a new Eclipse in the lab and have been running my > Comet + TPP pipeline successfully on a lot of data downloaded from PRIDE > lately, but have run into an error with the new DDA data generated on the > Eclipse. It seems to be failing at the protein prophet step and the error > doesn't make much sense to me. Any idea what is going on? > > I'm running TPP 6.1 and Comet 2022.01 rev. 1 although the error below is > from the output of the Comet search through the TPP interface. I get a > similar error on the command line at the same step. > > > Here's the error message: > > WARNING: no data - output file will be empty > > command "C:/TPP/bin/ProteinProphet "interact.pep.xml" "interact.prot.xml"" > failed: Operation not permitted > > command "C:/TPP/bin/ProteinProphet "interact.pep.xml" "interact.prot.xml"" > exited with non-zero exit code: 1 > QUIT - the job is incomplete > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to spctools-discuss+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/1a4f392c-7ec1-411b-8300-90c0f6b48158n%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/1a4f392c-7ec1-411b-8300-90c0f6b48158n%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CACyS9bpz3OQJpNGv9hv4t_STkRfyACf-BY4mjvFvSiurckx96Q%40mail.gmail.com.
