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zfyuan / EpiProfile2.0_Family

EpiProfile 2.0: A Computational Platform for Processing Epi-Proteomics Mass Spectrometry Data
GNU General Public License v3.0
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Running Plasmodium samples #4

Open mukhtarsadykov opened 3 years ago

mukhtarsadykov commented 3 years ago

Dear Dr. Yuan,

Thanks for making the tool! It is awesome!

I have a difficulty running EpiProfile2.0_PlasmodiumFalciparum. I have Xcalibur and Matlab + necessary packages installed. When I run EpiProfile, it shows "convert RAW to MS1 and MS2" all the time (tested for > 5 hours on a powerful PC), without stopping or giving any error messages. When I check the working folder, I see that it creates MS1 and MS2 folders, MS1 contains one MS1 file, while MS2 is empty. I run 3 samples, but it seems that it is stuck in on the first sample. Do you know what could be the reason for that?

a091601 commented 2 years ago

Dear scooby111, Hi, I have the same problem as you，how did you solve it ?

HYTang69 commented 2 years ago

Dear Everyone, I too have the same problem and I wonder if anyone has a solution to this? Thanks.

gliebsch commented 2 years ago

Dear everyone, maybe it is still of interest for you. I experienced the same issue and found out that the problem is that the xtract.exe is not working properly and asking for an update. This is also stated in the troubleshooting section of the User guide. But, the link given in the xtract.exe it is impossible to update the software. Hence, I looked for a work around and found that pFind has renamed the software tool to pXtract (http://pfind.org/software/pXtract/index.html). So I downloaded the software and extracted it into the same folder as xtract.exe (in the EpiProfile folder). As the tool is now called xtract_raw.exe, I renamed in the RAW2MS.m file the following and saved it: xtract_file = fullfile(pwd,'xtract_raw.exe'); When running Epiprofile.m, the extraction is working and I get results :)