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atc3 / maxquant_linux_guide

A guide to running MaxQuant in Linux
http://atchen.me/research/2019/03/21/mq-linux.html
MIT License
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ExternalProcess False_Cannot find the variable modification: Phospho (K)_ at MsLib.Data.ModPep.ModPepUtil.ReadParametersModPepSet #8

Open yang001-find opened 3 years ago

yang001-find commented 3 years ago

I want to add Phospho (K) in \ block, and this succeed on windows platform, but failed on linux platform and get the error messages "ExternalProcess FalseCannot find the variable modification: Phospho (k) at MsLib.Data.ModPep.ModPepUtil.ReadParametersModPepSet". How to fix it?[

atc3 commented 3 years ago

Hi,

I never had a problem with using the modifications file on linux. Could it be a spelling/capitalization error? i.e., Phospho (K) instead of Phospho (k)? I would also make sure that the modifications.xml file you used on Windows is the exact same modifications.xml file you use on Linux - the guide should say that these files need to be the same, if not I'll edit the text.

Let me know if that helps

yang001-find commented 3 years ago

Hi,

I never had a problem with using the modifications file on linux. Could it be a spelling/capitalization error? i.e., Phospho (K) instead of Phospho (k)? I would also make sure that the modifications.xml file you used on Windows is the exact same modifications.xml file you use on Linux - the guide should say that these files need to be the same, if not I'll edit the text.

Let me know if that helps

  1. when I used the same modifications.xml file at windows platform, the process just stayed at "preparing searches" step for more than 48 hours and not throw any error messages. The same process at windows platform takes 40 minutes. Following is the modification of 'Phospho (k)' part in modifications.xml file: `

    anywhere Standard none `

  2. I also tried Phospho (K) instead of Phospho (k), both modified this in mqpar.xml and modifications.xml, the process stayed at "preparing searches" and didn't throw error messages.

  3. I also used MaxQuantCmd.exe on windows cmd, the process stayed at "preparing searches" and didn't throw error messages. I am sure this is a bug for MaxQuantCmd.exe to deal with Phospho (k).

atc3 commented 3 years ago

Can you check if the CPU is running when it's stuck at "preparing searches"? I've had a few runs where it seems stuck at this step but it's actually still running under the hood - just running slowly.

In the combined/proc folder there should also be more details at what it's doing exactly under the "preparing searches" step - there are many parts to the "preparing searches" step, and modification searches like with phospho can definitely blow up the search space and result in long preparation times