Wasim Aftab,

If I may ask, is there any particular reason as to why you're using the latest upstream version of mono and not any other "released" version provided by your distribution of choice (MaxQuant's documentation mentions that any version equal to or above 5.4.1 should work fine)?

Also, what instructions are you using to build mono from source?

@Firas Khalil Khana

are you able to work successfully with any other versions?

Instructions for installations are given on the github link mentioned in the question.

Wasim Aftab,

I haven't tried to reproduce the error if that's what you mean.

Are you referring to the instructions from the README.md file? If so did you read the following:

"Note that building from Git assumes that you already have Mono installed, so please download and install the latest Mono release before trying to build from Git. This is required because the Mono build relies on a working Mono C# compiler to compile itself (also known as bootstrapping)."

You should already have a working version of Mono installed before attempting to build a new version from git as it bootstraps itself.

I suppose you ran the following (without having a working mono installed) (the README.md clearly states that this approach is risky as it just contains enough to run the 'mcs' compiler):

$ git clone https://github.com/mono/mono

$ cd mono

$ ./autogen.sh

$ make get-monolite-latest

$ make

When you should've run (with a working mono installed):

$ git clone --recursive [email protected]:mono/mono

$ cd mono

$ git submodule update --init --recursive

$ ./autogen.sh

$ make

$ make install

Firas Khalil Khana

NO.

"Note that building from Git assumes that you already have Mono installed, so please download and install the latest Mono release before trying to build from Git."

Of course, I've read that, I installed mono from following the link, which is reachable from mono GitHub page via another link

https://download.mono-project.com/sources/mono/

Thanks for your time.

Wasim Aftab,

I see. Well there's not much that you can do without root access.

I'd double check if mono was installed system-wide, and try to get my hands on a working binary version of mono that's built on a specified architecture similar to the intended host architecture (where it'll run).

Hope that helps.

Wasim Aftab,

A bit of research lead me to the following:

- MQ only works from the command line on Linux; the GUI isn't currently working.

- You need to have a working version of MQ already installed on Windows, and set up correctly without running it just yet (the Windows version has to be identical with the Linux compatible version).

- You need to save the parameters to a xml file, then switch to Linux.

- Now that you're back on Linux, edit the parameters (I suppose you're using ./gen_mqpar.py for this task).

- Unfortunately, Bruker file reading isn't supported on Linux yet (raw/Thermo files work fine though), as it's up to Bruker to make their tools linux/mono-compatible.

- You have to convert the Bruker files to mzxml with tools like Msconvert:

http://disq.us/url?url=http%3A%2F%2Fproteowizard.sourceforge.net%2Ftools%2Fmsconvert.html%29%3A3rCzhkcR9jlTMswqYNbLSXtBdjk&cuid=5759920

or by following the instructions in the following link:

http://www.codems.de/reports/mzxml_for_maxquant/

I've also compiled a list of links that (hopefully) will be useful:

- https://www.msi.umn.edu/sw/maxquant

- https://www.uio.no/english/services/it/research/hpc/abel/help/software/maxquant.html

- https://wiki.rc.usf.edu/index.php/MaxQuant

- https://www.mono-project.com/docs/compiling-mono/parallel-mono-environments/

- https://research.csc.fi/-/maxquant?redirect=https%3A%2F%2Fresearch.csc.fi%2Fsoftware-details%3Fp_p_id%3D101_INSTANCE_qvEXMgE3ObVa%26p_p_lifecycle%3D0%26p_p_state%3Dnormal%26p_p_mode%3Dview%26p_p_col_id%3Dcolumn-2%26p_p_col_pos%3D1%26p_p_col_count%3D4

Hope that helps.

Firas Khalil Khana "Unfortunately, Bruker file reading isn't supported on Linux yet"- I beg to disagree with that. Please see my original question I said:

"But when I run MaxQuant on my local Linux (Ubuntu 16.04) machine, I do not get that error, everything runs smoothly."

Wasim Aftab,

Hmm, that's weird indeed. Then it's mostly related to mono, but I'm still skeptical.

Kindly check the following link as there seems to be a relatively recent comment regarding the problem you're facing:

https://atchen.me/research/2019/03/21/mq-linux.html

Firas Khalil Khana I already contacted Albert Chen, the guy who wrote the webpage that you provided but, he himself is facing the problem of processing Brucker data on Linux cluster. see the issue in GitHub which I created some time back.

https://github.com/blahoink/maxquant_linux_guide/issues/1

Hi Wasim,

Have you made any progress with your problem? I have what looks like the identical issue. I can process Bruker files on a standalone Ubuntu (16.04). I can also run Thermo files on a multicore CentOS server, but get an error when trying to load Bruker files (using MaxQuantGui) i.e. the C# Redistributalbe is required to read Bruker data. From what I can see,t he server has mono-complete installed system wide. Same versions of MaxQuant (1.6.10.43) on both machines, mono on CentOS is 6.8, mono on Ubuntu is 6.6.

Caitriona

Hi All,

The error is fixed. cscaife (https://github.com/cscaife) figured that out. :)

I had to update gcc. To update it to 9.1.0 , download and run the following script

https://github.com/darrenjs/howto/blob/master/build_scripts/build_gcc_9.sh

for more information about the fix see this

https://github.com/blahoink/maxquant_linux_guide/issues/1