Installing and running MaxQuant on GNU/Linux
After a first analysis of 20 plasma samples, we wanted to compare the results of a single acquisition against a fractionation of the same samples over 7 fractions, tallying a total of 140 raw files. This required a more powerful computer… running GNU/Linux.
Installation
My first reference was the following video by Pavel Sinitcyn, a post-doc in the MaxQuant team. There’s no actual installation of MaxQuant - the binaries simply need to be downloaded and unzipped. The challenge is however to install the infrastructure to run MaxQuant’s C# code on Linux.
The instructions in the video suggested to install dotnet, as
documented
here. This
didn’t work under Ubuntu 22.04 LTS.
I am not sure of the reason… I had to install dotnet 3.1 (even
though 2.1 was mentioned in the video above), an older version than
the one available by default on Ubuntu 22.04 LTS. dotnet version 3.1
itself depended of an older version of libssl, namely libss1, that
wasn’t available on ubuntu (again, libssl3 was the default
version). I had to download and compile libss1 by hand, which seemed
to be successful, but ended up with a crashing MaxQuant.
Next, I followed these
instructions, that
suggested to use mono, and installing it via conda. This proved to
be successful. I will be using that setup in the following sections.
# create the environment
conda create -n maxquant -c conda-forge mono
# activate the environment
conda activate maxquant
# run any maxquant version
mono /path/to/maxquant/bin/MaxQuantCmd.exe mqpar.xml
It is worth noting that there’s also a MaxQuant docker container, but for an older version of MQ, 1.6.5.0, while the current one (at the time of writing) is 2.2.0.0.
docker run -it nickdg/maxquant
I couldn’t find a up-to-date MaxQuant container elsewhere.
Running and debugging
Once installed, running MaxQuant is only a matter of passing it a parameter file.
mono /path/to/maxquant/bin/MaxQuantCmd.exe mqpar.xml
That parameter can be generated using the GUI on Windows, and adapted
for linux by changing the paths to the data and fasta file folders
using the --changeFolder argument . This is described in detail in
the instruction video above.
Debugging
The run crashed after just under a week’s continuous run. I started
the job remotely and lost the output, so didn’t have any error
messages to try to identify the cause. I knew that the first MS/MS
search was underway and thus resumed the run at that step/job, using
the -p argument. To find that job index, one can perform a dry run
with the --dryrun argument. This will list all the steps as defined
in the parameter file and their respective ids.
mono /path/to/maxquant/bin/MaxQuantCmd.exe --dryrun mqpar.xml
Take note the index N of the step you want to resume your run with
and run it with:
mono /path/to/maxquant/bin/MaxQuantCmd.exe -p N mqpar.xml
And, as expected, the error happened again, but this time I managed to capture the output:
Reading search engine results
Preparing reverse hits
Finish search engine results
Filter identifications (MS/MS)
Calculating PEP
Unhandled Exception:
System.Exception: Exception during execution of external process: 1302419 Error: Garbage collector could not allocate 16384u bytes of memory for major heap section.
at QueueingSystem.WorkDispatcher.ProcessSingleRunExternalProcess (System.Int32 taskIndex, System.Int32 threadIndex) [0x0009d] in <48f64397b7dc4fdd807bfd54c44c2941>:0
at QueueingSystem.WorkDispatcher.DoWork (System.Int32 taskIndex, System.Int32 threadIndex) [0x0001e] in <48f64397b7dc4fdd807bfd54c44c2941>:0
at QueueingSystem.WorkDispatcher.Work (System.Object threadIndex) [0x00054] in <48f64397b7dc4fdd807bfd54c44c2941>:0
at System.Threading.ThreadHelper.ThreadStart_Context (System.Object state) [0x00025] in <aa5dff9b31c64fce86559bbbf6cd364f>:0
at System.Threading.ExecutionContext.RunInternal (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00071] in <aa5dff9b31c64fce86559bbbf6cd364f>:0
at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00000] in <aa5dff9b31c64fce86559bbbf6cd364f>:0
at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state) [0x0002b] in <aa5dff9b31c64fce86559bbbf6cd364f>:0
at System.Threading.ThreadHelper.ThreadStart (System.Object obj) [0x0000f] in <aa5dff9b31c64fce86559bbbf6cd364f>:0
[ERROR] FATAL UNHANDLED EXCEPTION: System.Exception: Exception during execution of external process: 1302419 Error: Garbage collector could not allocate 16384u bytes of memory for major heap section.
at QueueingSystem.WorkDispatcher.ProcessSingleRunExternalProcess (System.Int32 taskIndex, System.Int32 threadIndex) [0x0009d] in <48f64397b7dc4fdd807bfd54c44c2941>:0
at QueueingSystem.WorkDispatcher.DoWork (System.Int32 taskIndex, System.Int32 threadIndex) [0x0001e] in <48f64397b7dc4fdd807bfd54c44c2941>:0
at QueueingSystem.WorkDispatcher.Work (System.Object threadIndex) [0x00054] in <48f64397b7dc4fdd807bfd54c44c2941>:0
at System.Threading.ThreadHelper.ThreadStart_Context (System.Object state) [0x00025] in <aa5dff9b31c64fce86559bbbf6cd364f>:0
at System.Threading.ExecutionContext.RunInternal (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00071] in <aa5dff9b31c64fce86559bbbf6cd364f>:0
at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00000] in <aa5dff9b31c64fce86559bbbf6cd364f>:0
at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state) [0x0002b] in <aa5dff9b31c64fce86559bbbf6cd364f>:0
at System.Threading.ThreadHelper.ThreadStart (System.Object obj) [0x0000f] in <aa5dff9b31c64fce86559bbbf6cd364f>:0
Thanks to Kristina’s help, addressing the error was simply a matter of increasing the size of the heap with
sudo sysctl -w vm.max_map_count=655350
I then re-resumed the search with at step 25, corresponding to the calculation of posterior error probabilites:
mono /path/to/maxquant/bin/MaxQuantCmd.exe -p 25 mqpar_linux.xml
and… after just over a week of total run time, success!
Calculating PEP
Copying identifications
Applying FDR
Assembling second peptide MS/MS
Combining second peptide files
Second peptide search
Reading search engine results (SP)
Finish search engine results (SP)
Filtering identifications (SP)
Applying FDR (SP)
Re-quantification
Reporter quantification
Retention time alignment
Matching between runs 1
Matching between runs 2
Matching between runs 3
Matching between runs 4
Prepare protein assembly
Assembling proteins
Assembling unidentified peptides
Finish protein assembly
Updating identifications
iBAQ
Label-free preparation
Label-free normalization
Label-free quantification
Label-free collect
Estimating complexity
Prepare writing tables
Writing tables
Finish writing tables
Acknowledgements
Thank you very much to Kristina Gomoryova for her help in finding the relevant information, advising during installation and debugging, and generating the parameter file.
