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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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[ERROR] FATAL UNHANDLED EXCEPTION: System.Exception: Exception during execution of external process: 217362 #4

Open Jokendo-collab opened 4 years ago

Jokendo-collab commented 4 years ago

My Maxquant analysis runs smoothly then it fails at the FDR assignment stage. What could be causing this problem? Loading requirement: compilers/gcc820 python/anaconda-python-3.7 Configuring Testing fasta files Testing raw files Feature detection Calculating peak properties Combining apl files for first search Preparing searches MS/MS first search Read search results for recalibration Mass recalibration MS/MS preparation for main search Combining apl files for main search MS/MS main search Preparing combined folder
Calculating masses Correcting errors Reading search engine results Preparing reverse hits Finish search engine results Filter identifications (MS/MS) Applying FDR

Unhandled Exception: System.Exception: Exception during execution of external process: 217362 at BaseLibS.Util.WorkDispatcher.ProcessSingleRunExternalProcess (System.Int32 taskIndex, System.Int32 threadIndex) [0x001a1] in <3fc1eb7cc45041de8ce7f41aa00f3311>:0 at BaseLibS.Util.WorkDispatcher.DoWork (System.Int32 taskIndex, System.Int32 threadIndex) [0x0001e] in <3fc1eb7cc45041de8ce7f41aa00f3311>:0 at BaseLibS.Util.WorkDispatcher.Work (System.Object threadIndex) [0x00054] in <3fc1eb7cc45041de8ce7f41aa00f3311>:0 at System.Threading.ThreadHelper.ThreadStart_Context (System.Object state) [0x00025] in <6e7e1f2771fe4be7978e37d9d240b9d4>:0 at System.Threading.ExecutionContext.RunInternal (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x0 0071] in <6e7e1f2771fe4be7978e37d9d240b9d4>:0 at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00000] in

<6e7e1f2771fe4be7978e37d9d240b9d4>:0 at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state) [0x0002b] in <6e7e1f2771fe4be7978e37d9d240b9 d4>:0 at System.Threading.ThreadHelper.ThreadStart (System.Object obj) [0x0000f] in <6e7e1f2771fe4be7978e37d9d240b9d4>:0 [ERROR] FATAL UNHANDLED EXCEPTION: System.Exception: Exception during execution of external process: 217362 at BaseLibS.Util.WorkDispatcher.ProcessSingleRunExternalProcess (System.Int32 taskIndex, System.Int32 threadIndex) [0x001a1] in <3fc1eb7cc45041de8ce7f41aa00f3311>:0 at BaseLibS.Util.WorkDispatcher.DoWork (System.Int32 taskIndex, System.Int32 threadIndex) [0x0001e] in <3fc1eb7cc45041de8ce7f41aa00f3311>:0 at BaseLibS.Util.WorkDispatcher.Work (System.Object threadIndex) [0x00054] in <3fc1eb7cc45041de8ce7f41aa00f3311>:0 at System.Threading.ThreadHelper.ThreadStart_Context (System.Object state) [0x00025] in <6e7e1f2771fe4be7978e37d9d240b9d4>:0 at System.Threading.ExecutionContext.RunInternal (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x0 0071] in <6e7e1f2771fe4be7978e37d9d240b9d4>:0 at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00000] in <6e7e1f2771fe4be7978e37d9d240b9d4>:0 at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state) [0x0002b] in <6e7e1f2771fe4be7978e37d9d240b9 d4>:0 at System.Threading.ThreadHelper.ThreadStart (System.Object obj) [0x0000f] in <6e7e1f2771fe4be7978e37d9d240b9d4>:0
atc3 commented 4 years ago

How many files are you processing? It's my anecdotal experience that the FDR calculation can be memory-heavy so maybe you are running out of RAM.

You can also check the combined/proc folder for the Applying FDR step, as a file, to maybe get a more detailed error message.

Jokendo-collab commented 4 years ago

Hi @blahoink I am processing 200 raw files and I don't know how to go about this problem

atc3 commented 4 years ago

In your output folder for your run (MaxQuant calls this the "combined" folder), go into combined/proc and look for a file named Applying_FDR 11.error.txt (or something like that). Inside that file should be more detailed information about why MaxQuant crashed.

If this is an out-of-memory error, then in your SLURM script you can increase the memory per cpu by adding:

#SBATCH --mem-per-cpu=1000

to the top of your submission script. In the above example I'm setting 1000MB (1GB) of memory per core, but depending on your cluster configuration you can increase this until MaxQuant has enough memory to complete the run.