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maxquant index out of bounds #393

Open bernt-matthias opened 4 years ago

bernt-matthias commented 4 years ago 
Template of the MaxQuant parameter file '/gpfs1/work/songalax/galaxy/database/jobs_directory/032/32862/working/mqpar.xml' is created.
Traceback (most recent call last):
  File "/gpfs1/data/galaxy_server/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/8bac3cc5c5de/maxquant/mqwrapper.py", line 110, in <module>
    m.add_infiles([os.path.join(os.getcwd(), name) for name in fnames_with_ext], True)
  File "/gpfs1/data/galaxy_server/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/8bac3cc5c5de/maxquant/mqparam.py", line 196, in add_infiles
    if i > -1 and design['Name'][i]:
IndexError: list index out of range

command line was

python3 '/gpfs1/data/galaxy_server/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/8bac3cc5c5de/maxquant/mqwrapper.py' --num_threads=${GALAXY_SLOTS:-1} --substitution_rx='[^\w-\s.]' --raw_files='/gpfs1/data/galaxy_server/galaxy/database/files/082/dataset_82189.dat,/gpfs1/data/galaxy_server/galaxy/database/files/082/dataset_82188.dat,/gpfs1/data/galaxy_server/galaxy/database/files/081/dataset_81871.dat,/gpfs1/data/galaxy_server/galaxy/database/files/081/dataset_81870.dat,/gpfs1/data/galaxy_server/galaxy/database/files/081/dataset_81869.dat,/gpfs1/data/galaxy_server/galaxy/database/files/081/dataset_81868.dat,/gpfs1/data/galaxy_server/galaxy/database/files/081/dataset_81867.dat,/gpfs1/data/galaxy_server/galaxy/database/files/081/dataset_81866.dat,/gpfs1/data/galaxy_server/galaxy/database/files/081/dataset_81865.dat,/gpfs1/data/galaxy_server/galaxy/database/files/081/dataset_81860.dat,/gpfs1/data/galaxy_server/galaxy/database/files/081/dataset_81857.dat,/gpfs1/data/galaxy_server/galaxy/database/files/081/dataset_81856.dat,/gpfs1/data/galaxy_server/galaxy/database/files/081/dataset_81855.dat,/gpfs1/data/galaxy_server/galaxy/database/files/081/dataset_81854.dat,/gpfs1/data/galaxy_server/galaxy/database/files/081/dataset_81853.dat,/gpfs1/data/galaxy_server/galaxy/database/files/081/dataset_81852.dat,/gpfs1/data/galaxy_server/galaxy/database/files/081/dataset_81851.dat,/gpfs1/data/galaxy_server/galaxy/database/files/081/dataset_81850.dat,/gpfs1/data/galaxy_server/galaxy/database/files/081/dataset_81849.dat,/gpfs1/data/galaxy_server/galaxy/database/files/081/dataset_81848.dat,/gpfs1/data/galaxy_server/galaxy/database/files/081/dataset_81847.dat,/gpfs1/data/galaxy_server/galaxy/database/files/081/dataset_81846.dat,/gpfs1/data/galaxy_server/galaxy/database/files/081/dataset_81845.dat,/gpfs1/data/galaxy_server/galaxy/database/files/081/dataset_81844.dat' --infile_names='21-12-2018_S83_GF_F4_HP.raw,21-12-2018_S83_GF_F3_HP.raw,21-12-2018_S83_GF_F5_HP.raw,21-12-2018_S83_GF_F2_HP.raw,21-12-2018_S83_GF_F1_HP.raw,21-12-2018_S83_C8_HP.raw,21-12-2018_S82_InSol_HP.raw,21-12-2018_S81_InSol_HP.raw,21-12-2018_S83_InSol_HP.raw,21-12-2018_S83_FASP_HP.raw,21-12-2018_S82_GF_F5_HP.raw,21-12-2018_S82_GF_F4_HP.raw,21-12-2018_S82_GF_F3_HP.raw,21-12-2018_S82_GF_F2_HP.raw,21-12-2018_S82_GF_F1_HP.raw,21-12-2018_S82_FASP_HP.raw,21-12-2018_S82_C8_HP.raw,21-12-2018_S81_GF_F5_HP.raw,21-12-2018_S81_GF_F4_HP.raw,21-12-2018_S81_GF_F3_HP.raw,21-12-2018_S81_GF_F2_HP.raw,21-12-2018_S81_GF_F1_HP.raw,21-12-2018_S81_FASP_HP.raw,21-12-2018_S81_C8_HP.raw' --version='1.6.3.4' --fasta_files='/gpfs1/data/galaxy_server/galaxy/database/files/081/dataset_81905.dat' --identifier_parse_rule='^>.|(.)|.$' --description_parse_rule='^>.|.|[^ ]+ (.) OS.*$' --exp_design='/gpfs1/data/galaxy_server/galaxy/database/files/082/dataset_82194.dat' --missed_cleavages=2 --min_peptide_len=7 --max_peptide_mass=4600 --min_unique_pep=1 --fixed_mods='Carbamidomethyl (C)' --var_mods='Oxidation (M)' --proteases='Trypsin' --evidence='None' --msms='None' --parameters='None' --peptides='None' --proteinGroups='/work/songalax/galaxy/database/jobs_directory/032/32862/galaxy_dataset_131705.dat' --allPeptides='None' --libraryMatch='None' --matchedFeatures='None' --modificationSpecificPeptides='None' --ms3Scans='None' --msmsScans='None' --mzRange='None' --peptideSection='None' --summary='None' --mzTab='None' --mqpar_out='None'

bernt-matthias commented 4 years ago

ping @dglaetzer

dglaetzer commented 4 years ago

can you give me the experimental design template that was used?

bernt-matthias commented 4 years ago

The mqpar.xml?

dglaetzer commented 4 years ago

no, this input


--exp_design='/gpfs1/data/galaxy_server/galaxy/database/files/082/dataset_82194.dat'
is causing the problem. Looks like the experimental design template misses one of the input raw-files. (if it is not a bug). In the first case the error message should be less cryptic i guess.
bernt-matthias commented 4 years ago

Here you go (renamed it to txt dataset_82194.txt )

dglaetzer commented 4 years ago

I count 24 input datasets but only 21 entries in the template. So that's what causes the error. There may be a problem with the fractions as well. They are required to be a numeric value (at least mq complains about anything else than numbers in the fraction string). I need to test whether it can handle the empty string. In general, it seems like i should add some (more) checks on the validity of the template and report their failure to the user with comprehensible error messages.

bernt-matthias commented 4 years ago

I will check with the user.

In general, it seems like i should add some (more) tests on the validity of the template and report their failure to the user with comprehensible error messages.

This would be great.

bernt-matthias commented 4 years ago

Ok. This fixed this problem: bringing us to the next one: 

Unhandled Exception:
System.ArgumentException: Path is empty
  at System.IO.Directory.CreateDirectory (System.String path) [0x00016] in <5f1285e60d884a0d8de43c8b1a7e4c2e>:0 
  at MaxQuantPLibS.Basic.MaxQuantTasks.InitWorkflow (System.String combinedFolder, System.String mqparFile) [0x00022] in <ec730be64cdf4721a46ab6e809265226>:0 
  at MaxQuantPLibS.Work.InitializeWorkflow.Calculation (System.String[] args) [0x00001] in <ec730be64cdf4721a46ab6e809265226>:0 
  at MaxQuantPLibS.Work.MaxQuantWorkDispatcherUtil.PerformTask (System.Int32 taskType, System.String[] args) [0x00007] in <ec730be64cdf4721a46ab6e809265226>:0 
  at MaxQuantTask.Program.Function (System.String[] args) [0x00012] in <b866e35d5f424ce395a48bbb7863bb06>:0 
  at Utils.Util.ExternalProcess.Run (System.String[] args, System.Boolean debug) [0x00132] in <6139b99aa81348d4bab4aab61c6b8770>:0 
  at MaxQuantTask.Program.Main (System.String[] args) [0x00007] in <b866e35d5f424ce395a48bbb7863bb06>:0 
[ERROR] FATAL UNHANDLED EXCEPTION: System.ArgumentException: Path is empty
  at System.IO.Directory.CreateDirectory (System.String path) [0x00016] in <5f1285e60d884a0d8de43c8b1a7e4c2e>:0 
  at MaxQuantPLibS.Basic.MaxQuantTasks.InitWorkflow (System.String combinedFolder, System.String mqparFile) [0x00022] in <ec730be64cdf4721a46ab6e809265226>:0 
  at MaxQuantPLibS.Work.InitializeWorkflow.Calculation (System.String[] args) [0x00001] in <ec730be64cdf4721a46ab6e809265226>:0 
  at MaxQuantPLibS.Work.MaxQuantWorkDispatcherUtil.PerformTask (System.Int32 taskType, System.String[] args) [0x00007] in <ec730be64cdf4721a46ab6e809265226>:0 
  at MaxQuantTask.Program.Function (System.String[] args) [0x00012] in <b866e35d5f424ce395a48bbb7863bb06>:0 
  at Utils.Util.ExternalProcess.Run (System.String[] args, System.Boolean debug) [0x00132] in <6139b99aa81348d4bab4aab61c6b8770>:0 
  at MaxQuantTask.Program.Main (System.String[] args) [0x00007] in <b866e35d5f424ce395a48bbb7863bb06>:0 

Unhandled Exception:
System.Exception: Exception during execution of external process: 167422
  at BaseLibS.Util.WorkDispatcher.ProcessSingleRunExternalProcess (System.Int32 taskIndex, System.Int32 threadIndex) [0x0013b] in <39823f48f4784f749e0ec29211c52eb8>:0 
  at BaseLibS.Util.WorkDispatcher.DoWork (System.Int32 taskIndex, System.Int32 threadIndex) [0x0001c] in <39823f48f4784f749e0ec29211c52eb8>:0 
  at BaseLibS.Util.WorkDispatcher.Work (System.Object threadIndex) [0x00054] in <39823f48f4784f749e0ec29211c52eb8>:0 
  at System.Threading.ThreadHelper.ThreadStart_Context (System.Object state) [0x00025] in <5f1285e60d884a0d8de43c8b1a7e4c2e>:0 
  at System.Threading.ExecutionContext.RunInternal (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00071] in <5f1285e60d884a0d8de43c8b1a7e4c2e>:0 
  at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00000] in <5f1285e60d884a0d8de43c8b1a7e4c2e>:0 
  at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state) [0x0002b] in <5f1285e60d884a0d8de43c8b1a7e4c2e>:0 
  at System.Threading.ThreadHelper.ThreadStart (System.Object obj) [0x0000f] in <5f1285e60d884a0d8de43c8b1a7e4c2e>:0 
[ERROR] FATAL UNHANDLED EXCEPTION: System.Exception: Exception during execution of external process: 167422
  at BaseLibS.Util.WorkDispatcher.ProcessSingleRunExternalProcess (System.Int32 taskIndex, System.Int32 threadIndex) [0x0013b] in <39823f48f4784f749e0ec29211c52eb8>:0 
  at BaseLibS.Util.WorkDispatcher.DoWork (System.Int32 taskIndex, System.Int32 threadIndex) [0x0001c] in <39823f48f4784f749e0ec29211c52eb8>:0 
  at BaseLibS.Util.WorkDispatcher.Work (System.Object threadIndex) [0x00054] in <39823f48f4784f749e0ec29211c52eb8>:0 
  at System.Threading.ThreadHelper.ThreadStart_Context (System.Object state) [0x00025] in <5f1285e60d884a0d8de43c8b1a7e4c2e>:0 
  at System.Threading.ExecutionContext.RunInternal (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00071] in <5f1285e60d884a0d8de43c8b1a7e4c2e>:0 
  at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00000] in <5f1285e60d884a0d8de43c8b1a7e4c2e>:0 
  at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state) [0x0002b] in <5f1285e60d884a0d8de43c8b1a7e4c2e>:0 
  at System.Threading.ThreadHelper.ThreadStart (System.Object obj) [0x0000f] in <5f1285e60d884a0d8de43c8b1a7e4c2e>:0 
Traceback (most recent call last):
  File "/gpfs1/data/galaxy_server/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/8bac3cc5c5de/maxquant/mqwrapper.py", line 136, in <module>
    subprocess.run(cmd, check=True, cwd='./')
  File "/gpfs1/data/galaxy_server/galaxy/database/dependencies/_conda/envs/mulled-v1-88194d212d404fa1b66e7626414cd5e03962c42532a28f317b7bc004d3e11dd9/lib/python3.7/subprocess.py", line 487, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['maxquant', '/gpfs1/work/songalax/galaxy/database/jobs_directory/032/32899/working/mqpar.xml']' returned non-zero exit status 1.

Just a wild guess on the error: the mqpar.xml contained: 

        <filePaths/>
        <experiments/>
        <fractions/>
        <ptms/>
bernt-matthias commented 4 years ago

Was stiil a problem in the file. there it was .raw

dglaetzer commented 4 years ago

ok, that one looks more serious. Can you give me the mqpar.xml and the new experimental design template?

bernt-matthias commented 4 years ago

I already debugged it a bit. The problem was that the design template had the file extensions (.raw) in the names and then the Names array got [None, None, ....]

dglaetzer commented 4 years ago

So, more checks and more precise documentation... But there is a bug with the handling of the empty fraction column as well. In the current version the user must write 32767 (which is MQ's internal value for 'no fraction') instead of leaving it empty.

bernt-matthias commented 4 years ago

Thanks for the comment. Will test.

bernt-matthias commented 4 years ago

Another one for you that might be nice to catch: The file ... appears to be corrupt:

Unhandled Exception:
System.Exception: System.Exception: The file '/gpfs1/work/songalax/galaxy/database/jobs_directory/032/32916/working/21-12-2018_S81_GF_F3_HP.thermo.raw' appears to be corrupt. Try to open it with vendor software. ---> ThermoFisher.CommonCore.Data.Business.NoSelectedDeviceException: RunHeaderEx
  at ThermoFisher.CommonCore.RawFileReader.RawFileAccessBase.RequireDevice (System.String reason) [0x0001c] in <b3390dbff2b6498bb045a64033412ba7>:0 
  at ThermoFisher.CommonCore.RawFileReader.RawFileAccessBase.get_RunHeaderEx () [0x00000] in <b3390dbff2b6498bb045a64033412ba7>:0 
  at PluginRawThermo2.ThermoRawFile.get_FirstScanNumber () [0x00017] in <f54c00f43b894295a90a0e0a8dd71965>:0 
  at BaseLibS.Ms.RawFile.InitFromRawFileImpl () [0x00017] in <39823f48f4784f749e0ec29211c52eb8>:0 
  at BaseLibS.Ms.RawFile.InitFromRawFile () [0x00017] in <39823f48f4784f749e0ec29211c52eb8>:0 
  at BaseLibS.Ms.RawFile.Init (System.String path1) [0x00058] in <39823f48f4784f749e0ec29211c52eb8>:0 
  at MsLib.Raw.RawFileUtil.CreateRawFile (System.String path) [0x00042] in <c10c647f874849a58167c9895ff49fe2>:0 
  at MaxQuantPLibS.Basic.MaxQuantTasks.TestFile1 (System.String rawFilePath) [0x00001] in <ec730be64cdf4721a46ab6e809265226>:0 
  at MaxQuantPLibS.Basic.MaxQuantTasks.TestFile (System.Int32 taskIndex, System.String mqparFile) [0x0004f] in <ec730be64cdf4721a46ab6e809265226>:0 
   --- End of inner exception stack trace ---
  at MaxQuantPLibS.Basic.MaxQuantTasks.TestFile (System.Int32 taskIndex, System.String mqparFile) [0x0007c] in <ec730be64cdf4721a46ab6e809265226>:0 
  at MaxQuantPLibS.Work.RawFileTester.Calculation (System.String[] args) [0x00009] in <ec730be64cdf4721a46ab6e809265226>:0 
  at MaxQuantPLibS.Work.MaxQuantWorkDispatcherUtil.PerformTask (System.Int32 taskType, System.String[] args) [0x00007] in <ec730be64cdf4721a46ab6e809265226>:0 
  at MaxQuantTask.Program.Function (System.String[] args) [0x00012] in <b866e35d5f424ce395a48bbb7863bb06>:0 
  at Utils.Util.ExternalProcess.Run (System.String[] args, System.Boolean debug) [0x00132] in <6139b99aa81348d4bab4aab61c6b8770>:0 
  at MaxQuantTask.Program.Main (System.String[] args) [0x00007] in <b866e35d5f424ce395a48bbb7863bb06>:0 
[ERROR] FATAL UNHANDLED EXCEPTION: System.Exception: System.Exception: The file '/gpfs1/work/songalax/galaxy/database/jobs_directory/032/32916/working/21-12-2018_S81_GF_F3_HP.thermo.raw' appears to be corrupt. Try to open it with vendor software. ---> ThermoFisher.CommonCore.Data.Business.NoSelectedDeviceException: RunHeaderEx
  at ThermoFisher.CommonCore.RawFileReader.RawFileAccessBase.RequireDevice (System.String reason) [0x0001c] in <b3390dbff2b6498bb045a64033412ba7>:0 
  at ThermoFisher.CommonCore.RawFileReader.RawFileAccessBase.get_RunHeaderEx () [0x00000] in <b3390dbff2b6498bb045a64033412ba7>:0 
  at PluginRawThermo2.ThermoRawFile.get_FirstScanNumber () [0x00017] in <f54c00f43b894295a90a0e0a8dd71965>:0 
  at BaseLibS.Ms.RawFile.InitFromRawFileImpl () [0x00017] in <39823f48f4784f749e0ec29211c52eb8>:0 
  at BaseLibS.Ms.RawFile.InitFromRawFile () [0x00017] in <39823f48f4784f749e0ec29211c52eb8>:0 
  at BaseLibS.Ms.RawFile.Init (System.String path1) [0x00058] in <39823f48f4784f749e0ec29211c52eb8>:0 
  at MsLib.Raw.RawFileUtil.CreateRawFile (System.String path) [0x00042] in <c10c647f874849a58167c9895ff49fe2>:0 
  at MaxQuantPLibS.Basic.MaxQuantTasks.TestFile1 (System.String rawFilePath) [0x00001] in <ec730be64cdf4721a46ab6e809265226>:0 
  at MaxQuantPLibS.Basic.MaxQuantTasks.TestFile (System.Int32 taskIndex, System.String mqparFile) [0x0004f] in <ec730be64cdf4721a46ab6e809265226>:0 
   --- End of inner exception stack trace ---
  at MaxQuantPLibS.Basic.MaxQuantTasks.TestFile (System.Int32 taskIndex, System.String mqparFile) [0x0007c] in <ec730be64cdf4721a46ab6e809265226>:0 
  at MaxQuantPLibS.Work.RawFileTester.Calculation (System.String[] args) [0x00009] in <ec730be64cdf4721a46ab6e809265226>:0 
  at MaxQuantPLibS.Work.MaxQuantWorkDispatcherUtil.PerformTask (System.Int32 taskType, System.String[] args) [0x00007] in <ec730be64cdf4721a46ab6e809265226>:0 
  at MaxQuantTask.Program.Function (System.String[] args) [0x00012] in <b866e35d5f424ce395a48bbb7863bb06>:0 
  at Utils.Util.ExternalProcess.Run (System.String[] args, System.Boolean debug) [0x00132] in <6139b99aa81348d4bab4aab61c6b8770>:0 
  at MaxQuantTask.Program.Main (System.String[] args) [0x00007] in <b866e35d5f424ce395a48bbb7863bb06>:0 

Unhandled Exception:
System.Exception: Exception during execution of external process: 119416
  at BaseLibS.Util.WorkDispatcher.ProcessSingleRunExternalProcess (System.Int32 taskIndex, System.Int32 threadIndex) [0x0013b] in <39823f48f4784f749e0ec29211c52eb8>:0 
  at BaseLibS.Util.WorkDispatcher.DoWork (System.Int32 taskIndex, System.Int32 threadIndex) [0x0001c] in <39823f48f4784f749e0ec29211c52eb8>:0 
  at BaseLibS.Util.WorkDispatcher.Work (System.Object threadIndex) [0x00054] in <39823f48f4784f749e0ec29211c52eb8>:0 
  at System.Threading.ThreadHelper.ThreadStart_Context (System.Object state) [0x00025] in <5f1285e60d884a0d8de43c8b1a7e4c2e>:0 
  at System.Threading.ExecutionContext.RunInternal (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00071] in <5f1285e60d884a0d8de43c8b1a7e4c2e>:0 
  at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00000] in <5f1285e60d884a0d8de43c8b1a7e4c2e>:0 
  at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state) [0x0002b] in <5f1285e60d884a0d8de43c8b1a7e4c2e>:0 
  at System.Threading.ThreadHelper.ThreadStart (System.Object obj) [0x0000f] in <5f1285e60d884a0d8de43c8b1a7e4c2e>:0 
[ERROR] FATAL UNHANDLED EXCEPTION: System.Exception: Exception during execution of external process: 119416
  at BaseLibS.Util.WorkDispatcher.ProcessSingleRunExternalProcess (System.Int32 taskIndex, System.Int32 threadIndex) [0x0013b] in <39823f48f4784f749e0ec29211c52eb8>:0 
  at BaseLibS.Util.WorkDispatcher.DoWork (System.Int32 taskIndex, System.Int32 threadIndex) [0x0001c] in <39823f48f4784f749e0ec29211c52eb8>:0 
  at BaseLibS.Util.WorkDispatcher.Work (System.Object threadIndex) [0x00054] in <39823f48f4784f749e0ec29211c52eb8>:0 
  at System.Threading.ThreadHelper.ThreadStart_Context (System.Object state) [0x00025] in <5f1285e60d884a0d8de43c8b1a7e4c2e>:0 
  at System.Threading.ExecutionContext.RunInternal (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00071] in <5f1285e60d884a0d8de43c8b1a7e4c2e>:0 
  at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00000] in <5f1285e60d884a0d8de43c8b1a7e4c2e>:0 
  at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state) [0x0002b] in <5f1285e60d884a0d8de43c8b1a7e4c2e>:0 
  at System.Threading.ThreadHelper.ThreadStart (System.Object obj) [0x0000f] in <5f1285e60d884a0d8de43c8b1a7e4c2e>:0 
Traceback (most recent call last):
  File "/gpfs1/data/galaxy_server/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/8bac3cc5c5de/maxquant/mqwrapper.py", line 137, in <module>
    subprocess.run(cmd, check=True, cwd='./')
  File "/gpfs1/data/galaxy_server/galaxy/database/dependencies/_conda/envs/mulled-v1-88194d212d404fa1b66e7626414cd5e03962c42532a28f317b7bc004d3e11dd9/lib/python3.7/subprocess.py", line 487, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['maxquant', '/gpfs1/work/songalax/galaxy/database/jobs_directory/032/32916/working/mqpar.xml']' returned non-zero exit status 1.
Ebra55 commented 3 years ago

Dear bernt-matthias, I have this error with MaxQuant... in the Label-Free normalization step:

Label-free_normalization 0 Label-free_normalization (1/1) Process 57 C:\Users\mqpar.xml C:\Users\combined 8 0Index was outside the bounds of the array. at MaxQuantPLibS.Lfq.LfqCalc.CalcNormCoeffs(String mqparFile, String combinedFolder, Int32 nthreads, Int32 lfqInd) at MaxQuantPLibS.Work.LfqNorm.Calculation(String[] args, Responder responder) at MaxQuantPLibS.Work.MaxQuantWorkDispatcherUtil.PerformTask(Int32 taskType, String[] args, Responder responder) at MaxQuantTask.Program.Function(String[] args, Responder responder) at Utils.Util.ExternalProcess.Run(String[] args, Boolean debug)

How to fix it? Thank you

tannishthadas commented 5 months ago

Hi, I am getting this error - Label-free normalization

Unhandled Exception: System.Exception: Exception during execution of external process: 7065 Unhandled Exception: System.IndexOutOfRangeException: Index was outside the bounds of the array. at MaxQuantLibS.Domains.Peptides.ProteinTasks.ProteinAssembly.CalcNormCoeffsLfq (System.String mqparFile, System.String combinedFolder, System.Int32 nthreads, System.Int32 lfqInd) [0x0004c] in <2ccc08da14d74cffaf694e9e9a94f21e>:0 at MaxQuantLibS.Domains.Peptides.Work.LfqNorm.Calculation (System.String[] args, BaseLibS.Util.Responder responder) [0x00017] in <2ccc08da14d74cffaf694e9e9a94f21e>:0 at MaxQuantLibS.Domains.Peptides.Work.MaxQuantWorkDispatcherUtil.PerformTask (System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x00007] in <2ccc08da14d74cffaf694e9e9a94f21e>:0 at MaxQuantLibS.Base.MaxQuantUtils.Run (System.Int32 softwareId, System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x0003e] in <2ccc08da14d74cffaf694e9e9a94f21e>:0 at MaxQuantTaskCore.Program.Function (System.String[] args, BaseLibS.Util.Responder responder) [0x0001c] in <84143ecaa91a4c99adeae8279689607c>:0 at Utils.Util.ExternalProcess.Run (System.String[] args, System.Boolean debug) [0x00148] in :0 at MaxQuantTaskCore.Program.Main (System.String[] args) [0x00007] in <84143ecaa91a4c99adeae8279689607c>:0 [ERROR] FATAL UNHANDLED EXCEPTION: System.IndexOutOfRangeException: Index was outside the bounds of the array. at MaxQuantLibS.Domains.Peptides.ProteinTasks.ProteinAssembly.CalcNormCoeffsLfq (System.String mqparFile, System.String combinedFolder, System.Int32 nthreads, System.Int32 lfqInd) [0x0004c] in <2ccc08da14d74cffaf694e9e9a94f21e>:0 at MaxQuantLibS.Domains.Peptides.Work.LfqNorm.Calculation (System.String[] args, BaseLibS.Util.Responder responder) [0x00017] in <2ccc08da14d74cffaf694e9e9a94f21e>:0 at MaxQuantLibS.Domains.Peptides.Work.MaxQuantWorkDispatcherUtil.PerformTask (System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x00007] in <2ccc08da14d74cffaf694e9e9a94f21e>:0 at MaxQuantLibS.Base.MaxQuantUtils.Run (System.Int32 softwareId, System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x0003e] in <2ccc08da14d74cffaf694e9e9a94f21e>:0 at MaxQuantTaskCore.Program.Function (System.String[] args, BaseLibS.Util.Responder responder) [0x0001c] in <84143ecaa91a4c99adeae8279689607c>:0 at Utils.Util.ExternalProcess.Run (System.String[] args, System.Boolean debug) [0x00148] in :0 at MaxQuantTaskCore.Program.Main (System.String[] args) [0x00007] in <84143ecaa91a4c99adeae8279689607c>:0

at QueueingSystem.WorkDispatcher.ProcessSingleRunExternalProcess (System.Int32 taskIndex, System.Int32 threadIndex) [0x0009d] in :0 at QueueingSystem.WorkDispatcher.DoWork (System.Int32 taskIndex, System.Int32 threadIndex) [0x0001e] in :0 at QueueingSystem.WorkDispatcher.Work (System.Object threadIndex) [0x00054] in :0 at System.Threading.ThreadHelper.ThreadStart_Context (System.Object state) [0x00025] in <5dfd69ae4e3b402db546d8ded6fc755e>:0 at System.Threading.ExecutionContext.RunInternal (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00071] in <5dfd69ae4e3b402db546d8ded6fc755e>:0 at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00000] in <5dfd69ae4e3b402db546d8ded6fc755e>:0 at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state) [0x0002b] in <5dfd69ae4e3b402db546d8ded6fc755e>:0 at System.Threading.ThreadHelper.ThreadStart (System.Object obj) [0x0000f] in <5dfd69ae4e3b402db546d8ded6fc755e>:0 [ERROR] FATAL UNHANDLED EXCEPTION: System.Exception: Exception during execution of external process: 7065 Unhandled Exception: System.IndexOutOfRangeException: Index was outside the bounds of the array. at MaxQuantLibS.Domains.Peptides.ProteinTasks.ProteinAssembly.CalcNormCoeffsLfq (System.String mqparFile, System.String combinedFolder, System.Int32 nthreads, System.Int32 lfqInd) [0x0004c] in <2ccc08da14d74cffaf694e9e9a94f21e>:0 at MaxQuantLibS.Domains.Peptides.Work.LfqNorm.Calculation (System.String[] args, BaseLibS.Util.Responder responder) [0x00017] in <2ccc08da14d74cffaf694e9e9a94f21e>:0 at MaxQuantLibS.Domains.Peptides.Work.MaxQuantWorkDispatcherUtil.PerformTask (System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x00007] in <2ccc08da14d74cffaf694e9e9a94f21e>:0 at MaxQuantLibS.Base.MaxQuantUtils.Run (System.Int32 softwareId, System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x0003e] in <2ccc08da14d74cffaf694e9e9a94f21e>:0 at MaxQuantTaskCore.Program.Function (System.String[] args, BaseLibS.Util.Responder responder) [0x0001c] in <84143ecaa91a4c99adeae8279689607c>:0 at Utils.Util.ExternalProcess.Run (System.String[] args, System.Boolean debug) [0x00148] in :0 at MaxQuantTaskCore.Program.Main (System.String[] args) [0x00007] in <84143ecaa91a4c99adeae8279689607c>:0 [ERROR] FATAL UNHANDLED EXCEPTION: System.IndexOutOfRangeException: Index was outside the bounds of the array. at MaxQuantLibS.Domains.Peptides.ProteinTasks.ProteinAssembly.CalcNormCoeffsLfq (System.String mqparFile, System.String combinedFolder, System.Int32 nthreads, System.Int32 lfqInd) [0x0004c] in <2ccc08da14d74cffaf694e9e9a94f21e>:0 at MaxQuantLibS.Domains.Peptides.Work.LfqNorm.Calculation (System.String[] args, BaseLibS.Util.Responder responder) [0x00017] in <2ccc08da14d74cffaf694e9e9a94f21e>:0 at MaxQuantLibS.Domains.Peptides.Work.MaxQuantWorkDispatcherUtil.PerformTask (System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x00007] in <2ccc08da14d74cffaf694e9e9a94f21e>:0 at MaxQuantLibS.Base.MaxQuantUtils.Run (System.Int32 softwareId, System.Int32 taskType, System.String[] args, BaseLibS.Util.Responder responder) [0x0003e] in <2ccc08da14d74cffaf694e9e9a94f21e>:0 at MaxQuantTaskCore.Program.Function (System.String[] args, BaseLibS.Util.Responder responder) [0x0001c] in <84143ecaa91a4c99adeae8279689607c>:0 at Utils.Util.ExternalProcess.Run (System.String[] args, System.Boolean debug) [0x00148] in :0 at MaxQuantTaskCore.Program.Main (System.String[] args) [0x00007] in <84143ecaa91a4c99adeae8279689607c>:0

at QueueingSystem.WorkDispatcher.ProcessSingleRunExternalProcess (System.Int32 taskIndex, System.Int32 threadIndex) [0x0009d] in :0 at QueueingSystem.WorkDispatcher.DoWork (System.Int32 taskIndex, System.Int32 threadIndex) [0x0001e] in :0 at QueueingSystem.WorkDispatcher.Work (System.Object threadIndex) [0x00054] in :0 at System.Threading.ThreadHelper.ThreadStart_Context (System.Object state) [0x00025] in <5dfd69ae4e3b402db546d8ded6fc755e>:0 at System.Threading.ExecutionContext.RunInternal (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00071] in <5dfd69ae4e3b402db546d8ded6fc755e>:0 at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state, System.Boolean preserveSyncCtx) [0x00000] in <5dfd69ae4e3b402db546d8ded6fc755e>:0 at System.Threading.ExecutionContext.Run (System.Threading.ExecutionContext executionContext, System.Threading.ContextCallback callback, System.Object state) [0x0002b] in <5dfd69ae4e3b402db546d8ded6fc755e>:0 at System.Threading.ThreadHelper.ThreadStart (System.Object obj) [0x0000f] in <5dfd69ae4e3b402db546d8ded6fc755e>:0 What to do?

VioletZZH commented 5 months ago

@tannishthadas Hello,tannishthadas I also met the problem when using MaxDIA, detailed information is as follows: System. IndexOutOfRangeException: Index was outside the bounds of the array. Have you solved it now?

bernt-matthias commented 5 months ago

Maybe its better to ask the actual maxquant developers/community https://groups.google.com/g/maxquant-list?pli=1

VioletZZH commented 5 months ago

Maybe its better to ask the actual maxquant developers/community https://groups.google.com/g/maxquant-list?pli=1

Okay, I'll try. Thank you very much，Dear bernt-matthias.

tannishthadas commented 4 months ago

@tannishthadas Hello,tannishthadas I also met the problem when using MaxDIA, detailed information is as follows: System. IndexOutOfRangeException: Index was outside the bounds of the array. Have you solved it now? @VioletZZH Hi, No this is this unresolved :( Please let me know if you get any leads. Thanks