Closed emhumphries closed 3 years ago
Invalid maximum heap size: -Xmx-1G
Can you tell us how much free memory available in your computer?
Best,
Fengchao
Hi Fengchao, Thanks for your help. I'm running on a server so I'm not sure which one below:
I am also don't know Windows server very well, but "Available Physical Memory 1.53 GB" looks like the one we are looking for.
FragPipe automatically uses (int) freeMem - 2
if users don't specified the memory explicitly. If you think your task can be done with 1 GB memory, you can put 1 in the RAM
in the workflow
tab:
. Otherwise, you need to free some memory in your computer.
We will put a warning in FragPipe if (int) freeMem - 2 < 0
in the next release.
Best,
Fengchao
Manually setting the memory to 40GB solved the problem. Could be an MSFragger and windows server communication issue.
Hi All,
I'm trying to perform a closed search for a TMT16 workflow however I've got the same error as https://github.com/Nesvilab/MSFragger/issues/19 except using more recent updates of FragPipe and Java. I've tried reinstalling Java and rebooting the computer with no success. Do you have any suggestions to help solve this issue? Thank you in advance, Erin Humphries.
`System OS: Windows Server 2016, Architecture: AMD64 Java Info: 1.8.0_281, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
Version info: FragPipe version 15.0 MSFragger version 3.2 Philosopher version 3.4.13 (build 1611589727)
LCMS files: Experiment/Group:
18 commands to execute: WorkspaceCleanInit [Work dir: C:\Users\ehumphries\Documents\MSFragger\210414_output] C:\Progs\philosopher_v3.4.13\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: C:\Users\ehumphries\Documents\MSFragger\210414_output] C:\Progs\philosopher_v3.4.13\philosopher.exe workspace --init --nocheck MSFragger [Work dir: C:\Users\ehumphries\Documents\MSFragger\210414_output] java -jar -Dfile.encoding=UTF-8 -Xmx-1G C:\Progs\MSFragger-3.2\MSFragger-3.2\MSFragger-3.2.jar C:\Users\ehumphries\Documents\MSFragger\210414_output\fragger.params C:\Users\ehumphries\Documents\MSFragger\210414_output\7\210408_EMH_T1-2_ADV_Phos_QE1_D_1_05.mzML MSFragger move pepxml java -cp C:\Progs\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar;/C:/Progs/FragPipe-15.0/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove C:\Users\ehumphries\Documents\MSFragger\210414_output\7\210408_EMH_T1-2_ADV_Phos_QE1_D_1_05.pepXML C:\Users\ehumphries\Documents\MSFragger\210414_output\210408_EMH_T1-2_ADV_Phos_QE1_D_1_05.pepXML PeptideProphet: Workspace init [Work dir: C:\Users\ehumphries\Documents\MSFragger\210414_output\fragpipe-210408_EMH_T1-2_ADV_Phos_QE1_D_1_05.pepXML-temp] C:\Progs\philosopher_v3.4.13\philosopher.exe workspace --init --nocheck PeptideProphet [Work dir: C:\Users\ehumphries\Documents\MSFragger\210414_output\fragpipe-210408_EMH_T1-2_ADV_Phos_QE1_D_1_05.pepXML-temp] C:\Progs\philosopherv3.4.13\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\Users\ehumphries\Documents\MSFragger\2021-04-14-decoys-contam-20190717_RRP_SWISS_Canon_human_with_BUGS.fasta.fas ..\210408_EMH_T1-2_ADV_Phos_QE1_D_1_05.pepXML PeptideProphet: Delete temp java -cp C:\Progs\FragPipe-15.0\fragpipe\lib\fragpipe-15.0.jar com.github.chhh.utils.FileDelete C:\Users\ehumphries\Documents\MSFragger\210414_output\fragpipe-210408_EMH_T1-2_ADV_Phos_QE1_D_1_05.pepXML-temp Rewrite pepxml [Work dir: C:\Users\ehumphries\Documents\MSFragger\210414_output] java -cp C:\Progs\FragPipe-15.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml C:\Users\ehumphries\Documents\MSFragger\210414_output\interact-210408_EMH_T1-2_ADV_Phos_QE1_D_1_05.pep.xml C:\Users\ehumphries\Documents\MSFragger\210414_output\7\210408_EMH_T1-2_ADV_Phos_QE1_D_1_05.mzML Delay java -cp C:\Progs\FragPipe-15.0\fragpipe\lib/ com.dmtavt.fragpipe.util.DoNothing 1000 PtmProphet [Work dir: C:\Users\ehumphries\Documents\MSFragger\210414_output] C:\Progs\philosopher_v3.4.13\philosopher.exe ptmprophet --keepold --static --em 1 --nions b --mods STY:79.966331,M:15.9949 --minprob 0.5 --maxthreads 63 interact-210408_EMH_T1-2_ADV_Phos_QE1_D_1_05.pep.xml ProteinProphet [Work dir: C:\Users\ehumphries\Documents\MSFragger\210414_output] C:\Progs\philosopher_v3.4.13\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined C:\Users\ehumphries\Documents\MSFragger\210414_output\interact-210408_EMH_T1-2_ADV_Phos_QE1_D_1_05.pep.xml PhilosopherDbAnnotate [Work dir: C:\Users\ehumphries\Documents\MSFragger\210414_output] C:\Progs\philosopher_v3.4.13\philosopher.exe database --annotate C:\Users\ehumphries\Documents\MSFragger\2021-04-14-decoys-contam-20190717_RRP_SWISS_Canon_human_withBUGS.fasta.fas --prefix rev PhilosopherFilter [Work dir: C:\Users\ehumphries\Documents\MSFragger\210414_output] C:\Progs\philosopherv3.4.13\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml C:\Users\ehumphries\Documents\MSFragger\210414_output --protxml C:\Users\ehumphries\Documents\MSFragger\210414_output\combined.prot.xml FreeQuant [Work dir: C:\Users\ehumphries\Documents\MSFragger\210414_output] C:\Progs\philosopher_v3.4.13\philosopher.exe freequant --ptw 0.4 --tol 10 --isolated --dir C:\Users\ehumphries\Documents\MSFragger\210414_output\7 Quant (Isobaric) [Work dir: C:\Users\ehumphries\Documents\MSFragger\210414_output] C:\Progs\philosopher_v3.4.13\philosopher.exe labelquant --tol 20 --level 2 --plex 16 --annot C:\Users\ehumphries\Documents\MSFragger\210414_output\7\annotation.txt --brand tmt --dir C:\Users\ehumphries\Documents\MSFragger\210414_output\7 PhilosopherReport [Work dir: C:\Users\ehumphries\Documents\MSFragger\210414_output] C:\Progs\philosopher_v3.4.13\philosopher.exe report TmtIntegrator [Work dir: C:\Users\ehumphries\Documents\MSFragger\210414_output] java -cp "C:\Progs\FragPipe-15.0\fragpipe\tools\tmt-integrator-2.4.0.jar" TMTIntegrator C:\Users\ehumphries\Documents\MSFragger\210414_output\tmt-integrator-conf.yml C:\Users\ehumphries\Documents\MSFragger\210414_output\psm.tsv WorkspaceClean [Work dir: C:\Users\ehumphries\Documents\MSFragger\210414_output] C:\Progs\philosopher_v3.4.13\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: C:\Users\ehumphries\Documents\MSFragger\210414_output] C:\Progs\philosopher_v3.4.13\philosopher.exe workspace --clean --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\Users\ehumphries\Documents\MSFragger\210414_output] C:\Progs\philosopher_v3.4.13\philosopher.exe workspace --init --nocheck INFO[10:10:06] Executing Workspace v3.4.13
INFO[10:10:06] Removing workspace
INFO[10:10:06] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[10:10:06] Executing Workspace v3.4.13
INFO[10:10:06] Creating workspace
INFO[10:10:06] Done
MSFragger [Work dir: C:\Users\ehumphries\Documents\MSFragger\210414_output] java -jar -Dfile.encoding=UTF-8 -Xmx-1G C:\Progs\MSFragger-3.2\MSFragger-3.2\MSFragger-3.2.jar C:\Users\ehumphries\Documents\MSFragger\210414_output\fragger.params C:\Users\ehumphries\Documents\MSFragger\210414_output\7\210408_EMH_T1-2_ADV_Phos_QE1_D_1_05.mzML Invalid maximum heap size: -Xmx-1G Error: Could not create the Java Virtual Machine. Error: A fatal exception has occurred. Program will exit. Process 'MSFragger' finished, exit code: 1 Process returned non-zero exit code, stopping