fcyu
commented
3 years ago Hi Miguel,
It looks like your computer is set to use "," as the decimal separator. You need to change the configuration to use "." as the decimal separator.
Also, if your GPF data has overlapped windows, like 2 m/z of adjacent windows are overlapped, you need to add a demultiplexing filter in msconvert conversion.
The last thing I want to mention is that you can try the MSFragger-DIA narrow window SpecLib workflow, which is supposed to be better for the GPF data compared to DIA-Umpire.
Best,
Fengchao
On Wed, Jul 28, 2021 at 6:33 AM Miguel Cosenza-Contreras < @.***> wrote:
Hello,
We are trying to generate a spectral library using DIA-Umpire from DDA files that were acquired following a gas-phase-fractionation method for library generation (scanning 100m/z areas with 25 windows at 4m/z).
The execution stops when loading the first mzML file:
WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by org.nustaq.serialization.FSTClazzInfo (file:/C:/Data_analysis_software/FragPipe/fragpipe_v16_2021_07_26/fragpipe/tools/DIA_Umpire_SE-2.2.1.jar) to field java.lang.String.value WARNING: Please consider reporting this to the maintainers of org.nustaq.serialization.FSTClazzInfo WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release 2021-07-28 11:50:08,942 ERROR [root] java.lang.NumberFormatException: For input string: "402,432800" at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(Unknown Source) at java.base/jdk.internal.math.FloatingDecimal.parseFloat(Unknown Source) at java.base/java.lang.Float.parseFloat(Unknown Source) at MSUmpire.SpectrumParser.mzXMLParser.ParseElutionIndex(mzXMLParser.java:887) at MSUmpire.SpectrumParser.mzXMLParser.ReadElutionAndScanIndex(mzXMLParser.java:633) at MSUmpire.SpectrumParser.mzXMLParser.
(mzXMLParser.java:622) at MSUmpire.SpectrumParser.SpectrumParserBase.GetInstance(SpectrumParserBase.java:84) at MSUmpire.DIA.DIAPack.GetSpectrumParser(DIAPack.java:162) at MSUmpire.DIA.DIAPack.BuildDIAWindows(DIAPack.java:184) at MSUmpire.DIA.DIAPack.process(DIAPack.java:176) at dia_umpire_se.DIA_Umpire_SE.main(DIA_Umpire_SE.java:376) 2021-07-28 11:50:08,942 ERROR [root] Read spectral file:D:\tmp-MQ\TW\lasttry\TW-GBM_GPF_1.mzML failed. Process 'UmpireSe' finished, exit code: 2 Process returned non-zero exit code, stopping
Cancelling 277 remaining tasks We are using a Windows Server 2019 machine with multiple users, and curiously, the error seems to not be consistent between server users. We first found the error while executing FragPipe from a User session. The same workflow with the same files is not crashing when executed by a system admin. We tried giving admin rights to the initial user, but the error is consistent on his end. We are using FragPipe v16 and EasyPQP 0.1.21. I am attaching the log file here. I would appreciate your support! Best, Miguel log_2021-07-28_11-50-09_TW.txt <https://github.com/Nesvilab/FragPipe/files/6892304/log_2021-07-28_11-50-09_TW.txt> — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <https://github.com/Nesvilab/FragPipe/issues/415>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABU27WZPZ4GFFNWI64DKJDTTZ7MHRANCNFSM5BECJYOA> .
-- Dr. Fengchao Yu Research Investigator University of Michigan
xbisteau
MiguelCos
guoci
Hello,
We are trying to generate a spectral library using DIA-Umpire from DDA files that were acquired following a gas-phase-fractionation method for library generation (scanning 100m/z areas with 25 windows at 4m/z).
The execution stops when loading the first mzML file:
We are using a Windows Server 2019 machine with multiple users, and curiously, the error seems to not be consistent between server users. We first found the error while executing FragPipe from a User session. The same workflow with the same files is not crashing when executed by a system admin. We tried giving admin rights to the initial user, but the error is consistent on his end.
We are using FragPipe v16 and EasyPQP 0.1.21.
I am attaching the log file here.
I would appreciate your support!
Best, Miguel
log_2021-07-28_11-50-09_TW.txt