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Nesvilab / IonQuant

A label free quantification tool.
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Install error #28

Closed panbei2022 closed 2 years ago

panbei2022 commented 2 years ago

Hi IonQuant Developer,

I meet a problem during IonQuant install process.

According to your guidance, I download IonQuant-1.7.17.jar and installed VC_redist.x64.exe on my computer.

Finally, I can ensure three software version match IonQuant manuel: java (1.8.0_221) Visual C++ 2015-2019 Redistributable (x64) - 14.29.30139

But I still meet the error you mentioned in the manule, please see details as bellow. Could you help me check this problem. Many thanks!

######################################################################### C:\Users\XXX>java -jar D:\software\IonQuant\IonQuant-1.7.17.jar --specdir D:\Analysis\IonQuant\A1.raw --threads 4 10:19:11.294 [main] ERROR umich.ms.fileio.filetypes.bruker.Timsdata - JNA could not load native Bruker library 10:19:11.294 [main] ERROR umich.ms.fileio.filetypes.bruker.Timsdata - The ext folder with timsdata-2-8-7-1.dll (Win) or libtimsdata-2-8-7-1.so (Linux) is needed. If you are using an old ext folder, please upgrade. IonQuant version IonQuant-1.7.17 Batmass-IO version 1.23.6 timsdata library version (c) University of Michigan System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_221, Java HotSpot(TM) Client VM, Oracle Corporation JVM started with 0 GB memory 2022-01-17 10:19:11 [ERROR] - There is no spectral directory provided with --specdir or --filelist. #####################################################################

fcyu commented 2 years ago

You need to have the ext folder from MSFragger-3.4.zip. We cannot ship that folder together with IonQuant due to license issue. Put that folder in the folder where IonQuant is so that IonQuant can find the library to read the spectral files.

BTW, we have FragPipe (https://fragpipe.nesvilab.org/) which is the easiest way to run MSFragger, Philosopher, IonQuant, and other tools. You can familiar yourself by using FragPipe first.

Best,

Fengchao

panbei2022 commented 2 years ago

Hi IonQuant Developer,

Many thanks for your quick reply and guidance. The problem was resolved. And your suggestion for Fragpipe I will do later.

But there is another error emerged, can you see it:

java -jar D:\software\IonQuant\IonQuant-1.7.17.jar --specdir D:\Analysis\IonQuant*.d -

Error Info : "2022-01-07 11:15:55 [ERROR] - Need pepXML file"

fcyu commented 2 years ago

Your command is not correct. Please read the document here (https://github.com/Nesvilab/IonQuant) carefully before running IonQuant with command line.

If you find it difficult to use the command line, please try FragPipe (https://fragpipe.nesvilab.org/).

Best,

Fengchao