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Nesvilab / Crystal-C

Crystal-C: A computational tool for refinement of open search results
https://nesvilab.github.io/Crystal-C/
Apache License 2.0
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Error: Invalid or corrupt jarfile CrystalC-1.2.1.jar #3

Closed PePito-M closed 3 years ago

PePito-M commented 4 years ago

I loaded last version of Crystal-C with wget. Tried to use Crystal-C by running the following command:

java -Xmx8g -jar Crystal/CrystalC-1.2.1.jar Crystal/Crystal-C.params *.pepXML

Error: Error: Invalid or corrupt jarfile Crystal/CrystalC-1.2.1.jar

I have tried different versions of Java and CrystalC but I get the same problem. Also tried running: java -Xmx8g -cp Crystal/CrystalC-1.2.1.jar CrystalC-1.2.1.Main Crystal/Crystal-C.params *.pepXML but then the issue is: Error: Could not find or load main class

sarah-haynes commented 4 years ago

Can you try downloading the JAR file from the releases page? Depending on your setup, it may be easiest to use FragPipe (which includes Crystal-C) for your analyses.

huiyinc commented 4 years ago

Hi,

Thanks for your interest in our tool. If you want to run Crystal-C independent from FragPipe, please use the following command:

(for mzML files) java -Xmx53G -cp "CrystalC-1.2.1.jar" crystalc.Run crystalc.params .pepXML (for Thermo RAW files) java -Dbatmass.io.libs.thermo.dir="D:\MSFragger-3.0\ext\thermo" -Xmx53G -cp "CrystalC-1.2.1.jar" crystalc.Run crystalc.params .pepXML

Please let me know if you have any questions. Thank you!

Huiyin

PePito-M notifications@github.com 於 2020年6月30日 週二 下午12:33寫道：

I loaded last version of Crystal-C with wget. Tried to use Crystal-C by running the following command:

java -Xmx8g -jar Crystal/CrystalC-1.2.1.jar Crystal/Crystal-C.params *.pepXML

Error: Error: Invalid or corrupt jarfile Crystal/CrystalC-1.2.1.jar

I have tried different versions of Java and CrystalC but I get the same problem. Also tried running: java -Xmx8g -cp Crystal/CrystalC-1.2.1.jar CrystalC-1.2.1.Main Crystal/Crystal-C.params *.pepXML but then the issue is: Error: Could not find or load main class

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-- Hui-Yin Chang, 張彙音 Research Fellow Department of Pathology University of Michigan

PePito-M commented 4 years ago

Downloading the jar file instead of wget works! Thanks!

huiyinc commented 4 years ago

No problem! Huiyin

PePito-M notifications@github.com 於 2020年7月1日 上午7:25 寫道：

 Downloading the jar file instead of wget it works! Thanks!

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