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MSGFPlus / msgfplus

MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.
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Error: Unable to access jarfile edu.ucsd.msjava.msdbsearch.BuildSA #138

Closed Luxxii closed 2 years ago

Luxxii commented 2 years ago

Describe the question or problem Hey all, i wanted to index a FASTA database on the newest MSGFPlus-Release (2022.04.18)

Sadly i cannot get it to run on my system and was wondering if the problem is only on my side.

What i tried:

java -Xmx3500M -jar -cp /<FULLPATH>/MSGFPlus.jar edu.ucsd.msjava.msdbsearch.BuildSA

java -Xmx3500M -jar -cp MSGFPlus.jar edu.ucsd.msjava.msdbsearch.BuildSA

java -Xmx3500M -jar -cp ./<RELATIVE_PATH>/MSGFPlus.jar edu.ucsd.msjava.msdbsearch.BuildSA

However, running: java -Xmx3500M -jar MSGFPlus.jar is working correctly.

Is it possible that this problem lies within the jar? Or do i have to prepare the java-environment in a specific way to get it working?

Useful extras java -version: openjdk version "17.0.3" 2022-04-19 OpenJDK Runtime Environment (build 17.0.3+7) OpenJDK 64-Bit Server VM (build 17.0.3+7, mixed mode) (i also tried with java 11 and java 8)

OS: Linux (Kernel 5.18.5)

MSGFPlus.jar via ls: -rw-r--r-- 1 luxii luxii 17M Jan 7 20:48 MSGFPlus.jar

Luxxii commented 2 years ago

I am closing it due to pure dumbness from my side (sorry!).

-jar and -cp do not work well together.

I got it working with: java -Xmx3500M -cp MSGFPlus.jar edu.ucsd.msjava.msdbsearch.BuildSA

(maybe this will help others, if they stumble upon this..)