Error reading mzid files

[enriquead1]

I get this error when I read a mzid file:
INFO: error:java.lang.reflect.InaccessibleObjectException: Unable to make field private final java.util.Map sun.reflect.annotation.AnnotationInvocationHandler.memberValues accessible: module java.base does not "opens sun.reflect.annotation" to unnamed module @1555094b

I am attaching the specific mzid file that I want to analyse. It comes from a data repository where there is an mzid file, but not a csv file. I was planning to use xiFDR in order to filter the CSMs and get a csv.

CM15_Xi1.7.6.7.zip

[grandrea]

Hello, thanks for the report. I cannot reproduce the bug. I manage to successfully open the file in xiFDR 2.3.4 . I just load it via input->mzIdentML instead of CSV. Could you share a few more details of what you are doing?

[grandrea]

(you can also upload mzID to xiview.org and export crosslinks to get a csv, it is probably easier)

[enriquead1]

Hello, thanks for your quick answer.

That is a good idea indeed, but at some point I will have to extend this to many files. I am trying to extract the most interesting fields with pyteomics right now, that is probably the best.

Regarding this error, I can provide a short screen recording of what happens in my system. My xiFDR version is 2.3.4 .

Screencast.from.04-02-25.16.47.04.webm

[grandrea]

thanks, i suspect this may be due to the encoding. Try running by clicking on startunix.sh as recommended and not on the .jar file

[enriquead1]

There is an error too. The same happens by running ./startUnix.sh.

Screencast.from.05-02-25.15.53.42.webm

[grandrea]

ok, try the fix suggested here https://github.com/Rappsilber-Laboratory/xiFDR?tab=readme-ov-file#mzidentml-output

by editing your startUnix.sh adding the following options

java -Dfile.encoding=UTF-8 -Xmx3g --add-opens java.base/java.lang=ALL-UNNAMED -jar %mypath%xiFDR-2.1.5.2.jar

what java version do you have