Default Protein Reports exits with a fatal error

[iquasere]

Running java -cp PeptideShaker-2.2.12/PeptideShaker-2.2.12.jar -Xmx51200M eu.isas.peptideshaker.cmd.ReportCLI -in path/to/ps_output.psdb -out_reports path/to/out_dir -reports 9 returns

Thu Sep 29 14:44:15 UTC 2022 Exporting. Please Wait...
10% 20% 30% 40% 50% 60% 70% 80% 90%#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007fd3291ad6a3, pid=29208, tid=29209
#
# JRE version: OpenJDK Runtime Environment (17.0.3) (build 17.0.3-internal+0-adhoc..src)
# Java VM: OpenJDK 64-Bit Server VM (17.0.3-internal+0-adhoc..src, mixed mode, sharing, tiered, compressed class ptrs, g1 gc, linux-amd64)
# Problematic frame:
# C  [sqlite-3.36.0.3-7c636d52-4f25-423e-864a-8c4c42bc83b9-libsqlitejdbc.so+0x116a3]
#
# Core dump will be written. Default location: Core dumps may be processed with "/usr/share/apport/apport -p%p -s%s -c%c -d%d -P%P -u%u -g%g -- %E" (or dumping to //core.29208)
#
# An error report file with more information is saved as:
# //hs_err_pid29208.log
#
# If you would like to submit a bug report, please visit:
#   https://bugreport.java.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#
Aborted (core dumped)

The report is written, apparently just fine. This also happens with the 10 report. All other reports seem to work fine, so it seems to be related to "Default_Protein_Report"s.

[hbarsnes]

Can you try updating to a more recent Java version and see if that solves the problem?

[hbarsnes]

Issue assumed resolved. If this is not the case, please let us know and we'll reopen the issue.

[iquasere]

Sorry, Harald, for not following up on this. I ended up just ignoring the error, as the most recent versions of peptide-shaker in Bioconda still threw this exception, while the report was generated just fine. This happened with reports 9 and 10.

[hbarsnes]

Ok, thanks for the update. I will just keep the issue closed then and maybe reopen it in the future if the problem is reported by more users.

[esraaelmligy]

Hello, i am currently running into the same error and have no idea why, i am running the processing on four different searchgui zips, all of which are run with the same ms files, same parameters and options, the only difference is the fasta databases.

Three of the four ran just fine, but the last one seems to give the same error over and over again.

A fatal error has been detected by the Java Runtime Environment: SIGSEGV (0xb) at pc=0x00007f3b6c523e17, pid=6022, tid=6023 JRE version: OpenJDK Runtime Environment (17.0.10+7) (build 17.0.10+7-Ubuntu-120.04.1) Java VM: OpenJDK 64-Bit Server VM (17.0.10+7-Ubuntu-120.04.1, mixed mode, sharing, tiered, compressed oops, compressed class ptrs, g1 gc, linux-amd64) Problematic frame: # C [sqlite-3.40.0.0-af5e724e-9e83-49af-ab11-a4c075641d9b-libsqlitejdbc.so+0x11e17] Core dump will be written. Default location: Core dumps may be processed with "/usr/share/apport/apport -p%p -s%s -c%c -d%d -P%P -u%u -g%g -- %E" (or dumping to /home/esraa/core.6022) If you would like to submit a bug report, please visit: # Unknown # The crash happened outside the Java Virtual Machine in native code. See problematic frame for where to report the bug.

[hbarsnes]

@esraaelmligy Can you try updating to a newer Java version and see if that solves the problem?

[esraaelmligy]

I updated to the latest java version but i still face the same error, and now when i try to rerun the old jobs again they also result in the same error.

Thu Apr 04 10:34:27 EET 2024 Exporting reports. Thu Apr 04 10:34:27 EET 2024 Exporting Certificate of Analysis. Thu Apr 04 10:34:27 EET 2024 Exporting Default PSM Report. Thu Apr 04 10:34:28 EET 2024 Exporting. Please Wait... 10% 20% 30% 40% 50% 60% 70% 80% 90%

A fatal error has been detected by the Java Runtime Environment: SIGSEGV (0xb) at pc=0x00007f3982d1fe17, pid=49677, tid=49678

JRE version: OpenJDK Runtime Environment (21.0.2+13) (build 21.0.2+13-Ubuntu-120.04.1) Java VM: OpenJDK 64-Bit Server VM (21.0.2+13-Ubuntu-120.04.1, mixed mode, sharing, tiered, compressed oops, compressed class ptrs, g1 gc, linux-amd64) Problematic frame: C [sqlite-3.40.0.0-60f1b6cf-47a1-4a1d-a128-f985c150c02d-libsqlitejdbc.so+0x11e17]

Core dump will be written. Default location: Core dumps may be processed with "/usr/share/apport/apport -p%p -s%s -c%c -d%d -P%P -u%u -g%g -- %E" (or dumping to /home/esraa/core.49677) An error report file with more information is saved as: /home/esraa/hs_err_pid49677.log [2827.665s][warning][os] Loading hsdis library failed

If you would like to submit a bug report, please visit: Unknown The crash happened outside the Java Virtual Machine in native code. See problematic frame for where to report the bug.

Aborted (core dumped)

[esraaelmligy]

hs_err_pid49677.log

This attached file is the log file generated by the error, it is to note that this is an external file and not the peptideshaker's log file