IGV Error: Failed to write main dump
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5.4 years ago
manubiomed20 ▴ 10

I can't open IGV on ubuntu 18.04.2 LTS terminal. The following error appears:

WARN [2019-07-26T08:22:22,691]  [Globals.java:138] [AWT-EventQueue-0]  Development mode is enabled
jul 26, 2019 8:22:22 AM java.util.prefs.FileSystemPreferences$1 run
INFORMAÇÕES: Created user preferences directory.
INFO [2019-07-26T08:22:22,741]  [DirectoryManager.java:179] [AWT-EventQueue-0]  IGV Directory: /home/Giulia/igv
INFO [2019-07-26T08:22:22,795]  [Main.java:155] [AWT-EventQueue-0]  Startup  IGV Version 2.4.17 01/26/2019 12:40 AM
INFO [2019-07-26T08:22:22,796]  [Main.java:156] [AWT-EventQueue-0]  Java 1.8.0_152-release
INFO [2019-07-26T08:22:22,796]  [DirectoryManager.java:84] [AWT-EventQueue-0]  Fetching user directory... 
INFO [2019-07-26T08:22:22,891]  [Main.java:157] [AWT-EventQueue-0]  Default User Directory: /home/Giulia
INFO [2019-07-26T08:22:22,891]  [Main.java:158] [AWT-EventQueue-0]  OS: Linux
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x0000000000000000, pid=12090, tid=0x00007f5ceffff700
#
# JRE version: OpenJDK Runtime Environment (8.0_152-b12) (build 1.8.0_152-release-1056-b12)
# Java VM: OpenJDK 64-Bit Server VM (25.152-b12 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# C  0x0000000000000000
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /home/Giulia/hs_err_pid12090.log
#
# If you would like to submit a bug report, please visit:
#   http://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
IGV • 1.8k views
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Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again

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Which version of IGV did you get? If you got the (all platforms version) then it needs Java 11 to run. /home/Giulia/hs_err_pid12090.log may also contain useful information.

IGV on ubuntu 18.04.2 LTS terminal

You will also need to have X11 configured to get GUI from IGV, if you are logging into a remote server.

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I put the command ulimit -c unlimited, but couldn't open igv. How can I solve this problem?

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What does /home/Giulia/hs_err_pid12090.log contain?

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what is your version of IGV. the last version of IGV runs with an embedded java 11. here you're using java 1.8

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version  IGV 2.4 and version java-jdk-8.0.92-1.
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