Fatal error fastQC on ubuntu

Question

[Benn]

I try to run fastqc in ubuntu (16.04) command line, but get an error. I am not sure what the problem is.

Command:

~/Drive/ben/Ubuntu/FastQC.v0.11.7/fastqc -q -o ~/Drive/ben/NGS/QC ~/Drive/ben/NGS/fastq/Sample01*

Error:

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007f0401edd009, pid=18570, tid=18599
#
# JRE version: OpenJDK Runtime Environment (9.0) (build 9-internal+0-2016-04-14-195246.buildd.src)
# Java VM: OpenJDK 64-Bit Server VM (9-internal+0-2016-04-14-195246.buildd.src, mixed mode, tiered, compressed oops, g1 gc, linux-amd64)
# Problematic frame:
# C  [libjava.so+0x1d009]  JNU_GetEnv+0x19
#
# Core dump will be written. Default location: Core dumps may be processed with "/usr/share/apport/apport %p %s %c %d %P" (or dumping to /home/nota001b/Drive/ben/core.18570)
#
# An error report file with more information is saved as:
# /home/nota001b/Drive/ben/NGS/hs_err_pid18570.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.
#

Is there something wrong with my java?

java -version
openjdk version "9-internal"
OpenJDK Runtime Environment (build 9-internal+0-2016-04-14-195246.buildd.src)
OpenJDK 64-Bit Server VM (build 9-internal+0-2016-04-14-195246.buildd.src, mixed mode)

Anyone seen this before?

Answer 1

[Pierre Lindenbaum]

fastqc is compiled with java 1.8, not the 'new' java 9.0, that could be the origin of the error. Switch to java 1.8.

[Benn]

Thank you Pierre, any fast solution you can think of?

[Pierre Lindenbaum]

no. Its looks like this IGV bug: https://github.com/igvteam/igv/issues/326

When I switch the openjdk 8 it worked.

[Benn]

Is it possible to run fastqc in windows 7 cmd line?

[Santosh Anand]

fastqc is written in Java. So it should normally run on windows with the right version of JVM.

[Benn]

Any hands on experience? Theory does not always match reality. In my case simply changing the direction of the slashes seems not to work.

[Santosh Anand]

Check the windows related README from here

https://www.bioinformatics.babraham.ac.uk/projects/fastqc/INSTALL.txt

Theory does not always match reality. In my case simply changing the direction of the slashes seems not to work.

Although I work mostly on Linux/Mac, I do not find any reason, whatsoever, that it will not run on Window. In case of difficulty, you may open a new thread and I'll loook into it (please tag me)

[Benn]

Yeah thanks, I tried but didn't work. I also work mostly on linux, that's why I asked. Installing java 8 on ubuntu was easier (although I encountered some issues there as well), I have no further ambition to continue on windows.

[Santosh Anand]

No problems, and glad to know that you can continue your work.

[Santosh Anand]

You may install multiple versions of java and use update-alternatives to switch between them https://askubuntu.com/questions/315646/update-java-alternatives-vs-update-alternatives-config-java

[Benn]

I installed 1.8, switched to 1.8 on ubuntu and it works, thanks for all input!

[Pierre Lindenbaum]

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.