Question: Fatal error fastQC on ubuntu
0
gravatar for b.nota
7 months ago by
b.nota6.1k
Netherlands
b.nota6.1k wrote:

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?

fastqc java • 362 views
ADD COMMENTlink written 7 months ago by b.nota6.1k
2
gravatar for Pierre Lindenbaum
7 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum116k wrote:

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.

ADD COMMENTlink modified 7 months ago • written 7 months ago by Pierre Lindenbaum116k

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

ADD REPLYlink written 7 months ago by b.nota6.1k
1

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

When I switch the openjdk 8 it worked.

ADD REPLYlink written 7 months ago by Pierre Lindenbaum116k

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

ADD REPLYlink written 7 months ago by b.nota6.1k

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

ADD REPLYlink written 7 months ago by Santosh Anand4.6k

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

ADD REPLYlink written 7 months ago by b.nota6.1k

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)

ADD REPLYlink written 7 months ago by Santosh Anand4.6k

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.

ADD REPLYlink written 7 months ago by b.nota6.1k

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

ADD REPLYlink written 7 months ago by Santosh Anand4.6k
1

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

ADD REPLYlink written 7 months ago by Santosh Anand4.6k

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

ADD REPLYlink modified 7 months ago • written 7 months ago by b.nota6.1k

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

Upvote|Bookmark|Accept

ADD REPLYlink written 7 months ago by Pierre Lindenbaum116k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1774 users visited in the last hour