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Fatal error fastQC on ubuntu

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
• 4,027 views • link
written by Benn Benn

1 answer

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.

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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

• 1 views • link
written by Benn Benn

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

• 1 views • link
written by Benn Benn

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

• 1 views • link
written by Santosh Anand Santosh Anand

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

• 1 views • link
written by Benn Benn

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)

• 1 views • link
written by Santosh Anand Santosh Anand

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.

• 1 views • link
written by Benn Benn

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

• 1 views • link
written by Santosh Anand Santosh Anand

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

• 1 views • link
written by Benn Benn

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

Upvote|Bookmark|Accept

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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