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Question: FastQC on Main Galaxy broken
0
gravatar for kirti
2.6 years ago by
kirti • 0
kirti • 0 wrote:

When I try and do FastQC on fastqsanger files at usegalaxy.org, I get:

Fatal error: Exit code 1 () Can't exec "java": No such file or directory at /galaxy/main/deps/FastQC/0.11.4/iuc/package_fastqc_0_11_4/a8f485b2efd9/fastqc line 277. Traceback (most recent call last): File "/galaxy/main/shed_tools/toolshed.g2.bx.psu.edu/

Is the main server down?
galaxy • 993 views
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modified 17 months ago by cpreviti • 0 • written 2.6 years ago by kirti • 0

Main server is not down but the fastqc tool is experiencing configuration issues. We are looking into it, thanks for reporting it.

ADD REPLY • link written 2.6 years ago by Martin Čech ♦♦ 4.9k
0
gravatar for Jennifer Hillman Jackson
2.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

FastQC is now functional again at http://usegalaxy.org. Thanks for reporting the problem.

Jen, Galaxy team
ADD COMMENT • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for cpreviti
17 months ago by
cpreviti • 0
cpreviti • 0 wrote:

Dear Galaxy Team,

We are having very similar issues with fastqc on our local Galaxy instance... Could you gives us some advice on how to fix this?

Cheers, Christopher
ADD COMMENT • link written 17 months ago by cpreviti • 0
0
gravatar for cpreviti
17 months ago by
cpreviti • 0
cpreviti • 0 wrote:

Never mind, it was the path to the java executable. It's hard-coded in fastqc and had to be adjusted to our cluster nodes.
ADD COMMENT • link written 17 months ago by cpreviti • 0
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