Question: FastQC on Main Galaxy broken
0
gravatar for kirti
21 months ago by
kirti0
kirti0 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 • 614 views
ADD COMMENTlink modified 6 months ago by cpreviti0 • written 21 months ago by kirti0

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

ADD REPLYlink written 21 months ago by Martin Čech ♦♦ 4.3k
0
gravatar for Jennifer Hillman Jackson
21 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

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

Jen, Galaxy team

ADD COMMENTlink written 21 months ago by Jennifer Hillman Jackson23k
0
gravatar for cpreviti
6 months ago by
cpreviti0
cpreviti0 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 COMMENTlink written 6 months ago by cpreviti0
0
gravatar for cpreviti
6 months ago by
cpreviti0
cpreviti0 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 COMMENTlink written 6 months ago by cpreviti0
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 16.09
Traffic: 109 users visited in the last hour