Question: Upload/Other tools at Galaxy Main https://usegalaxy.org producing errors -- Resolved, review for details
2
gravatar for trenton_woodham
12 weeks ago by
trenton_woodham30 wrote:

What is Internal Server Error (500)?

I am using Galaxy Main usegalaxy.org). About 1 to 1.5 hours ago, I became unable to upload any files to galaxy from my disk drive. I keep getting Internal Server Error (500) after 2% of my files upload. This is happening even for files which I had uploaded successfully earlier in the day. I am trying to upload with an empty history and only 800 MB of my 250 GB memory in use. I am using "Auto-Detect" for the file type and am not specifying a genome. The files I have been trying to upload are .fastq.gz files. Again, no issue uploading earlier today, only encountered trouble in the past couple hours. Am I doing something wrong? Have I exceeded some limit? What does Internal Server Error (500) mean, and is there anything on my end I can do to fix it?

upload usegalaxy.org galaxy • 314 views
ADD COMMENTlink modified 12 weeks ago by Jennifer Hillman Jackson25k • written 12 weeks ago by trenton_woodham30
1

I am experiencing a similar problem that started in the same time frame. I am not getting an Internal Server Error, but I also cannot upload any files. I am working with small (~4kb) interval files, but their upload fails almost immediately and only states "tool error".

ADD REPLYlink written 12 weeks ago by mlwright30

Hello - I can confirm that upload is slow to execute at https://usegalaxy.org but haven't had an error produced yet (nor a successful load) - the jobs are queued.

If one of you has time, could you please send in a bug report? Please include a link to this Biostars post so we can link the two.

Thanks & sorry for the troubles! Jen, Galaxy team

ADD REPLYlink written 12 weeks ago by Jennifer Hillman Jackson25k
1

I submitted a bug report earlier, but if it's possible to update it somehow, I'd be happy to update with a link to this post. As it stands, I am now able to get my files onto Galaxy, but downstream applications (in this case, Extract Genomic DNA) fail with "tool error" and "failure preparing job script" messages.

ADD REPLYlink written 12 weeks ago by mlwright30
1

I'm unable to to file a bug report normally because I cannot even get my dataset into my galaxy library, and clicking on the failed upload in the Upload interface just deletes the entry. I can send an email to galaxy-bugs@lists.galaxyproject.org if that is the right place to file reports.

ADD REPLYlink written 12 weeks ago by trenton_woodham30

We have a handle on what is going wrong so more bug reports are not needed right now. See the primary updated reply for current status. We'll update again once resolved. Thanks! Jen

ADD REPLYlink written 12 weeks ago by Jennifer Hillman Jackson25k
0
gravatar for Jennifer Hillman Jackson
12 weeks ago by
United States
Jennifer Hillman Jackson25k wrote:

UPDATE 7-27-2018

The server issues are resolved.

The exception is Trinity/Unicycler. Details in this post: https://biostar.usegalaxy.org/p/28871/

Thanks! Jen, Galaxy team

ADD COMMENTlink written 12 weeks ago by Jennifer Hillman Jackson25k
0
gravatar for Jennifer Hillman Jackson
12 weeks ago by
United States
Jennifer Hillman Jackson25k wrote:

Update:

Some jobs (not just Upload) are producing failure preparing job script or Disk quota exceeded types of errors. Others will stall during Upload.

My guess is that one of the cluster nodes is problematic. I've reported this to our administrators. More feedback soon.

Workaround until fixed: Try rerunning the job, not all will fail.

Thanks to all for sending in the bug reports about this. Jen

ADD COMMENTlink modified 12 weeks ago • written 12 weeks ago by Jennifer Hillman Jackson25k

Update:

  1. Jobs that fail with the quota problems should work now, please rerun.
  2. Upload may still be problematic in some cases. We are working on it.
  3. Issues with Trinity/Unicycler are also still being sorted out. Details in this post: https://biostar.usegalaxy.org/p/28871/
ADD REPLYlink written 12 weeks ago by Jennifer Hillman Jackson25k
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: 90 users visited in the last hour