Question: Problems with Trinity and Unicycler
3
gravatar for aleksas.lab
4 months ago by
aleksas.lab30
aleksas.lab30 wrote:

I am trying to build a transcriptome from RNA NGS data in FASTQ format using TRINITY. It has been well over two days and it still shows that the analysis data sets are "waiting" to be processed. Is that normal?

Thanks!

Alex

ADD COMMENTlink modified 4 months ago by Jennifer Hillman Jackson25k • written 4 months ago by aleksas.lab30

This is at https://usegalaxy.org, correct?

The job should have started by now. More feedback soon.

ADD REPLYlink written 4 months ago by Jennifer Hillman Jackson25k
1

We have confirmed that the problems with both Trinity and Unicyler jobs right now are server-side. We are working on the correction with our partners at PCS Bridges (who run the cluster these jobs run on).

ADD REPLYlink written 4 months ago by Jennifer Hillman Jackson25k

Any status updates as of 01/18, 8 a.m. PST? Have the problems been resolved? Thanks! --Lee

ADD REPLYlink written 4 months ago by lhp_sf4dem30

The cluster that runs these jobs might be having problems. We are working to fix/test this. Meanwhile, leave your jobs queued, our admin can probably restart these (if that is needed). If you need to rerun instead, we will let you know.

ADD REPLYlink written 4 months ago by Jennifer Hillman Jackson25k
1

Any status updates as of 01/18, 8 a.m. PST? Have the problems been resolved? Thanks! --Lee

ADD REPLYlink written 4 months ago by lhp_sf4dem30
1

Never mind! My process is running! Great news!

ADD REPLYlink written 4 months ago by lhp_sf4dem30

Glad this is working for you now! Please see my comments below for current status server-side and what to do should your jobs complete but have a metadata assignment warning.

ADD REPLYlink written 4 months ago by Jennifer Hillman Jackson25k
0
gravatar for Jennifer Hillman Jackson
4 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Update 1-18-2018 8pm EST

Previously stalled PSC Bridges jobs are starting up and some may be completed already.

Please note that the server correction is not 100% yet. Jobs may end with a metadata warning. This shows up as a yellow box within the result dataset(s) and look like this: https://imgur.com/a/sh3Ac

For our tests, the dataset content was complete/correct (as any green successful job should be) and just the metadata was in an odd state. If this occurs for anyone else, try resetting the dataset's metadata using 1) the link in the yellow warning box or 2) by clicking on the pencil icon and autodetecting metadata on the Edit Attributes forms.

If for some reason that doesn't work (example: problems using the data with downstream tools after metadata is corrected, or autodetect doesn't work for some reason), please let us know. Sending in a bug report from an error dataset would be the simplest way to share the information for troubleshooting. But direct email to our internal support mailing list with a share link to the history (with the input/output datasets left undeleted) is another way to report a problem. This is how to do both: https://galaxyproject.org/issues/#usage-problem-reporting

We will leave this ticket opened until the metadata issues are cleared or we have a tracking ticket for the pending fix to share.

Thanks to everyone for their feedback and patience!

ADD COMMENTlink modified 4 months ago • written 4 months ago by Jennifer Hillman Jackson25k
0
gravatar for Jennifer Hillman Jackson
4 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Final Update 1-19-2018

Both Trinity and Unicycler are working correctly now.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 4 months 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: 73 users visited in the last hour