Hi
I’m trying to run the Blast2GO tool in https://proteomics.usegalaxy.eu but keeps on giving me this error:
An error occurred with this dataset:
format tabular database ?
Blast2GO JAR file not found: /opt/b2g4pipe_v2.5/blast2go.jar
Please advise.
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Welcome, @Lizex
This looks like a technical problem, and might be related to the server status.
Blast2GO JAR file not found: /opt/b2g4pipe_v2.5/blast2go.jar
Please follow this topic or the EU chat for updates: Jobs not running usegalaxy.eu
Once that is cleared up, try a rerun first. If that also fails, to help you more the moderators will need input/parameter setting to assist with troubleshooting. See Troubleshooting errors
Hi @Lizex
Please try the tool again now.
Hi Jenna
The error still persists:
An error occurred with this dataset:
format tabular database ?
Blast2GO JAR file not found: /opt/b2g4pipe_v2.5/blast2go.jar
Hi @Lizex The EU moderators will be back Monday their time. This error could be technical or some problem with the data/parameters.
Please post back these details: screenshots or a shared history link. You can also send in a bug report directly from the red error dataset at the same time – please include a link to this topic in the free text comments so they can link the two.
Thanks Jenna
I tried again running the Blast2GO tool this morning but got the same error.
Lizex
Hi
I want to use the Blast2GO tool. I did a Blast P search for my sequences and downloaded the .xml file that is needed. I uploaded the file into Galaxy and hit the run button. I still get the same error since I reported the issue.
An error occurred with this dataset:
format tabular database ?
Blast2GO JAR file not found: /opt/b2g4pipe_v2.5/blast2go.jar
I’ve been reporting this problem since last week and still no solution?
We can’t help more without more details. The FAQ I posted explains how to do all of these.
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Sharing your history is one option. This is the fastest option for your case.
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Posting back the full contents of the Job information page is another, specifically the Tool Parameters and Job Information sections with expanded stderr/stdout, plus screenshots of the expanded input datasets (to reveal the datatype, database, and “peek” view of a few lines).
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Submitting a bug report is another. Not all get a direct reply: instead server admins review these for potential server-side/tool bug issues (then apply appropriate fixes) then if there is time get back about potential usage help (content, format, metadata, parameters).
Why is this needed? The job details matter to isolate what exactly is going wrong. Errors like the one you have could be due to input/parameter problems (likely would result even if running the tool outside of Galaxy) OR an actual technical bug (tool wrapper, server, dependencies). Most issues are the first but some can be the latter. You can try to troubleshoot input/parameters issues yourself then ask for advice. Server/tool issues need to be fixed by the server admins or tool developers.
Hi Jenna
Thanks for your reply. Does the Blast2GO tool work on your end if you would run it on any random set of sequences. I don’t do any thing different then uploading the .xml from NCBI Blastp and run the tool as default.
I already reported (bug report) the issue.
Sorry if I can’t give more information since I cannot post a link in this post.
Regards
Update:
Ping @wm75 @gallardoalba – the dependency is actually missing. Not sure if licensing is a factor, or if that recently became a factor. Last wrapper update was Oct 2022, and the development repo for the Galaxy wrapper is not linked from the ToolShed so I can’t dig into this more.
Thanks!
Hi @Lizex
This tool is a little bit special: no tool test data, older indexes (and only one, from 2013), and the wrapper was contributed by the developer community. It isn’t even hosted at all UseGalaxy.* servers … just this EU server.
The EU team is running an administrative training event this week, and those are the same people who scan bug reports and address that server’s technical issues.
I’ll start up a direct message that you should be able to post a share link into. What I can help with is adjusting any content/format/datatype issues with the input and confirming a missing index is the root problem. If for some reason the local index is actually not available, or doesn’t support your specific data, that will need to wait for the EU admins.
Hi Jenna
Just a follow up on this issue. Could the EU team resolve the issue on the Blast2GO problem?
Hi @Lizex
I don’t have any updates.
Another way to ask the EU admins questions is through their chat (found at the bottom of their homepage). You can include a link to this question for extra context but also send in a bug report, then tell them when it was sent in and the tool name + error message again to make it easy to get oriented in a chat format.
Hi Jenna
Thanks for the advice. Will do that.
Hi Jenna
The EU admin/team never responded to my chat. What more can I do?
Consider using alternative methods?
- Review tool choices in the Annotation section of the tool panel.
- Or, do some direct data manipulations with tabular formatted data for the query and target. This is how everyone originally did Bioinformatics
When you come up with a custom process you like, consider creating a reusable workflow. You can “favorite” workflows and they will show up in the tool panel just like any other tool. Under the hood this is what all tools really are: groupings of manipulations.
References
- Data Manipulation Olympics
- Search Tutorials (query=workflow)
Hi Jenna
Thank you for responding to my email. I’ll look at your suggestions.
Kind regards
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