T coffee empty out put file

I followed the workflow provided by the author but the output file was 0 line,


Dataset Information

Number: 172
Name: T-Coffee on data 19: newick.dnd
Created: Mon Sep 28 03:16:34 2020 (UTC)
Filesize: 0 bytes
Dbkey: ?
Format: nhx

Job Information

Galaxy Tool ID: toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/11.0.8
Galaxy Tool Version: 11.0.8
Tool Version:
Tool Standard Output: stdout
Tool Standard Error: stderr
Tool Exit Code: 0
History Content API ID: 11ac94870d0bb33a8068581fb7ea1e74
Job API ID: 11ac94870d0bb33a3db1d70c47d76282
History API ID: 7fb32d3aa2f6df0e
UUID: 0c32b1eb-35ff-4b17-b9ff-969c19099a93
Full Path: /data/dnb03/galaxy_db/files/0/c/3/dataset_0c32b1eb-35ff-4b17-b9ff-969c19099a93.dat

Tool Parameters

Input Parameter Value
Filter FASTA input? no
FASTA sequences * 19: hcluster_sg on data 15
Pairwise Structual Method Nothing selected.
Multiple Sequence Alignment Methods t_coffee_msa
Pairwise Sequence Alignment Methods Nothing selected.
Output formats dnd
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even with a simple alignment file, T coffee gives 0 lines.

I think the error is “Invalid dataset ID or you are not allowed to access this dataset

You can see that by clicking on stderr, I personally don’t know what is means but maybe it helps you.


Just found out this is a galaxy specific error. Maybe this helps https://biostar.usegalaxy.org/p/19306/


@gbbio is correct. You may not have permission to use the dataset. If it was shared with you by someone else, ask them to re-share with permissions granted.

How that is set up by default can differ by Galaxy server, but this is how to manage permissions on all running a current release: FAQ: https://galaxyproject.org/learn/privacy-features/

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Thank you very much for your answers, and I have another question, is there a tool or workflow in galaxy to visualize homologs gene cluster between different species.@Jennifer @gbbio
thank you very much again.

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A post was split to a new topic: Visualization functions: view, graph, edit

thank you very much @jennaj ,I did not make my question clear enough, i want something similar to the workflow GeneSeqToFamily, I have gene clusters I am interested to compare and visualize between different species, but when i follow the workflow GeneSeqToFamily, T coffee fails every time, therefore i am wondering if there is another way to do a blast,align the best hit, visualize the surrounding genes close to it and also do family tree from those alignments.
I am still a beginner and I am sorry if i don’t make sense.
thank you very much for your reply.

1 Like

Hi @Ola_Alessa

If one tool is failing because of permissions problems with your input datasets, then other tools will too. There are other options but not exact options and most are in that same tool group. But reviewing again that doesn’t address the root issue. Permissions to view your data linked from this forum have nothing to do with you having permissions problems – and this error doesn’t seem to actually be that. I misread the error/actual issue, apologies. The problem is no output.

We need more details to help you. It could be a bug or a usage issue, or possibly the workflow has problems when run under the current release of Galaxy. Have you tried running the tool using the example data in the publication? If it works, then there is likely a content or format issue with your own data.

The full error message is sometimes nested on the Job Details page (what you posted here) inside the linked stderr or stdout files. Other times the bug report has the information. You don’t have to submit a bug report – it can be just viewed for troubleshooting. Reviewing those places can also help you to solve problems. Sometimes an internet search with the important parts of an error message finds help for a usage solution – even if that Q&A happened outside of Galaxy.

If you need help after that, please post back the full tool name that includes the version, note which server you are working on (actually usegalaxy.eu?), and post the error messages – not links to the error messages – those cannot be read by anyone but you. If you have modified the workflow – it can be posted back as a shared link (Workflows > use the pull-down menu > Share > Create the share link). If you just post back the URL in the browser that you see – to anything – others won’t be able to review it (external permissions problems again). Use Galaxy’s share function to grant others the ability to review.

If you want to keep this private, then it might be a good idea to submit the bug report to the EU administrators. Include a link to this topic in the comments (it can be read by anyone since this topic is already public) – plus any other details.

We should keep the conversation in this thread for now, since the original problem was misinterpreted. We can break it out if needed later, depending on your reply. Thanks!

Ping @nsoranzo (he is one of the authors of that publication/workflow and may have more advice) ref: https://pubmed.ncbi.nlm.nih.gov/29425291/