Question: Align.seq Mothur error message
0
gravatar for genevieve.laperriere
12 weeks ago by
genevieve.laperriere0 wrote:

Hi I got an error message (TERM environment variable not set) with the command align.seq in Mothur. What can I do to solve the problem ? My input data are ok and I tried with several dataset.

ADD COMMENTlink modified 11 weeks ago • written 12 weeks ago by genevieve.laperriere0
0
gravatar for Jennifer Hillman Jackson
12 weeks ago by
United States
Jennifer Hillman Jackson25k wrote:

Hi,

Thanks for sending in the bug report.

The warning about the TERM variable is a side-warning that doesn't describe the problem in detail when there is an input problem. Instead, review the full error message in the bug report. If you send this in just to get a copy and solve the problem yourself using that information, we would appreciate a reply email letting us know.

Yours has this included:

[ERROR]: your sequences are not the same length, aborting.

Your custom template did not meet the specification for the expected template input (in a few ways). To learn more about the formatting and template sources, please see: https://www.mothur.org/wiki/Alignment_database

Note: Combining line-command data with Galaxy wrapped tools (even if seemingly produced from the same tool) can lead to problems due to tool version conflicts, especially with complicate packages like this one. So, please try to avoid that if you can, as the best (and sometimes, only) solution is to rerun the line-command tools within Galaxy, using the most current/compatible tool versions for all steps. Or, run all line-command.

Mothur tool usage is described in the Galaxy tutorials and includes a versioned reference template for 16S analysis: https://galaxyproject.org/learn/

  • Tutorials by Galaxy Training Network >> Metagenomics

If you think an actual tool bug is presenting with the rerun or any other steps, when using Galaxy tools for all steps, note that in the new bug report sent in and we can take a closer look to rule that out or to request a tool wrapper correction.

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 12 weeks ago • written 12 weeks ago by Jennifer Hillman Jackson25k
0
gravatar for genevieve.laperriere
11 weeks ago by
genevieve.laperriere0 wrote:

Thank its a lot of information for me. I have a small question. If I want to use a other reference dataset for the Align.seqs can I ? Because for my samples (ITS2 fungal sequences) I would like to use the UNITE reference data base more appropriate for fungus. In the galaxy training they propose the silva.v4.fasta reference file. Is this can explain why I have the error report, because the software doesn'T reconize the UNITE.fasta ?

Thank

ADD COMMENTlink written 11 weeks ago by genevieve.laperriere0

I just asked one of the Mothur Galaxy wrapper developers about this and some changes to the Galaxy 16S tutorial and the Mothur tool forms to better explain usage and improve warnings about improper inputs are future goals.

Meanwhile, for general usage questions about Mothur, she suggested Q&A here as an alternative resource for when there isn't a Galaxy-specific problem: https://www.mothur.org/forum/

I also found some help around the web from others doing ITS analysis. This is just one post: https://www.researchgate.net/post/Mothur-formatted_UNITE_database, but review the others linked, the SOP included with the Mothur suite, or also do a search to read how others are using the tools for ITS/fungal analysis.

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by Jennifer Hillman Jackson25k

Yes I saw the same post. I'll try it

Thank for your help :)

ADD REPLYlink written 11 weeks ago by genevieve.laperriere0
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