Question: "Count.seqs" not running
0
gravatar for Ali
10 months ago by
Ali20
United States
Ali20 wrote:

Hello, I am getting this error "TERM environment variable not set" when running toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.36.1.0 I appreciate your help, Best, Ali

ADD COMMENTlink modified 12 weeks ago by genevieve.laperriere0 • written 10 months ago by Ali20

Could you check quickly that all of the input datasets have content? The only other time I have seen this is when an empty input dataset was given to the tool.

ADD REPLYlink written 10 months ago by Jennifer Hillman Jackson25k

Hi Jennifer, All input data are fine, I tried count.seqs with the 16 Microbial Analysis with Mothur demo and it seemed to give this error as well! Thanks for your help, Ali

ADD REPLYlink written 10 months ago by Ali20

Ok, thanks for feedback. You are working at https://usegalaxy.org, correct? I bug report could be sent in. I'll also review the tutorial and our tests, to see if can determine the problem.

ADD REPLYlink written 10 months ago by Jennifer Hillman Jackson25k
1

Yes I am working at https://usegalaxy.org

ADD REPLYlink written 10 months ago by Ali20

Hi, I am getting the same error message ("TERM environment variable not set. TERM environment variable not set") when I try running Mothur align.seqs on usegalaxy.org. I've double checked that all parameters are set, tried different datasets, tried different alignment methods. Same error every time. Did anyone ever determine how to fix this error? Thanks for your help.

ADD REPLYlink written 4 months ago by jennifer.polinski0

Hello, I started reviewing your bug report about this yesterday and will get back to you through email with the results. We have two reports similar to yours.

Thanks! Jen, Galaxy team

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

Hello,

I cannot reproduce the error with proper inputs (including the tutorial data) and have been unable to locate your account at https://usegalaxy.org. This does not necessarily mean that a tool issue isn't a factor - and if there is one, we'll want to fix it. If the issue turns out to be usage, we can provide direct help. This could include updating the tool help and/or tutorial to aid others in avoiding the issue.

So, would you please send in a bug report from the error dataset? Be sure to leave the inputs and outputs undeleted. In the comments, include a link to this post and any other info you would like to add. From there, we'll troubleshoot the problem through email using the bug report as a reference. All bug report data is private to our small internal team and is never made public.

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 10 months ago • written 10 months ago by Jennifer Hillman Jackson25k

Update: input issue identified and usage is clarified in this tutorial if anyone else runs into the same error: https://galaxyproject.github.io/training-material/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.html

ADD REPLYlink written 9 months ago by Jennifer Hillman Jackson25k
0
gravatar for genevieve.laperriere
12 weeks ago by
genevieve.laperriere0 wrote:

Hi I got the same error message (TERM environment variable not set) with the command align.seq in Mothur. What you did to solve the problem ? Same thing for me my input data are ok and I tried with several dataset.

ADD COMMENTlink written 12 weeks ago by genevieve.laperriere0

https://biostar.usegalaxy.org/p/28166/

ADD REPLYlink written 12 weeks ago by Jennifer Hillman Jackson25k
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