"Count.seqs" not running

Question: "Count.seqs" not running

13 months ago by

Ali • 20

United States

Ali • 20 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

mothur software error usegalaxy.org • 495 views

ADD COMMENT • link •

modified 6 months ago by genevieve.laperriere • 0 • written 13 months ago by Ali • 20

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 REPLY • link written 13 months ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 13 months ago by Ali • 20

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 REPLY • link written 13 months ago by Jennifer Hillman Jackson ♦ 25k

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

ADD REPLY • link written 13 months ago by Ali • 20

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 REPLY • link written 8 months ago by jennifer.polinski • 0

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 REPLY • link written 8 months ago by Jennifer Hillman Jackson ♦ 25k

13 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link modified 13 months ago • written 13 months ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 13 months ago by Jennifer Hillman Jackson ♦ 25k

6 months ago by

genevieve.laperriere • 0

genevieve.laperriere • 0 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 COMMENT • link written 6 months ago by genevieve.laperriere • 0

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

ADD REPLY • link written 6 months ago by Jennifer Hillman Jackson ♦ 25k

Please log in to add an answer.

Similar posts • Search »