This problem was solved ? I am having the same problem , Please guide me.
Welcome, @Farah_Zahoor_RAJPUT
The post from 5 years ago was about a tool bug long since resolved. Let’s start over in something fresh. 
The best place to get help with tools in the Mothur package are the tutorials linked on the bottom of the tool forms. The idea would be to prepare the data inputs, to import the workflow then run it, and then to use the example results as a sort of “answer key” reference history to compare the usage against. I did this last a few weeks ago, so I can also share with you the copy I’ve been using for testing.
- https://usegalaxy.org/u/jen-galaxyproject/h/training-16s-rrna-sequencing-with-mothur-main-tutorial-5
Please give that a review. You could even import the tutorial workflow again, use my history for the data, then send the output into a new history to create a brand new output. This can be an interesting way to learn how powerful workflows can be! That workflow can also be used as a template – maybe change parts of it for your own purposes? These tools have data outputs named in very similar ways and mixing things up is pretty easy to do (and frustrating!). Using a workflow can help to simplify the usage in a predicable way when tuning parameters, adding more steps, reruns on new/more samples, etcetera.
And, if you are still stuck after reviewing, please also share some details about your error, and we can try to help with more specificity. How to generate a history share link (same as I did above) is covered in the FAQ linked in the banner at this forum, also see here directly. → How to get faster help with your question 
Greetings,
I am still having the same problem , I am attaching ss
Thank you
Ok – this is with your own data, correct?
The tool is failing when creating a data index – internal to the Mothur tool itself, not the Galaxy server. This can be due to a content problem within the file, or with the logic of the query you are running.
Does that input file have 31053 samples inside of it? If the file doesn’t have that many, that could lead to a failure.
You could also test out a smaller sample size – maybe a few hundred. That would test if the input file is at least formatted Ok. Then try increasing it, maybe you can learn the limits for your specific data and this tool.
This tool also has an optional log file output. Try toggling that on, too.
