<Output File Name> did not exist.

Tomas Cumlin 1485

• June 29, 2022 08:23
• Edited

Hello,

I am attempting to create a Nextclade plugin in Geneious 2022.1.1. When running it, an error occurs and I am uncertain what it means. 
Here is what the error message says (I replaced some words with <>): 

___
Operation failed. The error was:  

Output file 

/home/<user>/.geneious2022.1data/transient/<numbers>/x/<batch number>/<Output File Name> did not exist. Maybe the operation failed. <plugin name> reported no error messages
___

Anyone who can help me understand what this type of error means and how I could solve it? 
Thank you!

0

• Official comment

  

  Tom Edwards

  • July 12, 2022 22:37

  Hi Tomas,

  Sorry for the late reply, it looks like you are using the wrapper plugin creator which is expecting the result of your Nextclade CLI command to produce an output file at the location /home/<user>/.geneious2022.1data/transient/<numbers>/x/<batch number>/<Output File Name>

  I would need more information about how you've setup the wrapper and what options you've used to help figure out why Nextclade doesn't seem to be producing any output. The most common reason is that there is a problem with the CLI command which causes no results to be produced.

  Cheers,
  Tom
• 

  Tomas Cumlin 1485

  • July 14, 2022 09:24

  Hi Tom,

  Thank you for your response. This is what my Nextclade CLI code looks like:

  _____________________________________________

  conda activate <path to the environment/environment name>

   

  nextclade run \

     --input-dataset <path to all required input files> \

     --output-all=/home/<user>/.geneious2022.1data/transient/<numbers>/x/ \

     --output-basename=$2 \

     $1

  ____________________________________________________

  Running the code in shell is no problem. It produces the expected output files. When I run this shell-file as a plugin in Geneious, it actually produces the expected output files as well and are located in the path specified in the “--output-all”. So the files appear in folder x, but no batch number is created and that error message appears, and no results appear in Geneious as well. 

  I’ve tried to change the path for the output files in various ways, such as including a batch number or tried a completely new path but the outcome is the same.

  I should add that it’s Nextclade 2.0.0 

  Kind regards,

  Tomas

  0
• 

  Tom Edwards

  • July 15, 2022 02:27

  Hi Tomas,

  Unfortunately it looks like you've run into a limitation of the wrapper plugin in that it doesn't support specifying a folder as the output, instead you will have to specify each file that you want to import into geneious individually using the small plus button to add output files. Here is a screenshot example:

  

  Hope that helps and let us know if you have any more questions.
  Tom

  0
• 

  Tomas Cumlin 1485

  • July 20, 2022 12:18

  Hi Tom,

  Thank you very much for your help! I specified each file that I wanted to import and the plugin seems to be working now.

  Kind regards,

  Tomas

  0

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