Request for Assistance: LEfSe Module File Upload Issue

Downstream analysis and statistics LEfSe
1

Dear professors,

I hope this email finds you well. I am currently using the LEfSe module on the Galaxy website to generate LEfSe plots. I am encountering an issue when trying to upload my own file, as the system displays the following warning: “Warning: Request Entity Too Large (413).”

Upon reviewing this, it appears that the file size of my data falls within the range of 1.3-2.9 megabytes. I suspect that the upload limitation may be causing this issue.

I am writing to seek your assistance in resolving this matter. Could you please provide guidance on whether it is possible to modify the file upload settings to accommodate larger files? Alternatively, if there are any specific guidelines or recommendations regarding file size that I may have overlooked, I would appreciate your insights.

I understand the importance of ensuring system efficiency, but my analysis requires the use of files within the mentioned size range. Your support in addressing this matter will be immensely helpful for my research.

Thank you very much for your time and consideration. I look forward to your guidance on resolving this file upload issue.

Best regards.

2

Hi @DocZ,

We do have a file size limit due to this being a shared resource for the community. For larger files I would suggest one of the two alternatives.

  1. Use of MaAsLin 2 in an R environment (through R/RStudio/linux etc.). MaAsLin is a newer tool we developed to do complementary tasks to LEfSe. With larger data especially, MaAsLin is robust to the compositionality and sparseness of these data types. The tutorial for MaAsLin can be found here.
  2. conda install LEfSe and run it on the command line. Further information for that method can be found here.

I hope this helps!
Best,
Kelsey

3

Thank you for your response and for providing alternative solutions to address the file size limitation in the Galaxy LEfSe module. I appreciate your efforts in maintaining a shared resource for the community！