The bioBakery help forum

Problem with LEFSe in Galaxy

Dear LEFSe team,

First of all, congrats for creating such an amazing tool!!!

I am a newbie with LEFSe analyses, I just started it on Monday, 05/18. I am using the galaxy interface and since yesterday evening when I try to format the data for LEFSe (item A), I get the following error: Uncaught exception in exposed API method

Can anybody help me with it? Is it a problem with my data or with Galaxy?

Thanks in advance.

Kind regards,

Cristiane

Hi Cristiane,
How big is the file you are trying to process?
Can you try to process the sample file we provide and let me know what happens?
Can you compare the structure of the sample file that we provide to the structure of the file you are trying to process ?
Let me know…
Best regards,
George Weingart PhD
Huttenhower Lab

Hello George,

To my mind it is quite big (7.8 Mb). I tried to attach it here, but got a message that new users can not upload…, still I would like you to have a look on it. I tried to format by hand the OTU table with taxonomy, because when comparing my file and the sample one, I noticed that the taxonomy does not repeat itself along the lines, but then got tired and used the make.lefse script on galaxy, where the same taxonomy repeats itself along the 40041 lines.
I followed the tutorial from https://bitbucket.org/biobakery/biobakery/wiki/lefse with the sample file and it worked perfectly. Then, with the file obtained with make.lefse (7.8Mb) I managed to run on galaxy. However, I am not sure that it is correct. For instance, I used the Silva release 138 in my analysis, so I would like to know how LEFSe deals with names like “028H05-P-BN-P5”, abbreviations such as “_fa” (family), “_ge (genus)” and “_unclassified”, should I removed them?

Huge thanks!
Best regards,
Cristiane

Hi Cristiane,

I don’t know, so I need to ask members of the Lab.

But, if I were you, I would remove in the mean time and compare the results- that way I think you”d get a faster answer.

Hello George,

I followed your suggestion and performed several tests with and without abbreviations, the results are very similar :wink:
Huge thanks!
Best wishes,
Cris

Hi Cris,

Thank you for reaching out to bioBakery support forum. I have removed the “new user file upload validation.” Can you please try uploading your file now ?

Thanks,
Sagun

Hello Sagun,

Thanks a lot for your reply and for removing the “new user file upload validation”. I generated the file from galaxy and then made several changes to use in LEFSe. Unfortunately, the file is too big to upload, but I can share the link to the file in my dropbox:
https://www.dropbox.com/s/52p103zkmsf8zl1/Galaxy7-[Make.lefse].txt?dl=0 -> original from Galaxy
https://www.dropbox.com/s/dvw0hv8tn4uzqz0/input_lefse2.txt?dl=0 -> removed _cl, _or, _fa, _ge, _unclassified

Please, let me know if you could access the tables.
Huge thanks in advance,
Best wishes,
Cris