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?