Problem with LEFSe in Galaxy

Downstream analysis and statistics LEfSe
1

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

3

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

4

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

5

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.

6

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

7

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

8

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

9

Hi, Could anyone can advise the reason why I got this error when I run Lefse analysis? My file size is about 6 M.b. Thank you
“Job ran longer than the maximum allowed execution time (runtime: 0:15:15, limit: 00:15:00), please try different inputs or parameters”

10

It may be that the size of the file makes it such that executing LEfSe exceeds the allowed time. I’d recommend trying to use the command line version, which has no such restrictions (lefse · biobakery/biobakery Wiki · GitHub)
Best,
Meg

[Edit]: It may also be worth trying to run it again on Galaxy, as your question came around the time we were having server trouble, and if so it may have been an issue on our end that has since resolved

11

Dear Meg,

Thank you so much for your feedback. I tried several times again but I still got the same error.

Is it true that I have to install C****onda to use the command line version?

Best regards,

Dat

---------- 원본 메일 ----------
보낸사람: “Meg Short via The bioBakery help forum” biobakery@discoursemail.com
받는사람: datle90@ncc.re.kr
날짜: 2021-06-05 (토) 04:52:56
제목: [The bioBakery help forum] [Downstream analysis and statistics/LEfSe] Problem with LEFSe in Galaxy

| mishort
June 4 |

  • | - |

It may be that the size of the file makes it such that executing LEfSe exceeds the allowed time. I’d recommend trying to use the command line version, which has no such restrictions (lefse · biobakery/biobakery Wiki · GitHub)
Best,
Meg

[Edit]: It may also be worth trying to run it again on Galaxy, as your question came around the time we were having server trouble, and if so it may have been an issue on our end that has since resolved

12

From the installation instructions:
LEfSe can be installed with Conda or run from a Docker image. Please note, if you are using bioBakery (Vagrant VM or cloud) you do not need to install LEfSe because the tool and its dependencies are already installed.

Install with Conda: $ conda install -c biobakery lefse

Install with Docker: $ docker run -it biobakery/lefse bash

So, you need either Conda or Docker installed on your computer.
Best,
Meg