LEfSE after Qiime2 new problem

Dear All,

I am newby to Qiime2, but with firum supprt I have solved a series of probem.
Thank in advance.

But I have a trouble with the LEfSE analysis. Briefly, I have follwed the indication of the Dr Bemjamin obtaining the file in txt. I have tried to modified this file adding two raws in order to include Class- Subclass but when I switch to Galaxy there is this problem:

File “/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/format_input.py”, line 433, in feats = add_missing_levels(feats) File "/shed_tools/testtoolshed.g2.bx.psu.edu/

I thought that y file was correctly formatted but I do not understand the problem or how to provide a correct txt.

Thanks a lot for your help

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Show us the file context or upload it. Ben

collapse.frequency.table.txt (202.3 KB)
This the file generated frim qiime2 follwing your guide.

To complete the file I follwed the instruction found on this forum: by using excel (to add the lacking information) and then saving in txt. I also controlled, example file on galaxy.
I do not understand the trouble. Is possibile that step in excel has modified the file?

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Edit your headers - you need columns that say class, sub-class, ID


I have modified in this way. Unfortunaty, I did not obtain any result.

Cartel1.txt (160.3 KB)

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I’m going to run it with my installed LEFSE, the huttenhower program is difficult to use. Ben

Your main problem is that it didn't recognize your use of "," as a "." I did a mass replacement on your data set and I got this:

The error that you cannot see that I can only see when I run LEFSE on my local machine is this: "ValueError: could not convert string to float: "5,31E+13" In my US-centric view of the world, the LEFSE program doesn't seem to recognize commas as decimal points.

Here is the actual file I passed. Cartel1.txt (122.4 KB)

Thank you so much for your help.
I was not able to sostitute all “,” in “.” in excel before creating the file.txt.

What LEFSE “software” do you use? , Becouse I tried on R with phyloseq object but I did not obtain any result. Additionaly, follwoing diverse tutorail on LEFSE-R-Phyloseq I am not able to have LEFSE analysis. in other words I had to use LEFSE con galaxy for this reasons.

Thank you in advance

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I installed from GitHub or bit bucket when they offered the code. Then I learned how to install it, so now I run it from a conda environment.

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Dear Ben,

I have tried with the txt file that you have provided in Galaxy.
If I discard the sub-class raw, for example, I can do the analysis, but without any result.
It is clear that one of the problem is the “,” in the file, but then I do not understand what is the mistake: class/ subclass?, define raw o column on galaxy?
I will try again strating from qiime2…(unfortunatly, some guides have been made for qiime1)

Yeah, I’ve had this debate in the past regarding classes/subclasses, if you read Segata’s publication it’s hard to interpret exactly what they mean by classes and subclasses - I think I can’t answer that for you as it would depend on your analysis. I can tell you that using the Mercurial/Github code from way back when that file runs. I get Porphorymonas with your classes/subclasses. I can go and delve into the code for you. Ben

I tried your suggestion to use mercurial/GitHub code. I would like to use phyloseq object, but it appears quit impossible in R 3.6.
LEfSe in Galaxy is not clear (data.txt or other parameters) or almost sets up for qiime1.
I would standardize my analysis from qiime2 (first stesps) to R (second steps and plotting).
Thank you in advance for your help