You did not provide a class

mothur bugs
1

I keep running the mothur function but it keeps saying that I did not provide a “class” even though I do have a class variable in the data frame

2
  1. Could you post the command you ran and the version of mothur you are using?
  2. I’d be happy to troubleshoot the issue for you if you send the input files to mothur.westcott@gmail.com?
3

When I run lefse, I use the command:

lefse(shared=Aris.HIvsHEU.shared, design=Aris.HIvsHEU.design, inputdir=MothurLEfSeProcessed_Data, class=HIV_Status)

I tried to see if putting a subclass (column of “Plasma”) would work but it doesn’t

when “class=HIV_Status”, it says that it cannot detect the two levels of the HIV_Status, despite there being two levels in the space deliminated file.

The design file is organized like (first few rows):

Group HIV_Status Subclass
DOM00004 HI Plasma
DOM00007 HEU Plasma
DOM00024 HI Plasma
DOM00031 HI Plasma
DOM00043 HI Plasma
DOM00086 HI Plasma

and the shared file (first few rows):

label Group num0tus Plasma_IFN_gamma Plasma_IL1_alpha Plasma_IL1_beta Plasma_IL2 Plasma_IL4 Plasma_IL5 Plasma_IL6 Plasma_IL8 Plasma_IL10 Plasma_MCP1 Plasma_TNF_alpha
0.03 DOM00004 11 1.1225435240687542 1.0153597554092142 0.9876662649262746 0.00860017176191757 0.7442929831226762 1.1179338350396415 0.2253092817258629 0.5705429398818975 0.7442929831226762 1.8940944273226987 1.335858911319818
0.03 DOM00007 11 1.1544239731146468 1.616580530085886 1.3197304943302246 0.6414741105040995 0.8312296938670634 0.4653828514484183 0.2966651902615311 0.4712917110589386 0.414973347970818 1.8365139988906714 1.3406423775607053
0.03 DOM00024 11 1.5059635180181261 1.085290578230065 0.6884198220027106 0.2787536009528289 0.6637009253896481 0.904715545278681 0.8808135922807914 0.3384564936046048 1.2068258760318498 1.792951708250132 1.5350408132511606
0.03 DOM00031 11 0.00860017176191757 0.00860017176191757 0.5211380837040362 0.00860017176191757 0.00860017176191757 0.617000341120899 0.29885307640970665 0.35410843914740087 1.6451273992583912 1.909609510490169 1.070037866607755
0.03 DOM00043 11 0.9863237770507653 1.0993352776859577 0.890979596989689 0.00860017176191757 0.48144262850230496 0.6374897295125107 0.561101383649056 0.9863237770507653 1.1332194567324942 2.252343224380086 1.2683439139510646

4

When I run your files with our latest version, I am not seeing the same error.

mothur > lefse(shared=Aris.HIvsHEU.shared, design=Aris.HIvsHEU.design, class=HIV_Status)

Comparing HI-HEU:

[ERROR]: 1.1225435240687542RAM used: 0.00840759Gigabytes . Total Ram: 36Gigabytes.

has occurred in the Utils class function mothurConvert-int. Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry

This error occurs because the file you are providing for the shared parameter is not a shared file. It is a relabund file. Shared files contain only integers.

5

Can you give me an example of a shared file in terms of how it is organized with its columns?

And I am assuming that there is no issue with the design file?

6

Sure, let’s look at a sample of the final.opti_mcc.shared file from Pat’s example analysis. The shared file contains the observed abundance for each sample within each otu. The abundances are integer values not floating point numbers. It’s the same format as the relabund file.

label Group numOtus Otu001 Otu002 Otu003 Otu004 Otu005 Otu006…

0.03 F3D0 531 499 306 394 403 632 356…

0.03 F3D1 531 351 311 189 64 73 117…

0.03 F3D141 531 388 335 301 482 425 279…

…

7

So the issue is the fact that my data has to be in terms of integers and not decimal values? What if I cannot use integer values and have to use my decimal values

8

Can I use the make.lefse() function to make the proper file for the lefse() function? Because I need the values to be in their decimal form

9

There isn’t currently an option to provide your own relative abundances to the lefse command. I will add the option to our feature request list.

10

One solution might be to multiple the relative abundances by 100 and then truncate the values to be integers. FWIW, you might also want to see this article showing problems with using relative abundances as a means of controlling for uneven sampling effort.

https://journals.asm.org/doi/10.1128/msphere.00354-23

Pat

11

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