I am using teh demo dataset to run LEfSe analysis. The data gets formatted, however the effect size is not calculated. There is an error, when i open to review details of error, following are the detail’s. Is LEfSE working on galaxy module or not? Please help. -B) LDA Effect Size (LEfSe)
Dataset Information
Number: 33
Name: B) LDA Effect Size (LEfSe) on data 32
Created: Thu Apr 4 16:09:22 2024 (UTC)
Filesize: 0 bytes
Dbkey: ?
Format: lefse_internal_res
Job Information
Galaxy Tool ID: LEfSe_run
Galaxy Tool Version: 1.0
Tool Version:
Tool Standard Output: stdout
Tool Standard Error: stderr
Tool Exit Code: 1
Job Messages
Fatal error: Exit code 1 ()
History Content API ID: 9b1b979e585e19dd
Job API ID: f937acaf11ccf7e7
History API ID: 22bdbe9d6e0775fe
UUID: 0d136d7d-910f-4c94-9729-cefffb5b365e
Tool Parameters
Input Parameter Value
Select data
32: A) Format Data for LEfSe on data 31
Alpha value for the factorial Kruskal-Wallis test among classes 0.05
Alpha value for the pairwise Wilcoxon test between subclasses 0.05
Threshold on the logarithmic LDA score for discriminative features 2.0
Do you want the pairwise comparisons among subclasses to be performed only among the subclasses with the same name? No
Set the strategy for multi-class analysis All-against-all (more strict)
Inheritance Chain
We cannot provide much help with issues specific to LEfSE tools not working, unfortunately. Your best chance is to try to contact someone that maintains the lefse galaxy server, possibly at https://forum.biobakery.org/.
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