LEfSe and MaAsLin2 issues and errors

LEfSe Galaxy Version 1.0
MaAsLin2 Galaxy Version 1.8.0

I’m having trouble running both LEfSe and MaAsLin2 on Galaxy. When I try to execute the “Format Data for LEfSe” step in LEfSe, I receive the following error:

Error: Cannot count lines in dataset format: lefse_internal_for, database: ? ERROR:galaxy.datatypes.data:Unable to count lines in file /export/galaxy-central/database/files/029/dataset_29667.dat

The table I’m using is shown below, named lefse_All_Samples_pathabundance_unstratified_relab_filtrada.tsv

Regarding MaAsLin2, the error occurs when I upload the TSV file. The error I receive is:

Traceback (most recent call last): File “/export/galaxy-central/tools/data_source/upload.py”, line 342, in main() File “/export/galaxy-central/tools/data_source/upload.py”, line 335, in main metadata.append(add_file(dataset,

The file in question is provided below with the name maaslin2_All_Samples_pathabundance_unstratified_relab_filtrada.tsv.

Any ideas about what is going on? I believe my files are in the correct format.

maaslin2_All_Samples_pathabundance_unstratified_relab_filtrada.tsv (85.5 KB)
lefse_All_Samples_pathabundance_unstratified_relab_filtrada.tsv (85.8 KB)

Hello @Poccia ,
For LEfSe Galaxy:
Please feel free to ignore the Unable to count lines error message for lefse. I just tried your dataset and all the steps run fine. (Our bioBakery Team will work on fixing this error message asap.)

For MaAsLin2 Galaxy:
Could you please also provide the metadata file for the MaAsLin2 please? It seems like the metadata file is missing for input.


The metadata was working fine, but I’ll upload here anyway.
metadados.tsv (2.9 KB)