LEfSe and MaAsLin2 issues and errors

Downstream analysis and statistics
1

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)

2

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.

Regards,
Sagun

3

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