Error: No motifs provided #58
Description
Hello,
I am trying to use the create_cistarget_motif_databases.py script to build a database for Arabidopsis thaliana, but I am consistently getting an Error: No motifs provided. even on a minimal test case where all inputs have been verified.
Here is my setup and what I have tried:
- Environment:
- I have a conda environment and it is activated.
- The cbust program was compiled manually and is in my $PATH. A direct manual call to cbust on a single motif file and the fasta file works correctly and produces scores.
-
Inputs (Minimal Test Case):
I created a small FASTA file: promoters_test.fasta.
I have a directory of motif files in the required raw matrix format: motifs_cb_format/.
I created a list with a single, existing motif file name: single_motif_test.list.
The content of single_motif_test.list is just one line: MA0001.1.cb
The file motifs_cb_format/MA0001.1.cb definitely exists. -
Command:
I am running the following command with absolute paths:
python /path/to/create_cistarget_motif_databases.py
-f /path/to/promoters_test.fasta
-M /path/to/motifs_cb_format
-m /path/to/single_motif_test.list
-o /path/to/my_athaliana_db_singletest
-t 8 -
The Error:
Despite all inputs being correct and cbust working manually, the script immediately fails with:
Error: No motifs provided.
This suggests the script is failing to read or process the motif list file (-m) correctly in my specific environment, before it even attempts to call cbust. Could you please provide any insights into what might be causing this pre-flight check to fail?
Thank you for your help.
Best wishes
Bui