Error: No motifs provided

[letaibui27-star]

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:

1. 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.

2. 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.

3. 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

4. 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