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

[ghuls]

What is the output of:

file /path/to/single_motif_test.list

[letaibui27-star]

What is the output of:

file /path/to/single_motif_test.list

Dear @ghuls
This is the output
/home/ug1737/motif/motifs.list: ASCII text
Thanks

[ghuls]

Could you share your input file in a zip file?
I don't see anything directly that could be wrong.

[letaibui27-star]

Could you share your input file in a zip file? I don't see anything directly that could be wrong.

Dear @ghuls
Sorry for the late reply. Here is the zip file with my inputs. Thanks a lot for your help!
bui_athaliana_db.zip

[ghuls]

@letaibui27-star Sorry for the delay.

Your motifs are not in Cluster-Buster format.

22      16      25      27      0       0       82      40      56      35      65      25      64      0       33      52      45      21
29      9       8       16      92      79      1       4       0       0       1       4       0       0       14      5       23      24
34      29      4       13      0       0       2       3       1       0       4       3       28      92      15      7       13      26
10      41      58      39      3       16      10      48      38      60      25      63      3       3       33      31      14      24

Cluster-Buster format looks like the following:

• Motif name: >motif_name
• counts for A, C, G and T on one row (with one row per position in the matrix.

>MA2042.1
22      29      34      10
16      9       29      41
25      8       4       58
27      16      13      39
0       92      0       3
0       79      0       16
82      1       2       10
40      4       3       48
56      0       1       38
35      0       0       60
65      1       4       25
25      4       3       63
64      0       28      3
0       0       92      3
33      14      15      33
52      5       7       31
45      23      13      14
21      24      26      24

With BioPython you can convert between motif formats:

import glob
from pathlib import Path

import Bio.motifs


def convert_jaspar_pfm_to_cluster_buster(jaspar_motif_filename, cluster_buster_motif_filename):
    with open(jaspar_motif_filename, "r") as jaspar_motif_fh:
        # Read JAPSAR motif.
        motif = Bio.motifs.read(jaspar_motif_fh, "pfm-four-rows")
        # Add motif name to motif object.
        motif.name = Path(motif_from_R).stem

        with open(cluster_buster_motif_filename, "w") as cluster_buster_motif_fh:
            print(Bio.motifs.write([motif], "clusterbuster"), file=cluster_buster_motif_fh)


for jaspar_motif_filename in glob.glob("motifs_cb_from_R/*.cb"):
    cluster_buster_filename = jaspar_motif_filename.replace(
        "motifs_cb_from_R", "motifs_cb"
    )
    print(jaspar_motif_filename, cluster_buster_filename)
    convert_jaspar_pfm_to_cluster_buster(jaspar_motif_filename, cluster_buster_filename)