build mm10 regions based databases

[WGLUN]

First thank for sharing such a powerful pipeline for chromatin and motif analysis.
I was trying build a mm10 database based on regions defined in ATACseq following your tutorial.
However, I encounter an unexpected error. It seems it is related to motif files and annotation file.
The motif files were download here:
https://resources.aertslab.org/cistarget/motif_collections/v10nr_clust_public/
Could you help on how to get this resolved?
Thanks

The output is like this,
Traceback (most recent call last):
File "/usr/local/cisTarget_databases/bin//create_cistarget_motif_databases.py", line 572, in
main()
File "/usr/local/cisTarget_databases/bin//create_cistarget_motif_databases.py", line 355, in main
) = get_motif_id_to_filename_and_nbr_motifs_dict(
File "/usr/local/cisTarget_databases/bin/clusterbuster.py", line 102, in get_motif_id_to_filename_and_nbr_motifs_dict
raise OSError(
OSError: Error: Cluster-Buster motif filename "/users/working/singletons/metacluster_196.3 EcR_usp EcR/usp bergman 1.1 Hnf4a 0 None None 0.265823 FBgn0003964 D. melanogaster gene is orthologous to FBgn0003964 in D. melanogaster (identity = 26%) which is directly annotated for motif.cb" does not exist for motif metacluster_196.3 EcR_usp EcR/usp bergman 1.1 Hnf4a 0 None None 0.265823 FBgn0003964 D. melanogaster gene is orthologous to FBgn0003964 in D. melanogaster (identity = 26%) which is directly annotated for motif.

[WGLUN]

I figured out what happened!
Please disregard or delete this topic.
Thanks

[jonhsussman]

Hi @WGLUN, I find the same issue; would you mind describing what the solution was?

Thanks,
Jonathan

[WGLUN]

Hi, @jonhsussman I followed this discussion here #4 to build the motif list.

[ghuls]

@jonhsussman You used the motif2TF file.

The motif file should contain only 1 column with the motif IDs (Cluster-Buster motif filename basename without extension):

cd v10nr_clust_public/singletons

ls -1 *.cb | sed -e 's/\.cb$//' > /tmp/v10nr_cbust_public.txt