Tutorial 10x multiome - AssertionError: Database "{fname}" doesn't exist.

[Tomoya89]

Describe the bug
Thank you for developing such a wonderful package!
First, I tried to follow the tutorial for 10x multiome, but I get the below error at the Motif enrichment analysis using pycistarget part.
I'm not sure if this is a problem with my environment, but could you please tell me how to solve this problem?
Thank you.

To Reproduce
from scenicplus.wrappers.run_pycistarget import run_pycistarget
run_pycistarget(
region_sets = region_sets,
species = 'homo_sapiens',
save_path = os.path.join(work_dir, 'motifs'),
ctx_db_path = rankings_db,
dem_db_path = scores_db,
path_to_motif_annotations = motif_annotation,
run_without_promoters = True,
n_cpu = 4,
#_temp_dir = os.path.join(tmp_dir, 'ray_spill'),
annotation_version = 'v10nr_clust',
)

Error output

AssertionError Traceback (most recent call last)
Cell In [60], line 2
1 from scenicplus.wrappers.run_pycistarget import run_pycistarget
----> 2 run_pycistarget(
3 region_sets = region_sets,
4 species = 'homo_sapiens',
5 save_path = os.path.join(work_dir, 'motifs'),
6 ctx_db_path = rankings_db,
7 dem_db_path = scores_db,
8 path_to_motif_annotations = motif_annotation,
9 run_without_promoters = True,
10 n_cpu = 4,
11 #_temp_dir = os.path.join(tmp_dir, 'ray_spill'),
12 annotation_version = 'v10nr_clust',
13 )

File ~/scenicplus/src/scenicplus/wrappers/run_pycistarget.py:182, in run_pycistarget(region_sets, species, save_path, custom_annot, save_partial, ctx_db_path, dem_db_path, run_without_promoters, biomart_host, promoter_space, ctx_auc_threshold, ctx_nes_threshold, ctx_rank_threshold, dem_log2fc_thr, dem_motif_hit_thr, dem_max_bg_regions, annotation, motif_similarity_fdr, path_to_motif_annotations, annotation_version, n_cpu, _temp_dir, exclude_motifs, exclude_collection, **kwargs)
180 ## CISTARGET
181 regions = region_sets[key]
--> 182 ctx_db = cisTargetDatabase(ctx_db_path, regions)
183 if exclude_motifs is not None:
184 out = pd.read_csv(exclude_motifs, header=None).iloc[:,0].tolist()

File ~/opt/anaconda3/envs/scenicplus/lib/python3.8/site-packages/pycistarget/motif_enrichment_cistarget.py:67, in cisTargetDatabase.init(self, fname, region_sets, name, fraction_overlap)
48 def init(self,
49 fname: str,
50 region_sets: Union[Dict[str, pr.PyRanges], pr.PyRanges] = None,
51 name: str = None,
52 fraction_overlap: float = 0.4):
53 """
54 Initialize cisTargetDatabase
55
(...)
65 Minimal overlap between query and regions in the database for the mapping.
66 """
---> 67 self.regions_to_db, self.db_rankings, self.total_regions = self.load_db(fname,
68 region_sets,
69 name,
70 fraction_overlap)

File ~/opt/anaconda3/envs/scenicplus/lib/python3.8/site-packages/pycistarget/motif_enrichment_cistarget.py:110, in cisTargetDatabase.load_db(self, fname, region_sets, name, fraction_overlap)
108 if name is None:
109 name = os.path.basename(fname)
--> 110 db = FeatherRankingDatabase(fname, name=name)
111 total_regions = db.total_genes
112 db_regions = db.genes

File ~/opt/anaconda3/envs/scenicplus/lib/python3.8/site-packages/ctxcore/rnkdb.py:106, in FeatherRankingDatabase.init(self, fname, name)
98 """
99 Create a new feather database.
100
101 :param fname: The filename of the database.
102 :param name: The name of the database.
103 """
104 super().init(name=name)
--> 106 assert os.path.isfile(fname), """Database "{fname}" doesn't exist."""
108 self._fname = fname
109 self.ct_db = CisTargetDatabase.init_ct_db(
110 ct_db_filename=self._fname, engine="pyarrow"
111 )

AssertionError: Database "{fname}" doesn't exist.

Version (please complete the following information):

• Python: [Python 3.8.14]
• SCENIC+: [0.1.dev454+g9320635]

[re-rosales]

Hi,
I got the same error. I would really appreciate any suggestions.

The versions I'm using:
Python: 3.9.12
scenicplus: 0.1.dev452+g22735ca

[tu4n-p]

I'd check if I had the ranking and score files for motifs or not.

[Tomoya89]

Thank you for your reply.
Yes, it seems I miss these files.
rankings_db = os.path.join(db_fpath, 'cluster_SCREEN.regions_vs_motifs.rankings.v2.feather')
scores_db = os.path.join(db_fpath, 'cluster_SCREEN.regions_vs_motifs.scores.v2.feather')
motif_annotation = os.path.join(motif_annot_fpath, 'motifs-v10-nr.hgnc-m0.00001-o0.0.tbl')

Could you please teach me how to prepare these files to proceed the tutorial?
I don't have the staging folder yet and maybe I might not have been able to successfully create the singularity image.

[tu4n-p]

You can download files here or you can create your database from scratch

[SeppeDeWinter]

@tu4n-p

Thanks for replying to the issue 😄

[ramadatta]

Hi,

Thank you for the wonderful tool. I have the same issue as above while running PBMC tutorial.

As you stated in the above replies, I checked here, and found motifs-v10-nr.hgnc-m0.00001-o0.0.tbl file, but could not find the

1. cluster_SCREEN.regions_vs_motifs.scores.v2.feather
2. cluster_SCREEN.regions_vs_motifs.rankings.v2.feather

to download.

Could I know from where I can download these files?

[ramadatta]

Hi, thanks, I think my question is already answered here.