Couldn't generate menr.pkl file for SCENIC+

[Jay2942023]

Hello,

I am trying to get familiar with SCENIC+ workflow using 10x multiome pbmc tutorial. However, pycistarget couldn't generate menr.pkl file for SCENIC+ input. All I get are a few lists of html file for different topics. Here I attached the code and error message.

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 = 8,
_temp_dir = os.path.join(tmp_dir, 'ray_spill'),
annotation_version = 'v10nr_clust',
)

[Jay2942023]

Here is the error:
File "/usr/local/lib/python3.8/site-packages/pycistarget/motif_enrichment_dem.py", line 319, in init
self.run(dem_db.db_scores, **kwargs)
File "/usr/local/lib/python3.8/site-packages/pycistarget/motif_enrichment_dem.py", line 365, in run
region_groups = [create_groups(contrast = contrasts[x],
File "/usr/local/lib/python3.8/site-packages/pycistarget/motif_enrichment_dem.py", line 365, in
region_groups = [create_groups(contrast = contrasts[x],
File "/usr/local/lib/python3.8/site-packages/pycistarget/motif_enrichment_dem.py", line 534, in create_groups
bg_pr_overlap = pr.PyRanges(region_names_to_coordinates(background)).count_overlaps(annotation)
File "/usr/local/lib/python3.8/site-packages/pycistarget/utils.py", line 33, in region_names_to_coordinates
regiondf.columns=['Chromosome', 'Start', 'End']
File "/usr/local/lib/python3.8/site-packages/pandas/core/generic.py", line 5920, in setattr
return object.setattr(self, name, value)
File "pandas/_libs/properties.pyx", line 69, in pandas._libs.properties.AxisProperty.set
File "/usr/local/lib/python3.8/site-packages/pandas/core/generic.py", line 822, in _set_axis
self._mgr.set_axis(axis, labels)
File "/usr/local/lib/python3.8/site-packages/pandas/core/internals/managers.py", line 228, in set_axis
self._validate_set_axis(axis, new_labels)
File "/usr/local/lib/python3.8/site-packages/pandas/core/internals/base.py", line 70, in _validate_set_axis
raise ValueError(
ValueError: Length mismatch: Expected axis has 0 elements, new values have 3 elements

[SeppeDeWinter]

Hi @Jay2942023

Can you check wether the chromosome names in your sets of regions map with the chromosome names in the genome annotation (pr_annot).

All the best,

Seppe

[mairamirza]

Hi @SeppeDeWinter

I am encountering the same 'ValueError: Length mismatch: Expected axis has 0 elements, new values have 3 elements' on this code chunk

for DAR in markers_dict.keys():
regions = markers_dict[DAR].index[markers_dict[DAR].index.str.startswith('chr')]
region_sets['DARs'][DAR] = pr.PyRanges(region_names_to_coordinates(regions))

my annot has following chromosome names:
`

Chromosome	Start	Strand	Gene	Transcript_type
chr2	154551776	1	Actl10	protein_coding
chrX	31117674	1	Btbd35f29	protein_coding
chr7	84915781	1	Olfr290	protein_coding
chrY	90839177	-1	Gm21748	protein_coding
chr4	108719649	1	3110021N24Rik	protein_coding
...	...	...	...	...
chr6	134791334	-1	Dusp16	protein_coding
chr14	51203391	1	Ear14	protein_coding
chr14	51203689	1	Ear14	protein_coding
chr12	85274286	1	Zc2hc1c	protein_coding
chr12	85288591	1	Zc2hc1c	protein_coding

`

and my markers_dict has following chromosome details:
`{'AP, cycling': Log2FC Adjusted_pval Contrast
chr1:146160518-146161018 2.952461 6.024392e-25 AP, cycling
chr18:33138394-33138894 2.950420 5.393040e-25 AP, cycling
chr2:120537711-120538211 2.950420 5.393040e-25 AP, cycling
chr1:64330705-64331205 2.906402 5.527621e-25 AP, cycling
chr7:125731094-125731594 2.904940 6.708995e-25 AP, cycling
... ... ... ...
chr15:10746557-10747057 0.586071 2.838126e-08 AP, cycling
chr7:89400669-89401169 0.586049 8.302689e-14 AP, cycling
chr17:23726623-23727123 0.585742 3.541455e-20 AP, cycling
chr8:54724231-54724731 0.585447 2.128771e-21 AP, cycling
chr6:120471574-120472074 0.585394 3.926210e-09 AP, cycling

[11247 rows x 3 columns],
'BP, neurogenic': Log2FC Adjusted_pval Contrast
chr12:52020608-52021108 4.009526 1.576404e-79 BP, neurogenic
chr2:96499436-96499936 3.983610 1.576404e-79 BP, neurogenic`

Could you please help me fix this error? Thanks