export_pseudobulk error

[mtrebelo]

Hi! I am using SCENIC+ and I am having an issue in the 'Generate pseudobulk ATAC-seq profiles, call peaks and generate a consensus peak set' step.

I am using the following code to create the bed and bw files:

from pycisTopic.pseudobulk_peak_calling import export_pseudobulk
bw_paths, bed_paths = export_pseudobulk(input_data = cell_data,
                 variable = 'cell_type',                                                                     # variable by which to generate pseubulk profiles, in this case we want pseudobulks per celltype
                 sample_id_col = 'sample_id',
                 chromsizes = chromsizes,
                 bed_path = 'work_dir',  # specify where pseudobulk_bed_files should be stored
                 bigwig_path = 'wor_dir',# specify where pseudobulk_bw_files should be stored
                 path_to_fragments = fragments_dict,                                                        # location of fragment fiels
                 n_cpu = 8,                                                                                 # specify the number of cores to use, we use ray for multi processing
                 normalize_bigwig = True,
                 remove_duplicates = True,
                 _temp_dir = os.path.join(tmp_dir, 'ray_spill'),                       
                 split_pattern = '-')

The outup that I am getting is the following:

INFO worker.py:1538 -- Started a local Ray instance.
(export_pseudobulk_ray pid=34990) 2023-05-01 17:15:54,946 cisTopic     INFO     Creating pseudobulk for Endocrine_dorsal_pancreas
(export_pseudobulk_ray pid=34989) 2023-05-01 17:15:55,249 cisTopic     INFO     Creating pseudobulk for anteriorpharynx
(export_pseudobulk_ray pid=34993) 2023-05-01 17:15:55,563 cisTopic     INFO     Creating pseudobulk for blood
(export_pseudobulk_ray pid=34992) 2023-05-01 17:15:55,941 cisTopic     INFO     Creating pseudobulk for epithelium_ductalcells
(export_pseudobulk_ray pid=34988) 2023-05-01 17:15:56,248 cisTopic     INFO     Creating pseudobulk for liver
(export_pseudobulk_ray pid=34986) 2023-05-01 17:15:56,787 cisTopic     INFO     Creating pseudobulk for pharyngealendoderm
(export_pseudobulk_ray pid=34987) 2023-05-01 17:15:57,284 cisTopic     INFO     Creating pseudobulk for vasculature

It seems to be lacking the message that it has been done and the files are not created.

Any idea why this could be happening?

[SeppeDeWinter]

Hi @mtrebelo

Does any of cell type labels contain spaces or special characters?

Also I see that bigwig_path is set to 'wor_dir'`` instead of 'work_dir'`.

Besides these things you can try setting n_cpu to 1, this will reveal all error messages (ray is not passing them correctly).

I hope this helps!

Best,

Seppe

[MohammadIzadi]

Hi @SeppeDeWinter,

Thanks for your helping. I have similar issue and I can't get output files in "pseudobulk_bed_files" and "pseudobulk_bw_files" dir. Can you help me to solve this?

Best, Mahan

[SeppeDeWinter]

Hi @MohammadIzadi

Did you try running the code with single cpu core?

Best,

Seppe

[solvi808]

I got the same error, and it said the package pyrle was missing, so after installing pyrle the output files appeared. Perhaps it is not correctly defined in the dependencies?