export_eRegulons ValueError: cmds: ....stderr:b"Host hgdownload.cse.ucsc.edu not found --> Name or service not known\n\nnetConnect() failed\nCouldn't open https://hgdownload.cse.ucsc.edu/goldenpath/hg38/bigZips/hg38.chrom.sizes\n" stdout:b''

[wangdlpbr]

I ran to the last step, but a new problem arose, how should I solve this problem?Is it just a network link problem?

from scenicplus.wrappers.run_scenicplus import run_scenicplus
try:
    run_scenicplus(
        scplus_obj = scplus_obj,
        variable = ['GEX_celltype2'],
        species = 'hsapiens',
        assembly = 'hg38',
        tf_file = '/data4/litianqing/wangda/ref/scenicplus_database/utoronto_human_tfs_v_1.01.txt',
        save_path = os.path.join(work_dir, 'scenicplus'),
        biomart_host = biomart_host,
        upstream = [1000, 150000],
        downstream = [1000, 150000],
        calculate_TF_eGRN_correlation = True,
        calculate_DEGs_DARs = True,
        export_to_loom_file = True,
        export_to_UCSC_file = True,
        path_bedToBigBed = '/data4/litianqing/wangda/ref/scenicplus_database/',
        n_cpu = 15,
        _temp_dir = os.path.join(tmp_dir, 'ray_spill'))
except Exception as e:
    #in case of failure, still save the object
    dill.dump(scplus_obj, open(os.path.join(work_dir, 'scenicplus/scplus_obj.pkl'), 'wb'), protocol=-1)
    raise(e)

2024-03-15 15:37:14,811 SCENIC+_wrapper INFO     /data4/litianqing/wangda/E10E14-RNA-ATAC-addseq/E14_scenicplus/scenicplus folder already exists.
2024-03-15 15:37:14,814 SCENIC+_wrapper INFO     Calculating TF-eGRNs AUC correlation
2024-03-15 15:38:11,483 SCENIC+_wrapper INFO     Calculating DEGs/DARs
2024-03-15 15:38:11,486 SCENIC+      INFO     Calculating DEGs for variable GEX_celltype2
2024-03-15 15:38:18,759 SCENIC+      INFO     There are 4175 variable features

... storing 'ACC_sample_id' as categorical
... storing 'ACC_celltype2' as categorical

2024-03-15 15:38:29,586 SCENIC+      INFO     Finished calculating DEGs for variable GEX_celltype2
2024-03-15 15:38:29,587 SCENIC+      INFO     Calculating DARs for variable GEX_celltype2
2024-03-15 15:48:34,560 SCENIC+      INFO     There are 63807 variable features

... storing 'ACC_sample_id' as categorical
... storing 'ACC_celltype2' as categorical

2024-03-15 15:50:38,070 SCENIC+      INFO     Finished calculating DARs for variable GEX_celltype2
2024-03-15 15:50:38,077 SCENIC+_wrapper INFO     Exporting to loom file
2024-03-15 15:50:38,078 SCENIC+      INFO     Formatting data
2024-03-15 15:50:43,864 SCENIC+      INFO     Creating minimal loom
2024-03-15 15:50:59,991 SCENIC+      INFO     Adding annotations
2024-03-15 15:51:04,494 SCENIC+      INFO     Adding clusterings
2024-03-15 15:51:04,553 SCENIC+      INFO     Adding markers
2024-03-15 15:51:05,000 SCENIC+      INFO     Exporting
2024-03-15 15:51:16,347 SCENIC+      INFO     Formatting data
2024-03-15 15:54:12,790 SCENIC+      INFO     Creating minimal loom
2024-03-15 16:02:16,682 SCENIC+      INFO     Adding annotations
2024-03-15 16:03:14,353 SCENIC+      INFO     Adding clusterings
2024-03-15 16:03:14,413 SCENIC+      INFO     Adding markers
2024-03-15 16:03:22,873 SCENIC+      INFO     Exporting
2024-03-15 16:05:55,265 SCENIC+_wrapper INFO     Exporting to UCSC
2024-03-15 16:05:59,004 R2G          INFO     Downloading gene annotation from biomart, using dataset: hsapiens_gene_ensembl
2024-03-15 16:05:59,678 R2G          INFO     Formatting data ...
2024-03-15 16:06:35,558 R2G          INFO     Writing data to: /data4/litianqing/wangda/E10E14-RNA-ATAC-addseq/E14_scenicplus/scenicplus/r2g.rho.bed
2024-03-15 16:06:37,762 R2G          INFO     Writing data to: /data4/litianqing/wangda/E10E14-RNA-ATAC-addseq/E14_scenicplus/scenicplus/r2g.rho.bb
2024-03-15 16:07:01,283 R2G          INFO     Downloading gene annotation from biomart, using dataset: hsapiens_gene_ensembl
2024-03-15 16:07:01,844 R2G          INFO     Formatting data ...
2024-03-15 16:07:40,249 R2G          INFO     Writing data to: /data4/litianqing/wangda/E10E14-RNA-ATAC-addseq/E14_scenicplus/scenicplus/r2g.importance.bed
2024-03-15 16:07:42,554 R2G          INFO     Writing data to: /data4/litianqing/wangda/E10E14-RNA-ATAC-addseq/E14_scenicplus/scenicplus/r2g.importance.bb

Error output

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[11], line 23
     20 except Exception as e:
     21     #in case of failure, still save the object
     22     dill.dump(scplus_obj, open(os.path.join(work_dir, 'scenicplus/scplus_obj.pkl'), 'wb'), protocol=-1)
---> 23     raise(e)

Cell In[11], line 3
      1 from scenicplus.wrappers.run_scenicplus import run_scenicplus
      2 try:
----> 3     run_scenicplus(
      4         scplus_obj = scplus_obj,
      5         variable = ['GEX_celltype2'],
      6         species = 'hsapiens',
      7         assembly = 'hg38',
      8         tf_file = '/data4/litianqing/wangda/ref/scenicplus_database/utoronto_human_tfs_v_1.01.txt',
      9         save_path = os.path.join(work_dir, 'scenicplus'),
     10         biomart_host = biomart_host,
     11         upstream = [1000, 150000],
     12         downstream = [1000, 150000],
     13         calculate_TF_eGRN_correlation = True,
     14         calculate_DEGs_DARs = True,
     15         export_to_loom_file = True,
     16         export_to_UCSC_file = True,
     17         path_bedToBigBed = '/data4/litianqing/wangda/ref/scenicplus_database/',
     18         n_cpu = 15,
     19         _temp_dir = os.path.join(tmp_dir, 'ray_spill'))
     20 except Exception as e:
     21     #in case of failure, still save the object
     22     dill.dump(scplus_obj, open(os.path.join(work_dir, 'scenicplus/scplus_obj.pkl'), 'wb'), protocol=-1)

File /data4/litianqing/wangda/software/scenicplus/scenicplus/src/scenicplus/wrappers/run_scenicplus.py:370, in run_scenicplus(scplus_obj, variable, species, assembly, tf_file, save_path, biomart_host, upstream, downstream, region_ranking, gene_ranking, simplified_eGRN, calculate_TF_eGRN_correlation, calculate_DEGs_DARs, export_to_loom_file, export_to_UCSC_file, tree_structure, path_bedToBigBed, n_cpu, _temp_dir, save_partial, **kwargs)
    338     r2g_data = export_to_UCSC_interact(scplus_obj,
    339                         species,
    340                         os.path.join(save_path,'r2g.rho.bed'),
   (...)
    352                         subset_for_eRegulons_regions=True,
    353                         eRegulons_key='eRegulons')
    354     r2g_data = export_to_UCSC_interact(scplus_obj,
    355                         species,
    356                         os.path.join(save_path,'r2g.importance.bed'),
   (...)
    368                         subset_for_eRegulons_regions=True,
    369                         eRegulons_key='eRegulons')
--> 370     regions = export_eRegulons(scplus_obj,
    371             os.path.join(save_path,'eRegulons.bed'),
    372             assembly,
    373             bigbed_outfile = os.path.join(save_path,'eRegulons.bb'),
    374             eRegulon_metadata_key = 'eRegulon_metadata',
    375             eRegulon_signature_key = 'eRegulon_signatures',
    376             path_bedToBigBed=path_bedToBigBed)
    378 log.info('Saving object')         
    379 with open(os.path.join(save_path,'scplus_obj.pkl'), 'wb') as f:

File /data4/litianqing/wangda/software/scenicplus/scenicplus/src/scenicplus/utils.py:836, in export_eRegulons(scplus_obj, out_file, assembly, bigbed_outfile, eRegulon_metadata_key, eRegulon_signature_key, path_bedToBigBed)
    834     stdout, stderr = p.communicate()
    835     if p.returncode:
--> 836         raise ValueError(
    837             "cmds: %s\nstderr:%s\nstdout:%s" % (
    838                 " ".join(cmds), stderr, stdout)
    839         )
    840 return regions

ValueError: cmds: /data4/litianqing/wangda/ref/scenicplus_database/bedToBigBed /data4/litianqing/wangda/E10E14-RNA-ATAC-addseq/E14_scenicplus/scenicplus/eRegulons.bed https://hgdownload.cse.ucsc.edu/goldenpath/hg38/bigZips/hg38.chrom.sizes /data4/litianqing/wangda/E10E14-RNA-ATAC-addseq/E14_scenicplus/scenicplus/eRegulons.bb
stderr:b"Host hgdownload.cse.ucsc.edu not found --> Name or service not known\n\nnetConnect() failed\nCouldn't open https://hgdownload.cse.ucsc.edu/goldenpath/hg38/bigZips/hg38.chrom.sizes\n"
stdout:b''

[SeppeDeWinter]

Hi @wangdlpbr

This particular download link was down for some time, it might be that it if you rerun the code now that it will work.

That being said, you almost reached the end of the run_scenicplus function so if you managed to save your scenicplus_obj you will have all the results you need for downstream analysis.

All the best,

Seppe