Hacktoberfest 2026: le issue che i maintainer hanno segnato per ottobre, aperte e adatte ai principianti. Sfoglia le issue Hacktoberfest

RuntimeError: One of the processes exited with code -7

Aperta
  • Qualcosa non va?
#35 2 commenti 0 reazioni 0 assegnatari Vedi su GitHub

Nessuno ha ancora preso questa issue.

Valutazione

Difficoltà
4/5
Tempo stimato
3-5 giorni
Idoneità per principianti
25/100
Tipo di issue
Bug
Chiarezza
Da chiarire
Stato di attività
Ferma
Stack tecnologico
python
Ambito
data

Direzione di ricerca

Inizia da src/cell_type_mapper/cli/precompute_stats_abc.py e segui la chiamata fino a src/cell_type_mapper/diff_exp/precompute_from_anndata.py. Riproduci la precomputazione con la configurazione fornita, quindi esamina src/cell_type_mapper/utils/multiprocessing_utils.py e il percorso del worker attorno a _precompute_summary_stats_from_h5ad_and_lookup. Il lavoro è completato quando hai identificato perché un worker termina con il codice di uscita -7 e hai segnalato il problema sottostante oppure lo hai corretto con un test di regressione.

Scritto dal modello di indicizzazione a partire dal testo della issue.

Descrizione

Hi! I am using this wonderful tool to annotate cell types in my file. However, while creating the precomputed stats file, an error occurred (as listed below). I have no idea what is happening, could you help me with this error?

this is my code:


precompute_config = {
    'output_path': str(precompute_dir / 'precomputed_stats.h5'),
    'hierarchy': ['CCN20230722_CLAS',
                  'CCN20230722_SUBC',
                  'CCN20230722_SUPT',
                  'CCN20230722_CLUS'],
    'h5ad_path_list': h5ad_path_list,
    'cell_metadata_path': str(training_set_path),
    'cluster_annotation_path': str(cluster_annotation_path),
    'cluster_membership_path': str(cluster_membership_path),
    'n_processors': 4,
    'split_by_dataset': True, #v2和v3会分开各自生成一个
    'do_pruning': True,
    'tmp_dir': str(scratch_dir),
    'clobber': True
}

precomputation_runner = PrecomputationABCRunner(
    args=[],
    input_data=precompute_config
)

precomputation_runner.run()

this is error:

CREATED TAXONOMY
writing /cwStorage/nodecw_group/zy_data/Project_Spatial/Multiome/Other_data/Allen_BC/abc_atlas_mapping/scratch/precompute/precomputed_stats.WMB-10Xv2.h5 from dataset WMB-10Xv2

RuntimeError Traceback (most recent call last)
File :23

File /public/home/yzhang/zy_data/Project_AD_st/Multiome/tools/cell_type_mapper-main/src/cell_type_mapper/cli/precompute_stats_abc.py:102, in PrecomputationABCRunner.run(self)
99 else:
100 cell_set = None
--> 102 was_written = precompute_summary_stats_from_h5ad_list_and_tree(
103 data_path_list=self.args['h5ad_path_list'],
104 taxonomy_tree=taxonomy_tree,
105 rows_at_a_time=10000,
106 normalization=self.args['normalization'],
107 output_path=output_path,
108 cell_set=cell_set,
109 n_processors=self.args['n_processors'],
110 tmp_dir=self.args['tmp_dir'],
111 layer=self.args['layer'],
112 gene_id_col=self.args['gene_id_col'])
114 if was_written:
115 files_to_merge.append(output_path)

File /public/home/yzhang/zy_data/Project_AD_st/Multiome/tools/cell_type_mapper-main/src/cell_type_mapper/diff_exp/precompute_from_anndata.py:343, in precompute_summary_stats_from_h5ad_list_and_tree(data_path_list, taxonomy_tree, output_path, rows_at_a_time, normalization, cell_set, tmp_dir, n_processors, copy_data_over, layer, gene_id_col)
340 if cell_set is None or cell_str in cell_set:
341 cell_name_to_cluster_name[cell_str] = cluster
--> 343 was_written = precompute_summary_stats_from_h5ad_and_lookup(
344 data_path_list=data_path_list,
345 cell_name_to_cluster_name=cell_name_to_cluster_name,
346 cluster_to_output_row=cluster_to_output_row,
347 output_path=output_path,
348 rows_at_a_time=rows_at_a_time,
349 normalization=normalization,
350 tmp_dir=tmp_dir,
351 n_processors=n_processors,
352 copy_data_over=copy_data_over,
353 layer=layer,
354 gene_id_col=gene_id_col)
356 if was_written:
357 with h5py.File(output_path, 'a') as out_file:

File /public/home/yzhang/zy_data/Project_AD_st/Multiome/tools/cell_type_mapper-main/src/cell_type_mapper/diff_exp/precompute_from_anndata.py:448, in precompute_summary_stats_from_h5ad_and_lookup(data_path_list, cell_name_to_cluster_name, cluster_to_output_row, output_path, rows_at_a_time, normalization, tmp_dir, n_processors, copy_data_over, layer, gene_id_col)
443 buffer_dir = tempfile.mkdtemp(
444 dir=tmp_dir,
445 prefix='precomputation_data_buffer_')
447 try:
--> 448 flag = _precompute_summary_stats_from_h5ad_and_lookup(
449 data_path_list=data_path_list,
450 cell_name_to_cluster_name=cell_name_to_cluster_name,
451 cluster_to_output_row=cluster_to_output_row,
452 output_path=output_path,
453 rows_at_a_time=rows_at_a_time,
454 normalization=normalization,
455 tmp_dir=tmp_dir,
456 n_processors=n_processors,
457 buffer_dir=buffer_dir,
458 layer=layer,
459 gene_id_col=gene_id_col)
460 finally:
461 _clean_up(tmp_dir)

File /public/home/yzhang/zy_data/Project_AD_st/Multiome/tools/cell_type_mapper-main/src/cell_type_mapper/diff_exp/precompute_from_anndata.py:647, in _precompute_summary_stats_from_h5ad_and_lookup(data_path_list, cell_name_to_cluster_name, cluster_to_output_row, output_path, rows_at_a_time, normalization, tmp_dir, n_processors, buffer_dir, layer, gene_id_col)
644 process_list.append(p)
646 while len(process_list) >= n_processors:
--> 647 process_list = winnow_process_list(process_list)
649 while len(process_list) > 0:
650 process_list = winnow_process_list(process_list)

File /public/home/yzhang/zy_data/Project_AD_st/Multiome/tools/cell_type_mapper-main/src/cell_type_mapper/utils/multiprocessing_utils.py:31, in winnow_process_list(process_list)
29 to_pop.append(ii)
30 if process_list[ii].exitcode != 0:
---> 31 raise RuntimeError(
32 "One of the processes exited with code "
33 f"{process_list[ii].exitcode}")
34 for ii in to_pop:
35 process_list.pop(ii)

RuntimeError: One of the processes exited with code -7

Lingua principale
Python
Stelle
58
Fork
10
Nessuna PR unita negli ultimi 30g

Preparare l'ambiente

Come iniziare

  1. Leggi tutta la issue e poi la guida ai contributi del progetto.
  2. Commenta sulla issue per dire che te ne occupi tu — evita che due persone facciano lo stesso lavoro.
  3. Fai un fork del repository e lavora su un branch.
  4. Apri una pull request che faccia riferimento al numero della issue.

Altre issue di AllenInstitute/cell_type_mapper

Tutte le issue di AllenInstitute/cell_type_mapper

Issue simili

Altre issue su Python

Ricevi le nuove issue nella tua casella

Un breve riepilogo di issue GitHub adatte ai principianti.