Hello, this is the first time filling out a ticket so excuse the bad formatting, but I'm running into a problem with the package. Trying to do the following:
from mieaa import API
enrichment_list = ['hsa-miR-126-P2-v3_3p', 'hsa-miR-126-P2-v3_5p*', 'hsa-miR-142-P1-v3_5p*', 'hsa-miR-196-P4_5p', 'hsa-miR-21_5p', 'hsa-miR-221-P1a_3p', 'hsa-miR-223_3p', 'hsa-miR-23-P3_3p', 'hsa-miR-30-P1a_5p', 'hsa-miR-30-P2b_5p', 'hsa-miR-30-P2d_5p', 'hsa-miR-362-P3_3p', 'hsa-miR-423_5p', 'hsa-miR-486_3p*', 'hsa-miR-486_5p', 'hsa-let-7a-3p', 'hsa-let-7a-5p', 'hsa-let-7d-3p', 'hsa-miR-10396a-5p', 'hsa-miR-10396b-5p', 'hsa-miR-10400-5p', 'hsa-miR-10a-3p', 'hsa-miR-1228-3p', 'hsa-miR-125a-5p', 'hsa-miR-1260a', 'hsa-miR-1260b', 'hsa-miR-1287-5p', 'hsa-miR-130a-3p', 'hsa-miR-146a-5p', 'hsa-miR-150-5p', 'hsa-miR-15a-5p', 'hsa-miR-15b-5p', 'hsa-miR-181a-2-3p', 'hsa-miR-193a-5p', 'hsa-miR-193b-5p', 'hsa-miR-196a-5p', 'hsa-miR-1976', 'hsa-miR-22-3p', 'hsa-miR-222-5p', 'hsa-miR-23b-3p', 'hsa-miR-23b-5p', 'hsa-miR-2682-5p', 'hsa-miR-27a-3p', 'hsa-miR-3135b', 'hsa-miR-3154', 'hsa-miR-3161', 'hsa-miR-3180-5p', 'hsa-miR-3195', 'hsa-miR-3196', 'hsa-miR-323b-3p', 'hsa-miR-326', 'hsa-miR-335-5p', 'hsa-miR-3615', 'hsa-miR-363-3p', 'hsa-miR-3663-3p', 'hsa-miR-4285', 'hsa-miR-4326', 'hsa-miR-4466', 'hsa-miR-4488', 'hsa-miR-4492', 'hsa-miR-4521', 'hsa-miR-455-3p', 'hsa-miR-4634', 'hsa-miR-4683', 'hsa-miR-5100', 'hsa-miR-542-5p', 'hsa-miR-551a', 'hsa-miR-584-5p', 'hsa-miR-615-3p', 'hsa-miR-638', 'hsa-miR-6511b-3p', 'hsa-miR-656-3p', 'hsa-miR-663a', 'hsa-miR-663b', 'hsa-miR-6785-3p', 'hsa-miR-6858-3p', 'hsa-miR-6894-3p', 'hsa-miR-7704', 'hsa-miR-7977', 'hsa-miR-92a-3p', 'hsa-miR-9901']
mieaa_api = API()
mieaa_api.new_session()
mieaa_api.run_gsea(test_set = enrichment_list, categories = ['miRWalk_GO', 'GO_annotations_indirect', 'GO_Annotations', 'miRPathDB_GO_Biological_process', 'miRPathDB_GO_Cellular_component', 'miRPathDB_GO_Molecular_function', 'KEGG'], mirna_type = "mirna", species="hsa", significance_level = .99)
json = mieaa_api.get_results(check_progress_interval=20, retries=10)
This has worked up till within the past month-ish without a issue. The current output is the following:
Traceback (most recent call last):
File "C:\Users\kfeher\RNA_seq\__main__.py", line 26, in <module>
program_runner(miRNA_input_data, miRNA_geo_studies_path)
File "C:\Users\kfeher\RNA_seq\miRNA_seq\mirna_validation.py", line 427, in program_runner
mirna_obj.determine_selected_output(display_figs)
File "C:\Users\kfeher\RNA_seq\miRNA_seq\mirna_validation.py", line 372, in determine_selected_output
enrichment_subplot = self.perform_enrichment_analysis(sig_mirna)
File "C:\Users\kfeher\RNA_seq\miRNA_seq\mirna_validation.py", line 316, in perform_enrichment_analysis
enrichment_results = perform_enrichment(enrichment_list, self.study_w_sample_name, self.testing)
File "C:\Users\kfeher\RNA_seq\miRNA_seq\enrich_utils.py", line 17, in perform_enrichment
mieaa_api.run_gsea(test_set = enrichment_list, categories = ['miRWalk_GO', 'GO_annotations_indirect', 'GO_Annotations', 'miRPathDB_GO_Biological_process', 'miRPathDB_GO_Cellular_component', 'miRPathDB_GO_Molecular_function', 'KEGG'], mirna_type = "mirna", species="hsa", significance_level = .99)
File "C:\ProgramData\Miniconda3\envs\rna_sequencing\lib\site-packages\mieaa\mieaa_wrapper.py", line 457, in run_gsea
return self._start_analysis('GSEA', test_set, categories, mirna_type, species, '', **kwargs)
File "C:\ProgramData\Miniconda3\envs\rna_sequencing\lib\site-packages\mieaa\mieaa_wrapper.py", line 346, in _start_analysis
descriptive_http_error(response)
File "C:\ProgramData\Miniconda3\envs\rna_sequencing\lib\site-packages\mieaa\mieaa_wrapper.py", line 16, in descriptive_http_error
raise requests.HTTPError('{}\nResponse: {}'.format(err, response.text))
requests.exceptions.HTTPError: 500 Server Error: Internal Server Error for url: https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/enrichment_analysis/hsa/mirna/GSEA/
Response: OperationalError at /api/v1/enrichment_analysis/hsa/mirna/GSEA/
database or disk is full
I guess I just want to make sure that its on the server-side and not something on my end. Thanks in advance
Hello, this is the first time filling out a ticket so excuse the bad formatting, but I'm running into a problem with the package. Trying to do the following:
This has worked up till within the past month-ish without a issue. The current output is the following:
I guess I just want to make sure that its on the server-side and not something on my end. Thanks in advance