CRITICAL - Failed to get proper response to query #165
Description
POSTGAP never finishes my run, citing problems with VEP timing out for connection. It seems to be having problems with this SNP (not in the input dataset):
CRITICAL - Failed to get proper response to query: 10/21/2020 03:09:59 PM - root - CRITICAL - Failed to get proper response to query http://rest.ensembl.org/eqtl/variant_name/homo_sapiens/rs1473281?content-type=application/json;statistic=p-value
Here is the traceback I get when cancelling the POSTGAP prematurely, perhaps it provides some clues about what is going wrong? The test job is running fine and my input is formatted according to the requirements.
Traceback (most recent call last): File "POSTGAP.py", line 690, in <module> main() File "POSTGAP.py", line 127, in main res = postgap.Integration.diseases_to_genes(options.diseases, expanded_efo_iris, options.population, options.tissues) File "/home/user/postgap/lib/postgap/Integration.py", line 68, in diseases_to_genes return gwas_snps_to_genes(diseases_to_gwas_snps(diseases, efos), population, tissues) File "/home/user/postgap/lib/postgap/Integration.py", line 163, in gwas_snps_to_genes res = concatenate(cluster_to_genes(cluster, tissue_weights, population) for cluster in clusters) File "/home/user/postgap/lib/postgap/Utils.py", line 120, in concatenate return sum(filter(lambda elem: elem is not None, list), []) File "/home/user/postgap/lib/postgap/Integration.py", line 163, in <genexpr> res = concatenate(cluster_to_genes(cluster, tissue_weights, population) for cluster in clusters) File "/home/user/postgap/lib/postgap/Integration.py", line 457, in cluster_to_genes associations = ld_snps_to_genes([snp for snp in cluster.ld_snps if snp in ld], tissues) File "/home/user/postgap/lib/postgap/Integration.py", line 579, in ld_snps_to_genes cisreg = cisregulatory_evidence(ld_snps, tissues) # Hash of hashes SNP => Gene => Cisregulatory_Evidence File "/home/user/postgap/lib/postgap/Integration.py", line 665, in cisregulatory_evidence evidence = concatenate(source().run(ld_snps, tissues) for source in postgap.Cisreg.sources) File "/home/user/postgap/lib/postgap/Utils.py", line 120, in concatenate return sum(filter(lambda elem: elem is not None, list), []) File "/home/user/postgap/lib/postgap/Integration.py", line 665, in <genexpr> evidence = concatenate(source().run(ld_snps, tissues) for source in postgap.Cisreg.sources) File "/home/user/postgap/lib/postgap/Cisreg.py", line 386, in run list = concatenate(self.get(chunk) for chunk in chunks(snps, 1)) File "/home/user/postgap/lib/postgap/Utils.py", line 120, in concatenate return sum(filter(lambda elem: elem is not None, list), []) File "/home/user/postgap/lib/postgap/Cisreg.py", line 386, in <genexpr> list = concatenate(self.get(chunk) for chunk in chunks(snps, 1)) File "/home/user/postgap/lib/postgap/Cisreg.py", line 499, in get return postgap.REST.get(server, ext, data = {"ids" : [snp.rsID for snp in chunk]}) File "/home/user/postgap/lib/postgap/REST.py", line 227, in get time.sleep(60) # Sleep 1 minute while server cools down