I loaded everything and once i had proper credentials cold run everything according to instructions. I had 2 errors and I am not so sure that one isn't causing the other. For downloading cbiportal data with: synapse get -r --downloadLocation data/cbioportal syn5521835 I get IOError: [Errno 2] No such file or directory: 'data/cbioportal/SYNAPSE_METADATA_MANIFEST.tsv' When I try to verify a clinical file with python sage_processing/validateGENIE.py clinical data_clinical_supp_TJU.txt TJU I get: Traceback (most recent call last): File "sage_processing/validateGENIE.py", line 846, in perform_main(syn, args) File "sage_processing/validateGENIE.py", line 814, in perform_main message = main(syn, args.fileType, args.file, args.center, pool, args.oncotreeLink, args.offline, args.uploadToSynapse) File "sage_processing/validateGENIE.py", line 770, in main vital_status_mapping = getGenieMapping(syn, "syn10888675") File "sage_processing/validateGENIE.py", line 133, in getGenieMapping table_ent = syn.tableQuery('SELECT * FROM %s' %synId) File "/Library/Python/2.7/site-packages/synapseclient/client.py", line 2866, in tableQuery return CsvFileTable.from_table_query(self, query, **kwargs) File "/Library/Python/2.7/site-packages/synapseclient/table.py", line 1094, in from_table_query includeRowIdAndRowVersion=includeRowIdAndRowVersion) File "/Library/Python/2.7/site-packages/synapseclient/client.py", line 2978, in _queryTableCsv download_from_table_result = self._waitForAsync(uri=uri, request=download_from_table_request) File "/Library/Python/2.7/site-packages/synapseclient/client.py", line 2735, in _waitForAsync result = self.restGET(uri+'/get/%s'%async_job_id['token'], endpoint=endpoint) File "/Library/Python/2.7/site-packages/synapseclient/client.py", line 3383, in restGET exceptions._raise_for_status(response, verbose=self.debug) File "/Library/Python/2.7/site-packages/synapseclient/exceptions.py", line 140, in _raise_for_status raise SynapseHTTPError(message, response=response) synapseclient.exceptions.SynapseHTTPError: 403 Client Error: Forbidden You do not have READ permission for the requested entity. However I can verify a maf file: python sage_processing/validateGENIE.py maf data_mutations_extended_TJU_maf.txt TJU INFO:__main__:VALIDATING data_mutations_extended_TJU_maf.txt INFO:__main__:YOUR FILE IS VALIDATED! WARNING:__main__:Your mutation file does not have the column headers that can give extra information to the processed mutation file: T_REF_COUNT, N_DEPTH, N_REF_COUNT, N_ALT_COUNT.