I've tried using the command line tool (http://python-docs.synapse.org/build/html/CommandLineClient.html) and the recommend synapse_client Python code to download the fastq files and get the following error:
ValueError: Failed downloading syn8271842 to ~/TESLA_1_1.fastq.gz.synapse_download_68009016
I have access to the data and can read the file names from the TESLA Data Release Files. I have made the call from an AWS EC2 instance.
Can you recommend an approach or give insight into this error and how to avoid it?
thanks.
Full log:
Welcome, Charles Shale!
[####################]100.00% 1/1 Done...
Downloading [####################]100.00% 7.1kB/7.1kB (3.9MB/s) SYNAPSE_TABLE_QUERY_80465671.csv Done...
Traceback (most recent call last):
File "/usr/lib/python3.7/concurrent/futures/thread.py", line 57, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/charlesshale/.local/lib/python3.7/site-packages/synapseclient/core/multithread_download/download_threads.py", line 355, in _get_response_with_retry
) from cause
synapseclient.core.exceptions.SynapseError: Could not download the file: TESLA_1_1.fastq.gz, please try again.
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "synapse2.py", line 21, in
ent = syn.get(syn_id, downloadFile=True)
File "/home/charlesshale/.local/lib/python3.7/site-packages/synapseclient/client.py", line 728, in get
return self._getWithEntityBundle(entityBundle=bundle, entity=entity, **kwargs)
File "/home/charlesshale/.local/lib/python3.7/site-packages/synapseclient/client.py", line 845, in _getWithEntityBundle
self._download_file_entity(downloadLocation, entity, ifcollision, submission)
File "/home/charlesshale/.local/lib/python3.7/site-packages/synapseclient/client.py", line 907, in _download_file_entity
downloadPath = self._downloadFileHandle(entity.dataFileHandleId, objectId, objectType, downloadPath)
File "/home/charlesshale/.local/lib/python3.7/site-packages/synapseclient/client.py", line 1868, in _downloadFileHandle
expected_md5=fileHandle.get('contentMd5'))
File "/home/charlesshale/.local/lib/python3.7/site-packages/synapseclient/client.py", line 1909, in _download_from_url_multi_threaded
multithread_download.download_file(self, request)
File "/home/charlesshale/.local/lib/python3.7/site-packages/synapseclient/core/multithread_download/download_threads.py", line 236, in download_file
downloader.download_file(download_request)
File "/home/charlesshale/.local/lib/python3.7/site-packages/synapseclient/core/multithread_download/download_threads.py", line 313, in download_file
self._check_for_errors(request, completed_futures)
File "/home/charlesshale/.local/lib/python3.7/site-packages/synapseclient/core/multithread_download/download_threads.py", line 409, in _check_for_errors
raise ValueError(f"Failed downloading {request.object_id} to {request.path}") from exception
ValueError: Failed downloading syn8271842 to /home/charlesshale/.synapseCache/16/68009016/TESLA_1_1.fastq.gz.synapse_download_68009016