@liucy - is repeatedly getting this error message while downloading data from syn12137225
"$ synapse get -q "SELECT * FROM syn12137225 WHERE (("study"='iPSC') AND ("assay"='rnaSeq'))"
Synapse username: liucy
Password for liucy:
Welcome, Chunyu Liu!
[####################]100.00% 1/1 Done...
Downloading [####################]100.00% 343.5kB/343.5kB (3.4MB/s) Job-60973533554965171483468615.csv Done...
Downloading [####----------------]21.61% 2.0MB/9.3MB (6.9MB/s) aa759-149_010.Signal.Unique.strDownloading [#########-----------]43.21% 4.0MB/9.3MB (7.3MB/s) aa759-149_010.Signal.Unique.strDownloading [#############-------]64.82% 6.0MB/9.3MB (7.0MB/s) aa759-149_010.Signal.Unique.strDownloading [#################---]86.43% 8.0MB/9.3MB (7.3MB/s) aa759-149_010.Signal.Unique.strDownloading [####################]100.00% 9.3MB/9.3MB (7.7MB/s) aa759-149_010.Signal.Unique.str1.out(2).bg Done...
Downloading [####----------------]21.61% 2.0MB/9.3MB (8.5MB/s) aa759-149_010.Signal.Unique.strDownloading [#########-----------]43.21% 4.0MB/9.3MB (9.5MB/s) aa759-149_010.Signal.Unique.strDownloading [#############-------]64.82% 6.0MB/9.3MB (9.8MB/s) aa759-149_010.Signal.Unique.strDownloading [#################---]86.43% 8.0MB/9.3MB (9.9MB/s) aa759-149_010.Signal.Unique.strDownloading [####################]100.00% 9.3MB/9.3MB (10.2MB/s) aa759-149_010.Signal.Unique.str1.out(2).bg Done...
Downloading [####----------------]21.61% 2.0MB/9.3MB (9.6MB/s) aa759-149_010.Signal.Unique.strDownloading [#########-----------]43.21% 4.0MB/9.3MB (10.7MB/s) aa759-149_010.Signal.Unique.stDownloading [#############-------]64.82% 6.0MB/9.3MB (11.1MB/s) aa759-149_010.Signal.Unique.stDownloading [#################---]86.43% 8.0MB/9.3MB (11.1MB/s) aa759-149_010.Signal.Unique.stDownloading [####################]100.00% 9.3MB/9.3MB (11.3MB/s) aa759-149_010.Signal.Unique.str1.out(2).bg Done...
Downloading [####----------------]21.61% 2.0MB/9.3MB (6.8MB/s) aa759-149_010.Signal.Unique.strDownloading [#########-----------]43.21% 4.0MB/9.3MB (7.4MB/s) aa759-149_010.Signal.Unique.strDownloading [#############-------]64.82% 6.0MB/9.3MB (7.7MB/s) aa759-149_010.Signal.Unique.strDownloading [#################---]86.43% 8.0MB/9.3MB (7.8MB/s) aa759-149_010.Signal.Unique.strDownloading [####################]100.00% 9.3MB/9.3MB (8.0MB/s) aa759-149_010.Signal.Unique.str1.out(2).bg Done...
Downloading [####----------------]21.61% 2.0MB/9.3MB (8.8MB/s) aa759-149_010.Signal.Unique.strDownloading [#########-----------]43.21% 4.0MB/9.3MB (10.4MB/s) aa759-149_010.Signal.Unique.stDownloading [#############-------]64.82% 6.0MB/9.3MB (11.0MB/s) aa759-149_010.Signal.Unique.stDownloading [#################---]86.43% 8.0MB/9.3MB (11.2MB/s) aa759-149_010.Signal.Unique.stDownloading [####################]100.00% 9.3MB/9.3MB (11.5MB/s) aa759-149_010.Signal.Unique.str1.out(2).bg Done...
SynapseFileCacheError: Could not obtain a lock on the file cache within timeout: 0:01:10 Please try again later"
Created by Mette Peters Mette Hi,
I am an engineer working on the Python/Command-line client. It may take a while for us to investigate/fix the underlying bug, but I think this workaround should unblock you.
The lock on the file cache is actually just a empty folder that we create as we are writing metadata to your files cache. So the workaround is to delete all empty folders in the `.synapseCache` folder.
You can do so in Command Prompt using the following commands:
I am assuming that you did not change the location of the Synapse cache folder. If you did, please `cd` into wherever you specified the cache folder.
```
cd %userprofile%/.synapseCache
for /f "delims=" %i in ('dir /ad /s /b') do @rd "%i"
```
Source for deletion command:
https://superuser.com/questions/172981/how-can-i-recursively-delete-empty-folders my home directory is in local disk.
I rebooted computer. No improvement. Still stuck at the same loop. That would be an appropriate course of action. If you are blocked from doing other work because you cannot get these files, then I would do that.
If you are in a position to wait, I'm going to open an issue with our engineers to get better advise on how to proceed: https://sagebionetworks.jira.com/browse/SYNPY-749
One followup question: is your home directory (which is where the Synapse cache is by default) also on network attached storage? should I reboot the machine and try again? 2018-06-12 15:18:54,391 [client:390 - INFO]: Welcome, Chunyu Liu!
[####################]100.00% 1/1 Done...
Downloading [####################]100.00% 343.5kB/343.5kB (2.8MB/s) Job-6100818889103862926341806.csv Done...
Downloading [####----------------]21.61% 2.0MB/9.3MB (5.4MB/s) aa759-149_010.Signal.Unique.strDownloading [#########-----------]43.21% 4.0MB/9.3MB (6.0MB/s) aa759-149_010.Signal.Unique.strDownloading [#############-------]64.82% 6.0MB/9.3MB (6.2MB/s) aa759-149_010.Signal.Unique.strDownloading [#################---]86.43% 8.0MB/9.3MB (6.4MB/s) aa759-149_010.Signal.Unique.strDownloading [####################]100.00% 9.3MB/9.3MB (6.5MB/s) aa759-149_010.Signal.Unique.str1.out(3).bg Done...
2018-06-12 15:22:54,980 [client:1863 - DEBUG]:
Retrying download on error: [] after progressing 0 bytes
Traceback (most recent call last):
File "/usr/lib/python2.7/site-packages/synapseclient/client.py", line 1857, in _downloadFileHandle
self.cache.add(fileHandle['id'], downloaded_path)
File "/usr/lib/python2.7/site-packages/synapseclient/cache.py", line 229, in add
with Lock(self.cache_map_file_name, dir=cache_dir):
File "/usr/lib/python2.7/site-packages/synapseclient/lock.py", line 101, in __enter__
self.blocking_acquire()
File "/usr/lib/python2.7/site-packages/synapseclient/lock.py", line 87, in blocking_acquire
raise SynapseFileCacheError("Could not obtain a lock on the file cache within timeout: %s Please try again later" % str(timeout))
SynapseFileCacheError: Could not obtain a lock on the file cache within timeout: 0:01:10 Please try again later
Downloading [####----------------]21.61% 2.0MB/9.3MB (5.5MB/s) aa759-149_010.Signal.Unique.strDownloading [#########-----------]43.21% 4.0MB/9.3MB (6.2MB/s) aa759-149_010.Signal.Unique.strDownloading [#############-------]64.82% 6.0MB/9.3MB (6.5MB/s) aa759-149_010.Signal.Unique.strDownloading [#################---]86.43% 8.0MB/9.3MB (6.7MB/s) aa759-149_010.Signal.Unique.strDownloading [####################]100.00% 9.3MB/9.3MB (6.9MB/s) aa759-149_010.Signal.Unique.str1.out(3).bg Done...
2018-06-12 15:24:07,300 [client:1863 - DEBUG]:
Retrying download on error: [] after progressing 0 bytes
Traceback (most recent call last):
File "/usr/lib/python2.7/site-packages/synapseclient/client.py", line 1857, in _downloadFileHandle
self.cache.add(fileHandle['id'], downloaded_path)
File "/usr/lib/python2.7/site-packages/synapseclient/cache.py", line 229, in add
with Lock(self.cache_map_file_name, dir=cache_dir):
File "/usr/lib/python2.7/site-packages/synapseclient/lock.py", line 101, in __enter__
self.blocking_acquire()
File "/usr/lib/python2.7/site-packages/synapseclient/lock.py", line 87, in blocking_acquire
raise SynapseFileCacheError("Could not obtain a lock on the file cache within timeout: %s Please try again later" % str(timeout))
SynapseFileCacheError: Could not obtain a lock on the file cache within timeout: 0:01:10 Please try again later
Downloading [####----------------]21.61% 2.0MB/9.3MB (5.3MB/s) aa759-149_010.Signal.Unique.strDownloading [#########-----------]43.21% 4.0MB/9.3MB (6.0MB/s) aa759-149_010.Signal.Unique.strDownloading [#############-------]64.82% 6.0MB/9.3MB (6.2MB/s) aa759-149_010.Signal.Unique.strDownloading [#################---]86.43% 8.0MB/9.3MB (6.3MB/s) aa759-149_010.Signal.Unique.strDownloading [####################]100.00% 9.3MB/9.3MB (6.5MB/s) aa759-149_010.Signal.Unique.str1.out(3).bg Done...
2018-06-12 15:25:19,558 [client:1863 - DEBUG]:
Retrying download on error: [] after progressing 0 bytes
Traceback (most recent call last):
File "/usr/lib/python2.7/site-packages/synapseclient/client.py", line 1857, in _downloadFileHandle
self.cache.add(fileHandle['id'], downloaded_path)
File "/usr/lib/python2.7/site-packages/synapseclient/cache.py", line 229, in add
with Lock(self.cache_map_file_name, dir=cache_dir):
File "/usr/lib/python2.7/site-packages/synapseclient/lock.py", line 101, in __enter__
self.blocking_acquire()
File "/usr/lib/python2.7/site-packages/synapseclient/lock.py", line 87, in blocking_acquire
raise SynapseFileCacheError("Could not obtain a lock on the file cache within timeout: %s Please try again later" % str(timeout))
SynapseFileCacheError: Could not obtain a lock on the file cache within timeout: 0:01:10 Please try again later
Downloading [####----------------]21.61% 2.0MB/9.3MB (5.3MB/s) aa759-149_010.Signal.Unique.strDownloading [#########-----------]43.21% 4.0MB/9.3MB (5.5MB/s) aa759-149_010.Signal.Unique.strDownloading [#############-------]64.82% 6.0MB/9.3MB (5.8MB/s) aa759-149_010.Signal.Unique.strDownloading [#################---]86.43% 8.0MB/9.3MB (5.9MB/s) aa759-149_010.Signal.Unique.strDownloading [####################]100.00% 9.3MB/9.3MB (6.1MB/s) aa759-149_010.Signal.Unique.str1.out(3).bg Done...
Can you run your command with `--debug` to see if any additional output comes?
`"synapse --debug get -q "SELECT * FROM syn12137225 WHERE (("study"='iPSC') AND ("assay"='rnaSeq'))"` A related thread:
https://www.synapse.org/#!SynapseForum:threadId=572 I haven't seen this exactly with the download from a query, but I've seen file lock issues caused by either 1) too many open files, or 2) a time problem on the NAS. If your local system time and the time kept by the NAS server are not close, you can get errors like this. Win7.
try to download to a NAS. It downloaded 520 files, and stopped with this error. After that, I tried to re-run this command, hitting the same error again and again. Just repeating it. We've encountered things like this before - often it's a local filesystem problem.
@liucy can you provide more information on the system you are using?
1. Operating system
1. If the drive you are trying to store to is a network drive or physical drive attached to your machine?
Can you download other files with the same command?
Does it always stop at the same place?