Bug #3566
closedError making substacks in Appion
0%
Description
User Yihu Xie having trouble making substacks in Appion.
Job completed in Appion, but did not show up. Tried in command line with the following results:
[yxie@emgbox02 ~]$ /opt/myamisnap/bin/appion alignSubStack.py --description="open" --class-list-keep=5,18,11 --cluster-id=5 --max-shift=5 --write-file --commit --rundir=/emg/data00/appion/yxie/15sep11a/stacks/clustersub5d --runname=clustersub5d --projectid=47 --expid=684 --jobtype=makestack
... Time stamp: 15sep16q26
... Function name: alignSubStack
... Appion directory: /emg/sw/packages/myamisnap/appion
... Using split database
Connected to database: 'nyap_47'
... Committing data to database
... Run directory: /emg/data00/appion/yxie/15sep11a/stacks/clustersub5d
... Writing function log to: alignSubStack.log
... Uploading ScriptData....
... Found 4 processors on this machine
... Running Appion version 'trunk-r19165'
... Getting stack data for stackid=2
Old stack info: '1.5x box size?'
... Exclude list: []
... Include list: [5, 18, 11]
... Querying database for particles
... Completed in 0.51 sec... Parsing particle information
Traceback (most recent call last):
File "/emg/sw/packages/myamisnap/appion/bin/alignSubStack.py", line 293, in <module>
subStack.start()
File "/emg/sw/packages/myamisnap/appion/bin/alignSubStack.py", line 185, in start
shift = math.hypot(alignpart['xshift'], alignpart['yshift'])
File "/emg/sw/packages/myamisnap/appion/bin/alignSubStack.py", line 12, in <module>
from appionlib import appionScript
ImportError: No module named appionlib
TypeError: a float is required
/emg/sw/packages/myamisnap/appion/bin/alignSubStack.py
Traceback (most recent call last):
Updated by Anchi Cheng over 9 years ago
The error I got in repeating the command does not have the part about import error which is strange to see. The actual error is
File "/emg/sw/packages/myamisnap/bin/alignSubStack.py", line 185, in start
shift = math.hypot(alignpart['xshift'], alignpart['yshift'])
TypeError: a float is required
Updated by Anchi Cheng over 9 years ago
- Project changed from 138 to Appion
- Status changed from New to In Test
- Assignee set to Ed Eng
- Affected Version set to Appion/Leginon 3.2
This is caused by the unfortunate fact that cl2d does not output alignment parameters. Therefore, maximum shift and minimum score options can not be used to limit particles in the stack.
Yihu will have to avoid putting numbers to either options.
r19172, r19173, r19174 blocks users from using them.
Ed, please close the issue if no more related problem.