Appion

Moved data to /gpfs and Anchi updated database. Still not working. Running Maximum Liklihood manually after qsub -I:

[rice@guppy-19 ~]$ /opt/myamisnap/bin/appion maxlikeAlignment.py --description="maxlike 13244 stack 39" --stack=39 --lowpass=10 --highpass=2000 --num-part=13244 --num-ref=30 --bin=3 --angle-interval=5 --max-iter=15 --nproc=8 --fast --fast-mode=normal --mirror --savemem --commit --converge=normal --rundir=/gpfs/appion/rice/15sep24a/align/wjrmaxlike10 --runname=wjrmaxlike10 --projectid=33 --expid=755 --jobtype=partalign
Error:  image path is not writable: /emg/data00/leginon

 ... Time stamp: 15nov11j22
 ... Function name: maxlikeAlignment
 ... Appion directory: /opt/myamisnap/lib
 ... Using split database
Connected to database: 'nyap_33'
 ... Committing data to database
 ... Querying original particles from stackid=39
connecting
 ... Getting stack data for stackid=39
Old stack info: 'wjr further removal after serden som of xmipp max liklihood number 8  ... 13244 particle substack with 54,55,57,94,93,92,91,83,82,74,52,53,9,64,65,66,67 classes excluded'
 ... Run directory: /gpfs/appion/rice/15sep24a/align/wjrmaxlike10
!!! WARNING: directory '/gpfs/appion/rice/15sep24a/align/wjrmaxlike10' already exists.
 ... Writing function log to: maxlikeAlignment.log
 ... Uploading ScriptData....
 ... Found 1 processors on this machine
 ... Running Appion version 'myami-3.2'
self.params['maxlikejobid'] 20
 ... Getting stack data for stackid=39
Old stack info: 'wjr further removal after serden som of xmipp max liklihood number 8  ... 13244 particle substack with 54,55,57,94,93,92,91,83,82,74,52,53,9,64,65,66,67 classes excluded'
 ... Stack 39 pixel size: 1.47
 ... Getting stack data for stackid=39
Old stack info: 'wjr further removal after serden som of xmipp max liklihood number 8  ... 13244 particle substack with 54,55,57,94,93,92,91,83,82,74,52,53,9,64,65,66,67 classes excluded'
Estimated first iteration time: 2 hr 43 min
Traceback (most recent call last):
  File "/opt/myamisnap/bin/maxlikeAlignment.py", line 498, in <module>
    maxLike.start()
  File "/opt/myamisnap/bin/maxlikeAlignment.py", line 418, in start
    a.run()
  File "/opt/myamisnap/lib/appionlib/proc2dLib.py", line 45, in run
    self.approc2d.checkConflicts()
  File "/opt/myamisnap/lib/appionlib/proc2dLib.py", line 112, in checkConflicts
    self.inputNumParticles = self.inheader['nz']
TypeError: 'NoneType' object is unsubscriptable

I didn't look closely enough at Anchi's changes in r19115, it screwed up the recursive search. I fixed it now in r19338, this should be working again. Please try.

Can this be closed ?