... Time stamp: 11may04z17 ... Function name: sortJunkStack ... Appion directory: /leginon/appion/lib !!! WARNING: There is more than one appion directory in your PYTHONPATH !!! WARNING: There is more than one leginon directory in your PYTHONPATH !!! WARNING: Using split database Connected to database: 'ap16' ... Committing data to database ... Run directory: /leginon/rawimage/Titan/appion/feisun/11apr19f/stacks/sortjunk1 !!! WARNING: directory '/leginon/rawimage/Titan/appion/feisun/11apr19f/stacks/sortjunk1' already exists. ... Writing function log to: sortJunkStack.log ... Found 24 processors on this machine ... Running Appion version '2.1.3' ... Getting stack data for stackid=3 Old stack info: 'start image' Breaking up spider stack into single files, this can take a while ... processStack: Free memory: 34.9 GB ... processStack: Box size: 128 ... processStack: Memory used per part: 64.0 kB ... processStack: Max particles in memory: 571138 ... processStack: Particles allowed in memory: 28556 ... processStack: Number of particles in stack: 10034 ... processStack: Particle loop num chunks: 1 ... processStack: Particle loop step size: 10034 ... processStack: Splitting 10034 particles into 4 folders with 3344 particles per folder ... processStack: partnum 1 to 3344 of 10034 ... processStack: partnum 3345 to 6688 of 10034, 15.5 sec remain ... processStack: partnum 6689 to 10032 of 10034, 7.44 sec remain ... processStack: partnum 10033 to 10034 of 10034, 4.28 msec remain ... processStack: finished processing stack in 21.86 sec xmipp_sort_by_statistics -i partlist.doc WARNING: ** You are using an old file format (SELFILE) which is going to be deprecated in next Xmipp release ** Processing training set ... 0000/???? sec. ------------------------------------------------------------ 0/ 0 sec. 1/ 30 sec. . 1/ 20 sec. .. 1/ 15 sec. ... 1/ 12 sec. .... 2/ 20 sec. ..... 2/ 17 sec. ...... 2/ 15 sec. ....... 2/ 13 sec. ........ 3/ 18 sec. ......... 3/ 16 sec. .......... 3/ 15 sec. ........... 3/ 13 sec. ............ 4/ 17 sec. ............. 4/ 16 sec. .............. 4/ 15 sec. ............... 4/ 14 sec. ................ 5/ 16 sec. ................. 5/ 15 sec. .................. 5/ 15 sec. ................... 5/ 14 sec. .................... 6/ 16 sec. ..................... 6/ 15 sec. ...................... 6/ 15 sec. ....................... 6/ 14 sec. ........................ 7/ 16 sec. ......................... 7/ 15 sec. .......................... 7/ 15 sec. ........................... 7/ 14 sec. ............................ 8/ 16 sec. ............................. 8/ 15 sec. .............................. 8/ 15 sec. ............................... 9/ 16 sec. ................................ 9/ 15 sec. ................................. 9/ 15 sec. .................................. 9/ 15 sec. ................................... 10/ 16 sec. .................................... 10/ 15 sec. ..................................... 10/ 15 sec. ...................................... 10/ 15 sec. ....................................... 11/ 16 sec. ........................................ 11/ 15 sec. ......................................... 11/ 15 sec. .......................................... 11/ 15 sec. ........................................... 12/ 16 sec. ............................................ 12/ 15 sec. ............................................. 12/ 15 sec. .............................................. 12/ 15 sec. ............................................... 13/ 15 sec. ................................................ 13/ 15 sec. ................................................. 13/ 15 sec. .................................................. 13/ 15 sec. ................................................... 14/ 15 sec. .................................................... 14/ 15 sec. ..................................................... 14/ 15 sec. ...................................................... 14/ 15 sec. ....................................................... 15/ 15 sec. ........................................................ 15/ 15 sec. ......................................................... 15/ 15 sec. .......................................................... 15/ 15 sec. ........................................................... 15/ 15 sec. ............................................................ Sorting particle set ... 0000/???? sec. ------------------------------------------------------------ 0/ 0 sec. 0/ 0 sec. . 0/ 0 sec. .. 0/ 0 sec. ... 0/ 0 sec. .... 0/ 0 sec. ..... 0/ 0 sec. ...... 0/ 0 sec. ....... 0/ 0 sec. ........ 0/ 0 sec. ......... 0/ 0 sec. .......... 0/ 0 sec. ........... 0/ 0 sec. ............ 0/ 0 sec. ............. 0/ 0 sec. .............. 0/ 0 sec. ............... 0/ 0 sec. ................ 0/ 0 sec. ................. 0/ 0 sec. .................. 0/ 0 sec. ................... 0/ 0 sec. .................... 0/ 0 sec. ..................... 0/ 0 sec. ...................... 0/ 0 sec. ....................... 0/ 0 sec. ........................ 0/ 0 sec. ......................... 0/ 0 sec. .......................... 0/ 0 sec. ........................... 0/ 0 sec. ............................ 0/ 0 sec. ............................. 0/ 0 sec. .............................. 0/ 0 sec. ............................... 0/ 0 sec. ................................ 0/ 0 sec. ................................. 0/ 0 sec. .................................. 0/ 0 sec. ................................... 0/ 0 sec. .................................... 0/ 0 sec. ..................................... 0/ 0 sec. ...................................... 0/ 0 sec. ....................................... 0/ 0 sec. ........................................ 0/ 0 sec. ......................................... 0/ 0 sec. .......................................... 0/ 0 sec. ........................................... 0/ 0 sec. ............................................ 0/ 0 sec. ............................................. 0/ 0 sec. .............................................. 0/ 0 sec. ............................................... 0/ 0 sec. ................................................ 0/ 0 sec. ................................................. 0/ 0 sec. .................................................. 0/ 0 sec. ................................................... 0/ 0 sec. .................................................... 0/ 0 sec. ..................................................... 0/ 0 sec. ...................................................... 0/ 0 sec. ....................................................... 0/ 0 sec. ........................................................ 0/ 0 sec. ......................................................... 0/ 0 sec. .......................................................... 0/ 0 sec. ........................................................... 0/ 0 sec. ............................................................ Merging files into a stack, this can take a while ... Using 4096 particle per iteration ......................................... ... writing single particles to file /public/appion/feisun/11apr19f/stacks/sortjunk1/sorted-4096.hed ['/leginon/appion/lib', '/leginon/appion/3rPackage/EMAN1.9/bin', '/leginon/appion/3rPackage/EMAN1.9/lib'] ['/leginon/appion/lib', '/leginon/appion/3rPackage/EMAN1.9/bin', '/leginon/appion/3rPackage/EMAN1.9/lib'] Traceback (most recent call last): File "/leginon/appion/bin/sortJunkStack.py", line 153, in ? sortJunk.start() File "/leginon/appion/bin/sortJunkStack.py", line 59, in start apXmipp.gatherSingleFilesIntoStack("sort_junk.sel","sorted.hed") File "/leginon/appion/lib/appionlib/apXmipp.py", line 193, in gatherSingleFilesIntoStack apImagicFile.writeImagic(stackarray, stackname, msg=False) File "/leginon/appion/lib/appionlib/apImagicFile.py", line 250, in writeImagic shape = part.shape AttributeError: 'NoneType' object has no attribute 'shape'