Failed makestack in Appion

From Michael Derby who ran the following Appion script

makestack2.py --single=start.hed --selectionid=1 --no-invert --normalized --phaseflip --flip-type=ace2image --boxsize=112 --description="test" --projectid=3 --preset=upload --session=12may25z --runname=stack2 --rundir=/myamiImages/appion/12may25z/stacks/stack2 --no-rejects --no-wait --commit --continue

And did not got a successful stack made. Looking at standard output from the script is directly pasted into the terminal (would be in his /myamiImages/appion/12may25z/stacks/stack2/stack2.appionsub.log if submitted through Torque/PBS) got the Error log

Beginning Main Loop

Starting image 1 ( skip:0, remain:19 ) id:2, file: 12may25z_10-F7_01
 ... Pixel size: 1.57
 ... Found 117 particles
 ... Best CTF run info: runname='acetwo2', confidence=0.967, defocus=-1.711 um
 ... using ctfvaluesfile: /myamiImages/appion/12may25z/ctf/acetwo2/12may25z_10-F7_01.mrc.ctf.txt
 ... ace2 command: /usr/ace2correct.exe -ctf /myamiImages/appion/12may25z/ctf/acetwo2/12may25z_10-F7_01.mrc.ctf.txt -apix 1.570 -img /myamiImages/leginon/12may25z/rawdata/12may25z_10-F7_01.mrc -wiener 0.1 -out /myamiImages/appion/12may25z/stacks/stack2/12may25z_10-F7_01.mrc.corrected.mrc
 ... phaseflipping entire micrograph with defocus -1.617 microns
 ... boxing 117 particles into temp file: /myamiImages/appion/12may25z/stacks/stack2/12may25z_10-F7_01.hed
EMAN: batchboxer input=/myamiImages/appion/12may25z/stacks/stack2/12may25z_10-F7_01.mrc.corrected.mrc dbbox=/myamiImages/appion/12may25z/stacks/stack2/12may25z_10-F7_01.box output=/myamiImages/appion/12may25z/stacks/stack2/12may25z_10-F7_01.hed newsize=112
batchboxer: error while loading shared libraries: libEM.so: cannot open shared object file: No such file or directory
!!! WARNING: EMAN failed with subprocess error code 127

This results in crashing of Appion script

 ... reading stack from disk into memory: 12may25z_10-F7_01.hed
Traceback (most recent call last):
  File "/usr/makestack2.py", line 1145, in ?
    makeStack.run()
  File "/usr/lib/python2.4/site-packages/appionlib/appionLoop2.py", line 70, in run
    results = self.loopProcessImage(imgdata)
  File "/usr/lib/python2.4/site-packages/appionlib/appionLoop2.py", line 116, in loopProcessImage
    return self.processImage(imgdata)
  File "/usr/makestack2.py", line 1034, in processImage
    self.boxedpartdatas, self.imgstackfile, self.partmeantree = self.boxParticlesFromImage(imgdata)
  File "/usr/makestack2.py", line 256, in boxParticlesFromImage
    imagicdata = apImagicFile.readImagic(imgstackfile)
  File "/usr/lib/python2.4/site-packages/appionlib/apImagicFile.py", line 134, in readImagic
    headerdict = readImagicHeader(headerfilename)
  File "/usr/lib/python2.4/site-packages/appionlib/apImagicFile.py", line 164, in readImagicHeader
    headfile=open(headerfilename,'rb')
IOError: [Errno 2] No such file or directory: '/myamiImages/appion/12may25z/stacks/stack2/12may25z_10-F7_01.hed'

Replies (1)

RE: Failed makestack in Appion - Added by Anchi Cheng over 12 years ago

Derby,

It appears that EMAN's library is not in the path for EMAN batchboxer to run. It needs to be in LD_LIBRARY_PATH environment variable.

As a short test, you can copy just the command that runs the EMAN boxer as a test like this to launch batchboxer for this particular image:

batchboxer input=/myamiImages/appion/12may25z/stacks/stack2/12may25z_10-F7_01.mrc.corrected.mrc dbbox=/myamiImages/appion/12may25z/stacks/stack2/12may25z_10-F7_01.box output=/myamiImages/appion/12may25z/stacks/stack2/12may25z_10-F7_01.hed newsize=112

batchboxer append results to the output file. Once you are successful, if you want to run the appion script again, make sure that you clean up the two outputs before you try it:

/myamiImages/appion/12may25z/stacks/stack2/12may25z_10-F7_01.hed
/myamiImages/appion/12may25z/stacks/stack2/12may25z_10-F7_01.img

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