Error running task : 0

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Gábor Oroszlán

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Jul 21, 2021, 8:58:44 AM7/21/21
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Hi,
I am trying to make initial model with classes from negative stained images, and when I start the process I get this message:

NOT Writing notes, ppid=-1

Models will be 5.040 A/pix

Error running task :  0


The running task window says e2initialmodel.py is still running but I initiated it yesterday afternoon. iter 12 tries 30 (since I wanted to leave it for o/n I gave bigger number) shrink 3, sym d sym nr 2.

Does it mean there is zero error and it is still running it just takes long or 0 indicates an issue?

Thanks and Best,
Gabor

Steve Ludtke

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Jul 21, 2021, 9:07:47 AM7/21/21
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If you ever see the message "Error running task", something serious has gone wrong. If you are running with threaded parallelism you may find a file called "thread.out" containing useful error messages.
- how many class-averages did you use?
- what is the box size of the class-averages?
- what is the full command-line of the e2initialmodel command you ran?


--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)



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Gábor Oroszlán

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Jul 21, 2021, 3:07:12 PM7/21/21
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Hi Steve,
Sorry for disappearing, I did not get notification of your message. I did find thread.out, I attached it.

I have 36 class averages,
box size is 196
command:e2initialmodel.py --input=r2db_01/good_classes.hdf --iter=12 --tries=8 --shrink=3 --sym=c1 --automaskexpand=-1 --randorient --parallel=thread:4

thanks,
Gabor

Gábor Oroszlán

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Jul 21, 2021, 3:53:36 PM7/21/21
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Now I attached it for real

Gábor Oroszlán

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Jul 21, 2021, 3:55:12 PM7/21/21
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InvalidCallException at /Users/eman/miniconda3/conda-bld/eman2_1615226493600/work/libEM/aligner.cpp:2759: 'ERROR (RT2DTreeAligner): requires cubic images with even numbered box sizes' caught

InvalidCallException at /Users/eman/miniconda3/conda-bld/eman2_1615226493600/work/libEM/aligner.cpp:2759: 'ERROR (RT2DTreeAligner): requires cubic images with even numbered box sizes' caught
InvalidCallException at /Users/eman/miniconda3/conda-bld/eman2_1615226493600/work/libEM/aligner.cpp:2759: 'ERROR (RT2DTreeAligner): requires cubic images with even numbered box sizes' caught

InvalidCallException at /Users/eman/miniconda3/conda-bld/eman2_1615226493600/work/libEM/aligner.cpp:2759: 'ERROR (RT2DTreeAligner): requires cubic images with even numbered box sizes' caught


Traceback (most recent call last):
  File "/Users/gabor/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/Users/gabor/eman2-sphire-sparx/bin/e2initialmodel.py", line 224, in execute
    sim=cmponetomany(projs,ptcls[i],align=("rotate_translate_tree",{"flip":1,"maxshift":old_div(boxsize,5)}),alicmp=("ccc",{}),cmp=("ccc",{}))
  File "/Users/gabor/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2_utils.py", line 839, in cmponetomany
    ta=r[0].align(align[0],target,align[1],alicmp[0],alicmp[1])
RuntimeError: std::exception
Traceback (most recent call last):
  File "/Users/gabor/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/Users/gabor/eman2-sphire-sparx/bin/e2initialmodel.py", line 224, in execute
    sim=cmponetomany(projs,ptcls[i],align=("rotate_translate_tree",{"flip":1,"maxshift":old_div(boxsize,5)}),alicmp=("ccc",{}),cmp=("ccc",{}))
  File "/Users/gabor/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2_utils.py", line 839, in cmponetomany
    ta=r[0].align(align[0],target,align[1],alicmp[0],alicmp[1])
RuntimeError: std::exception
Traceback (most recent call last):
  File "/Users/gabor/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/Users/gabor/eman2-sphire-sparx/bin/e2initialmodel.py", line 224, in execute
    sim=cmponetomany(projs,ptcls[i],align=("rotate_translate_tree",{"flip":1,"maxshift":old_div(boxsize,5)}),alicmp=("ccc",{}),cmp=("ccc",{}))
  File "/Users/gabor/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2_utils.py", line 839, in cmponetomany
    ta=r[0].align(align[0],target,align[1],alicmp[0],alicmp[1])
RuntimeError: std::exception
Traceback (most recent call last):
  File "/Users/gabor/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/Users/gabor/eman2-sphire-sparx/bin/e2initialmodel.py", line 224, in execute
    sim=cmponetomany(projs,ptcls[i],align=("rotate_translate_tree",{"flip":1,"maxshift":old_div(boxsize,5)}),alicmp=("ccc",{}),cmp=("ccc",{}))
  File "/Users/gabor/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2_utils.py", line 839, in cmponetomany
    ta=r[0].align(align[0],target,align[1],alicmp[0],alicmp[1])
RuntimeError: std::exception
InvalidCallException at /Users/eman/miniconda3/conda-bld/eman2_1615226493600/work/libEM/aligner.cpp:2759: 'ERROR (RT2DTreeAligner): requires cubic images with even numbered box sizes' caught

Traceback (most recent call last):
  File "/Users/gabor/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/Users/gabor/eman2-sphire-sparx/bin/e2initialmodel.py", line 224, in execute
    sim=cmponetomany(projs,ptcls[i],align=("rotate_translate_tree",{"flip":1,"maxshift":old_div(boxsize,5)}),alicmp=("ccc",{}),cmp=("ccc",{}))
  File "/Users/gabor/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2_utils.py", line 839, in cmponetomany
    ta=r[0].align(align[0],target,align[1],alicmp[0],alicmp[1])
RuntimeError: std::exception
InvalidCallException at /Users/eman/miniconda3/conda-bld/eman2_1615226493600/work/libEM/aligner.cpp:2759: 'ERROR (RT2DTreeAligner): requires cubic images with even numbered box sizes' caught

Traceback (most recent call last):
  File "/Users/gabor/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/Users/gabor/eman2-sphire-sparx/bin/e2initialmodel.py", line 224, in execute
    sim=cmponetomany(projs,ptcls[i],align=("rotate_translate_tree",{"flip":1,"maxshift":old_div(boxsize,5)}),alicmp=("ccc",{}),cmp=("ccc",{}))
  File "/Users/gabor/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2_utils.py", line 839, in cmponetomany
    ta=r[0].align(align[0],target,align[1],alicmp[0],alicmp[1])
RuntimeError: std::exception
InvalidCallException at /Users/eman/miniconda3/conda-bld/eman2_1615226493600/work/libEM/aligner.cpp:2759: 'ERROR (RT2DTreeAligner): requires cubic images with even numbered box sizes' caught

InvalidCallException at /Users/eman/miniconda3/conda-bld/eman2_1615226493600/work/libEM/aligner.cpp:2759: 'ERROR (RT2DTreeAligner): requires cubic images with even numbered box sizes' caught

Traceback (most recent call last):
  File "/Users/gabor/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/Users/gabor/eman2-sphire-sparx/bin/e2initialmodel.py", line 224, in execute
    sim=cmponetomany(projs,ptcls[i],align=("rotate_translate_tree",{"flip":1,"maxshift":old_div(boxsize,5)}),alicmp=("ccc",{}),cmp=("ccc",{}))
  File "/Users/gabor/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2_utils.py", line 839, in cmponetomany
    ta=r[0].align(align[0],target,align[1],alicmp[0],alicmp[1])
RuntimeError: std::exception
Traceback (most recent call last):
  File "/Users/gabor/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/Users/gabor/eman2-sphire-sparx/bin/e2initialmodel.py", line 224, in execute
    sim=cmponetomany(projs,ptcls[i],align=("rotate_translate_tree",{"flip":1,"maxshift":old_div(boxsize,5)}),alicmp=("ccc",{}),cmp=("ccc",{}))
  File "/Users/gabor/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2_utils.py", line 839, in cmponetomany
    ta=r[0].align(align[0],target,align[1],alicmp[0],alicmp[1])
RuntimeError: std::exception
InvalidCallException at /Users/eman/miniconda3/conda-bld/eman2_1615226493600/work/libEM/aligner.cpp:2759: 'ERROR (RT2DTreeAligner): requires cubic images with even numbered box sizes' caught

Traceback (most recent call last):
  File "/Users/gabor/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/Users/gabor/eman2-sphire-sparx/bin/e2initialmodel.py", line 224, in execute
    sim=cmponetomany(projs,ptcls[i],align=("rotate_translate_tree",{"flip":1,"maxshift":old_div(boxsize,5)}),alicmp=("ccc",{}),cmp=("ccc",{}))
  File "/Users/gabor/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2_utils.py", line 839, in cmponetomany
    ta=r[0].align(align[0],target,align[1],alicmp[0],alicmp[1])
RuntimeError: std::exception
InvalidCallException at /Users/eman/miniconda3/conda-bld/eman2_1615226493600/work/libEM/aligner.cpp:2759: 'ERROR (RT2DTreeAligner): requires cubic images with even numbered box sizes' caught

Traceback (most recent call last):
  File "/Users/gabor/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/Users/gabor/eman2-sphire-sparx/bin/e2initialmodel.py", line 224, in execute
    sim=cmponetomany(projs,ptcls[i],align=("rotate_translate_tree",{"flip":1,"maxshift":old_div(boxsize,5)}),alicmp=("ccc",{}),cmp=("ccc",{}))
  File "/Users/gabor/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2_utils.py", line 839, in cmponetomany
    ta=r[0].align(align[0],target,align[1],alicmp[0],alicmp[1])
RuntimeError: std::exception
InvalidCallException at /Users/eman/miniconda3/conda-bld/eman2_1615226493600/work/libEM/aligner.cpp:2759: 'ERROR (RT2DTreeAligner): requires cubic images with even numbered box sizes' caught

Traceback (most recent call last):
  File "/Users/gabor/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/Users/gabor/eman2-sphire-sparx/bin/e2initialmodel.py", line 224, in execute
    sim=cmponetomany(projs,ptcls[i],align=("rotate_translate_tree",{"flip":1,"maxshift":old_div(boxsize,5)}),alicmp=("ccc",{}),cmp=("ccc",{}))
  File "/Users/gabor/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2_utils.py", line 839, in cmponetomany
    ta=r[0].align(align[0],target,align[1],alicmp[0],alicmp[1])
RuntimeError: std::exception
InvalidCallException at /Users/eman/miniconda3/conda-bld/eman2_1615226493600/work/libEM/aligner.cpp:2759: 'ERROR (RT2DTreeAligner): requires cubic images with even numbered box sizes' caught

Traceback (most recent call last):
  File "/Users/gabor/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
    try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
  File "/Users/gabor/eman2-sphire-sparx/bin/e2initialmodel.py", line 224, in execute
    sim=cmponetomany(projs,ptcls[i],align=("rotate_translate_tree",{"flip":1,"maxshift":old_div(boxsize,5)}),alicmp=("ccc",{}),cmp=("ccc",{}))
  File "/Users/gabor/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2_utils.py", line 839, in cmponetomany
    ta=r[0].align(align[0],target,align[1],alicmp[0],alicmp[1])
RuntimeError: std::exception

Ludtke, Steven J.

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Jul 21, 2021, 4:20:33 PM7/21/21
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Alas, 
196 is not compatible with shrink=3. The result after shrink= needs to be an even integer.

192 would work with shrink=4. For shrink=3 you need a box size which is a multiple of 6 or (better) 12. You could try shrink=2 with the existing box size, but it may take a while to run.




--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)



Gábor Oroszlán

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Jul 22, 2021, 9:25:56 AM7/22/21
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Hi Steve,

Thanks very much, I somehow missed the shrink part. 

Best,
Gabor

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