Tomogram reconstruction error

[ntall...@gmail.com]

Trying eman tomography processing for the first time and I am encountering an issue I am having issue troubleshooting. Any direction or advice would be appreciated as it could be my installation or an issue with how my input files are formatted.

Thanks,

Nathaniel

Command:

 /usr/local/eman2/bin/e2tomogram.py --alltiltseries --tltstep=3.0 --rawtlt=/jasper/jasper2/ntalledge/HIV2/TiltSeries/HIV2ts2/micrographs/CorrImages/tomograms_stacks/HIV2ts2_01/HIV2ts2-01.rawtlt --npk=20 --tltkeep=0.9 --outsize=2k --niter=2,1,1,1 --bytile --notmp --pkkeep=0.9 --compressbits=8 --clipz=-1 --bxsz=32 --correctrot --filterto=0.45 --extrapad --rmbeadthr=-1.0 --threads=12 --patchtrack=-1 --ppid=-2

Terminal Output:

 NOT Writing notes, ppid=-2

Reading tilt series tiltseries/HIV2ts2_01.hdf...

(41, 256, 256)

Traceback (most recent call last):

  File "/usr/local/eman2/bin/e2tomogram.py", line 2117, in <module>

    main()

  File "/usr/local/eman2/bin/e2tomogram.py", line 321, in main

    ret=calc_global_trans(imgs_500, options)

  File "/usr/local/eman2/bin/e2tomogram.py", line 1186, in calc_global_trans

    ts=-np.cumsum(ts, axis=0)

  File "<__array_function__ internals>", line 6, in cumsum

  File "/usr/local/eman2/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 2423, in cumsum

    return _wrapfunc(a, 'cumsum', axis=axis, dtype=dtype, out=out)

  File "/usr/local/eman2/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 58, in _wrapfunc

    return _wrapit(obj, method, *args, **kwds)

  File "/usr/local/eman2/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 47, in _wrapit

    result = getattr(asarray(obj), method)(*args, **kwds)

ValueError: operands could not be broadcast together with shapes (2,) (131072,) 

[MuyuanChen]

What is the version of EMAN you are using? Does the program work on any of the tutorial dataset? It is useful to try at least some steps of the small tutorial to figure out whether the issue is with the format of your own data or the program itself. Also turning off —notmp may give you some temporary files that may help debugging. 

Muyuan

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