Re: [scipion-users] GCTF -- black psdFile column

[Grigory S. <sha...@gm...>]

Hello Dmitry,

looking at the output, GCTF has failed to run. Most often this happens due
to incompatibility of the binary you used and cuda  / gpu cc version.

Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228 <+44%201223%20267228>
e-mail: gs...@mr...


On Thu, May 28, 2020 at 9:22 PM Dmitry A. Semchonok <sem...@gm...>
wrote:

> Dear colleagues,
>
>
>
> During testing the new hardware/software, we have one more issue –
>
> The gCTF results in the black frames output for the psdFile column.
>
>
> Could you please suggest the solution?
>
>
> Thank you
>
>
> Sincerely,
>
> Dmitry
>
>
>
>
> runstdout
>
> ………………………
>
> All 1 files to be searched and refined:
>
> 04024:
> Runs/003956_ProtGctf/tmp/mic_0024/20170629_00049_frameImage_aligned_mic.mrc
>
> 04025:   Warning in function gctf_open_sumlog(), file src/ctf.cu on line
> 2965:No output ctfstar file! You may have to extract CTF information from
> *_gctf.log!
>
> 04026:
> >>>>>>TIME<<<<<<
> PREPARATION: 0.363971s
>
> 04027:   Reading file:
> Runs/003956_ProtGctf/tmp/mic_0024/20170629_00049_frameImage_aligned_mic.mrc
>
> 04028:
> >>>>>>TIME<<<<<<
> READING: 0.031053s
>
> 04029:   .
>
> 04030:   >>>>>>TIME<<<<<<
>                                              FFT: 1.224681s
>
> 04031:
>
> 04032:      Defocus_U   Defocus_V       Angle          CCC
>
> 04033:        2450.00     2550.00       27.18        -nan  Final Values
>
> 04034:
>
> 04035:   >>>>>>TIME<<<<<<
>                                         1S2R: 0.003816s
>
> 04036:   Resolution limit estimated by EPA:  1.916
>
> 04037:   Estimated Bfactor:  -0.00
>
> 04038:
> >>>>>>TIME<<<<<<                                                    LOCAL
> REFINE: 0.000000s
>
> 04039:
> >>>>>>TIME<<<<<<                                                      PHASE
> FLIP: 0.000000s
>
> 04040:   Processing done successfully.
>
> 04041:
> -------------------------------------------------------------------------------------------------------------------------------
>
> 04042:
>
> 04043:   FINISHED: estimateCtfStep, step 24
>
> 04044:     2020-05-28 22:13:10.064454
>
> 04045:   STARTED: createOutputStep, step 25
>
> 04046:     2020-05-28 22:13:10.094255
>
> 04047:   FINISHED: createOutputStep, step 25
>
> 04048:     2020-05-28 22:13:10.095781
>
> 04049:   *** Last status is finished
>
> 04050:   Cleaning temp folder....
>
> 04051:   ------------------- PROTOCOL FINISHED
>
>
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