Hi,
> Afterwards, downsampling and refinement was performed in Relion 3.1_beta
> Now, when I try to upscale it using a Refine3D's star file, micrographs
> and autopick coords (same as used to down-sample), it's giving me
> following error.
Why do you need "autopick coords"?
Aren't you re-extracting run_data.star from Refine3D?
Then the problem shouldn't happen.
The error you quoted often happens when you run
autopicking in an external program (e.g. Topaz) and
then manually curate the result in a ManualPick job.
Topaz and RELION manual pick might give different sets
of columns and Extract might fail. I fixed this issue
in the latest commit.
https://github.com/3dem/relion/commit/e176a91de37f8059065332f601a8d4a56eaa184d#diff-25d902c24283ab8cfbac54dfa101ad31
> If I try to do this by going back to Relion 3.0 then it gives me an
> error saying columns not recognised which might be due to 3.1_beta has
> some different formats.
> What is the way to resolve this? Shouldn't there be some conversion module ?
We don't officially support converting 3.1 files into
3.0, but you can find some information in the archive
of this mailing list.
Best regards,
Takanori Nakane
> /ERROR:/
>
> /ERROR in appending metadata tables with not the same columns!/
>
> /=== Backtrace ===/
>
> //usr/local/relion-3.1/bin/relion_preprocess_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41)
> [0x4252e1]/
>
> //usr/local/relion-3.1/bin/relion_preprocess_mpi(_ZN13MetaDataTable6appendERKS_+0x1c1)
> [0x431bb1]/
>
> //usr/local/relion-3.1/bin/relion_preprocess_mpi(_ZN13Preprocessing16joinAllStarFilesEv+0x2c0)
> [0x445d00]/
>
> //usr/local/relion-3.1/bin/relion_preprocess_mpi(_ZN16PreprocessingMpi19runExtractParticlesEv+0x1de)
> [0x45ee9e]/
>
> //usr/local/relion-3.1/bin/relion_preprocess_mpi(_ZN16PreprocessingMpi3runEv+0x12)
> [0x45f4c2]/
>
> //usr/local/relion-3.1/bin/relion_preprocess_mpi(main+0x3b) [0x41dc9b]/
>
> //lib64/libc.so.6(__libc_start_main+0xf5) [0x7f73e7cc6505]/
>
> //usr/local/relion-3.1/bin/relion_preprocess_mpi() [0x41e5cf]/
>
> /==================/
>
> /ERROR: /
>
> /ERROR in appending metadata tables with not the same columns!/
>
> /--------------------------------------------------------------------------/
>
> /MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD/
>
> /with errorcode 1./
>
> //
>
> /NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes./
>
> /You may or may not see output from other processes, depending on/
>
> /exactly when Open MPI kills them./
>
> /--------------------------------------------------------------------------/
>
> --
> /Abhisek Mondal, Ph.D./
> /Cardiovascular Research Institute
> University of California San Francisco
> 555 Mission Bay Blvd. South. Rm 482
> Dan Minor's Lab
> San Francisco, CA 94158
>
> USPS address:
> UCSF
> Abhisek Mondal, Ph.D.
> Cardiovascular Research Institute, Box 3122
> 555 Mission Bay Blvd., Floor 4
> San Francisco, CA 94143/
>
> ------------------------------------------------------------------------
>
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