biochem-fan
commented
2 years ago You are selecting a wrong STAR file.
You should select a particle STAR file from an Extract (or Subset selection) job, not AutoPick coordinate STAR files.
Open njxisang opened 2 years ago
biochem-fan
commented
2 years ago You are selecting a wrong STAR file.
You should select a particle STAR file from an Extract (or Subset selection) job, not AutoPick coordinate STAR files.
gideonfemi
commented
3 months ago I have a similar error trying to run 3D initial reference on RELION. Please see the error message below.
ERROR: BUG: cannot find name for particle...
biochem-fan
commented
3 months ago Please write your full command line (see the note.txt in the job directory).
gideonfemi
commented
3 months ago Here is it.
++++ Executing new job on Thu May 30 14:18:44 2024
++++ with the following command(s):
which relion_refine --o Class3D/job003/run --i mtf_de20_300kV.star --ref emd_1056.mrc --firstiter_cc --trust_ref_size --ini_high 60 --dont_combine_weights_via_disc --pool 3 --pad 2 --ctf --iter 25 --tau2_fudge 4 --particle_diameter 200 --K 1 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --offset_range 5 --offset_step 2 --sym C1 --norm --scale --j 1 --pipeline_control Class3D/job003/
++++
biochem-fan
commented
3 months ago --i mtf_de20_300kV.star
This confirms that you have selected a wrong input file.
See my earlier comment:
You should select a particle STAR file from an Extract (or Subset selection) job
Is this your first time running RELION? Please go through the tutorial to learn the basics.
gideonfemi
commented
3 months ago Yes, this is my first time running RELION. Does it mean I can't run only the 3D classification if I have the .star file? Is it a sequential step from the Import to Motion Correction .......? Thank you
biochem-fan
commented
3 months ago You have a wrong STAR file. Please go through the tutorial first.
When I use the relion3.13 to the InitialModel, it report: WARNING: stack_0220_2x_SumCorr_autopick.star seems to be from a previous version of Relion. Attempting conversion... You should make sure metadata in the optics group table after conversion is correct. in: /mnt/e/relion/src/jaz/io/star_converter.cpp, line 185 ERROR: BUG: cannot find name for particle... === Backtrace === /mnt/e/relion/build/bin/relion_refine(_ZN11RelionErrorC2ERKNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x7d) [0x5626ffffcd9d] /mnt/e/relion/build/bin/relion_refine(+0x47e0d) [0x5626fffb5e0d] /mnt/e/relion/build/bin/relion_refine(_ZN16ObservationModel10loadSafelyENSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS_R13MetaDataTableS5_ib+0x414) [0x5627000ad014] /mnt/e/relion/build/bin/relion_refine(_ZN10Experiment4readE8FileNamebbbbi+0x10fa) [0x5627000f3e6a] /mnt/e/relion/build/bin/relion_refine(_ZN11MlOptimiser17initialiseGeneralEi+0x3a1) [0x562700050271] /mnt/e/relion/build/bin/relion_refine(_ZN11MlOptimiser10initialiseEv+0x43) [0x562700051f23] /mnt/e/relion/build/bin/relion_refine(main+0x5b) [0x5626fffedf4b] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0x7f1717391083] /mnt/e/relion/build/bin/relion_refine(_start+0x2e) [0x5626fffeec0e]
ERROR: BUG: cannot find name for particle...
I do not know how to resolve it.