Hi all,
I am running star.py to generate a new star file from cryosparc 3D particles and original extracted particles from Relion. It worked fine for the first dataset but I keep running into the following error with my second dataset.
/programs/x86_64-linux/pyem/20210211/pyem_extlib/pyem-20210211-gqx7/pyem/star.py:536: FutureWarning: Columnar iteration over characters will be deprecated in future releases.
df[UCSF.IMAGE_INDEX], df[UCSF.IMAGE_PATH] =
/programs/x86_64-linux/pyem/20210211/pyem_extlib/pyem-20210211-gqx7/pyem/star.py:544: FutureWarning: Columnar iteration over characters will be deprecated in future releases.
df[UCSF.IMAGE_ORIGINAL_INDEX], df[UCSF.IMAGE_ORIGINAL_PATH] =
Traceback (most recent call last):
File “/programs/x86_64-linux/pyem/20210211/pyem/star.py”, line 367, in
sys.exit(main(parser.parse_args()))
File “/programs/x86_64-linux/pyem/20210211/pyem/star.py”, line 149, in main
df = star.smart_merge(df, coord_star, fields=star.Relion.MICROGRAPH_COORDS, key=args.merge_key)
File “/programs/x86_64-linux/pyem/20210211/pyem_extlib/pyem-20210211-gqx7/pyem/star.py”, line 146, in smart_merge
s2 = s2.set_index(key, drop=False)
File “/programs/x86_64-linux/pyem/20210211/pyem_extlib/miniconda3-4.8.2-b5qb/lib/python3.8/site-packages/pandas/core/frame.py”, line 4555, in set_index
raise KeyError(f"None of {missing} are in the columns")
KeyError: ‘None of [None] are in the columns’
I assume it has something to do with smart merging. Attached below are the first few lines form the original star file (Relion particle extraction job) and the 3D refinement star file (cryosparc 3D refinement)
Original star file
opticsGroup1 1 0.440000 200.000000 2.700000 0.100000 1.760000 256 2
version 30001
data_particles
loop_
_rlnCoordinateX #1
_rlnCoordinateY #2
_rlnImageName #3
_rlnMicrographName #4
_rlnOpticsGroup #5
_rlnCtfMaxResolution #6
_rlnCtfFigureOfMerit #7
_rlnDefocusU #8
_rlnDefocusV #9
_rlnDefocusAngle #10
_rlnCtfBfactor #11
_rlnCtfScalefactor #12
_rlnPhaseShift #13
4127.000000 3813.000000 000001@Extract/job028/Movies1/Mouse_Ran_0001_Apr28.mrcs MotionCorr/job009/Movies1/Mouse_Ran_0001_Apr28.mrc 1 9.550302 0.069100 13129.773438 12800.386719 4.298743 0.000000 1.000000 0.000000
3229.000000 3619.000000 000002@Extract/job028/Movies1/Mouse_Ran_0001_Apr28.mrcs MotionCorr/job009/Movies1/Mouse_Ran_0001_Apr28.mrc 1 9.550302 0.069100 13129.773438 12800.386719 4.298743 0.000000 1.000000 0.000000
4701.000000 3618.000000 000003@Extract/job028/Movies1/Mouse_Ran_0001_Apr28.mrcs MotionCorr/job009/Movies1/Mouse_Ran_0001_Apr28.mrc 1 9.550302 0.069100 13129.773438 12800.386719 4.298743 0.000000 1.000000 0.000000
cryosparc star file (corrected for path)
data_optics
loop_
_rlnVoltage #1
_rlnSphericalAberration #2
_rlnAmplitudeContrast #3
_rlnOpticsGroup #4
_rlnImageSize #5
_rlnImagePixelSize #6
_rlnImageDimensionality #7
200.000000 2.700000 0.100000 2 256 1.760000 2
data_particles
loop_
_rlnImageName #1
_rlnAngleRot #2
_rlnAngleTilt #3
_rlnAnglePsi #4
_rlnOriginXAngst #5
_rlnOriginYAngst #6
_rlnDefocusU #7
_rlnDefocusV #8
_rlnDefocusAngle #9
_rlnPhaseShift #10
_rlnCtfBfactor #11
_rlnOpticsGroup #12
_rlnRandomSubset #13
_rlnClassNumber #14
000023@Extract/job028/Movies1/Mouse_Ran_0007_Apr28.mrcs -12.142051 49.854980 -39.672478 45.688500 -4.504500 19436.955078 17484.806641 5.979735 0.000000 0.000000 2 1 1
000030@Extract/job028/Movies1/Mouse_Ran_0008_Apr28.mrcs -7.319140 157.622406 -164.040695 -1.644500 -43.686499 17727.222656 16971.269531 16.456701 0.000000 0.000000 2 2 1
000037@Extract/job028/Movies1/Mouse_Ran_0012_Apr28.mrcs 127.329735 91.092255 -21.489674 20.949500 -10.653500 20354.275391 19938.802734 -29.649731 0.000000 0.000000 2 1 1
000008@Extract/job028/Movies1/Mouse_Ran_0017_Apr28.mrcs 117.662704 72.517395 -3.220111 -21.664500 -17.374500 18412.326172 17959.712891 14.052449 0.000000 0.000000 2 2 1
000032@Extract/job028/Movies1/Mouse_Ran_0023_Apr28.mrcs 104.336433 93.033707 43.894417 41.112500 -31.388501 18076.320312 17500.007812 13.061128 0.000000 0.000000 2 1 1
000004@Extract/job028/Movies1/Mouse_Ran_0032_Apr28.mrcs 30.459883 153.108765 -104.875526 -35.392500 16.659500 23033.207031 22183.183594 18.947712 0.000000 0.000000 2 2 1
Has anyone run into similar problem. Any suggestions to fix tis is highly appreciated.
Thanks
Abhilash.