RBMC error platform_read_file: fopen: Operation not permitted (version: 4.7)

Motion Correction
1

Hi

I am trying to run RBMC on a rather old dataset of ours (initially processed before path motion correction was available on Cryosprc) and am getting the following error:

Screenshot 2026-06-04 at 11.53.57
Screenshot 2026-06-04 at 11.53.57927×645 74.8 KB

I have checked the symbolic links and the permissions to the movie files and they seem to be fine. I have tried removing the movie that Cryosprc flagged and then restart RBMC. In that case cryosparc flagged another movie and the job died. I have re-imported the movies –> rerun patch motion correction –> reassigned the particles to the new patch motion correction and then tried RBMC. However the problem persists.

Since I could not think of anything else, I manually cleared the SSD cache but still no luck.

I am using Cryosparc version 4.7.0. I was wondering if any of you have faced a similar issue or have any suggestion to figure out what might be going on.

Thanks,

Indrajit

2

Hi @Indrajit:

Please can you post the outputs of these commands:

csprojectid=P99 # replace with actual project ID
csjobid=J199 # replace with actual rbmc job id
cryosparcm joblog $csprojectid $csjobid | tail -n 40
cryosparcm cli "get_job('$csprojectid', '$csjobid', 'job_type', 'version', 'input_slot_groups.connections', 'params_spec', 'status')"
3

Here is the output.

spuser@spgpu5:/data/spgpu2_lnk/data/Users/Anamika/eBIC_bi28576-21_m02_28_04_2023/CS-ebic-bi28576-21-appol$ cryosparcm joblog $csprojectid $csjobid | tail -n 40

data type: 0x10

frames:    \[0:-1\]

eer upsample factor: 1

eer number of fractions: 40.

movie 682382087437757538: J401/imported/000682382087437757538_FoilHole_28363737_Data_28306427_28306429_20230429_060038_fractions.tif

Total: 3956.513s

  iosys:2:

             iocb processing \[hits     660\]: 0.077303s 0.00% (1791.083554s 45.27% with children)

             iosys_sort_jobs \[hits     660\]: 0.004530s 0.00%

    iosys_open_cacheable_fds \[hits     660\]: 9.854870s 0.25%

    iosys_process_cached_fd_reads \[hits     660\]: 0.020064s 0.00% (38.355984s 0.97% with children)

            io_uring fill sq \[hits     660\]: 0.838919s 0.02%

              io_uring block \[hits     660\]: 37.496299s 0.95%

           io_uring drain cq \[hits     660\]: 0.000703s 0.00%

                   slow_path \[hits     660\]: 1742.790867s 44.05%

  iosys:1:

             iocb processing \[hits     716\]: 0.149255s 0.00% (1549.867631s 39.17% with children)

             iosys_sort_jobs \[hits     717\]: 0.006034s 0.00%

    iosys_open_cacheable_fds \[hits     717\]: 15.510005s 0.39%

    iosys_process_cached_fd_reads \[hits     717\]: 0.003144s 0.00% (54.042359s 1.37% with children)

            io_uring fill sq \[hits     717\]: 1.260170s 0.03%

              io_uring block \[hits     717\]: 52.778047s 1.33%

           io_uring drain cq \[hits     717\]: 0.000998s 0.00%

                   slow_path \[hits     716\]: 1480.159978s 37.41%

  iosys:0:

             iocb processing \[hits     654\]: 0.147551s 0.00% (1814.945699s 45.87% with children)

             iosys_sort_jobs \[hits     654\]: 0.004339s 0.00%

    iosys_open_cacheable_fds \[hits     654\]: 10.461533s 0.26%

    iosys_process_cached_fd_reads \[hits     654\]: 0.002326s 0.00% (39.847742s 1.01% with children)

            io_uring fill sq \[hits     654\]: 0.797075s 0.02%

              io_uring block \[hits     654\]: 39.047629s 0.99%

           io_uring drain cq \[hits     654\]: 0.000711s 0.00%

                   slow_path \[hits     654\]: 1764.484534s 44.60%

  MAIN THREAD:

========= main process now complete at 2026-06-04 13:56:53.199024.

========= monitor process now complete at 2026-06-04 13:56:53.991904.


spuser@spgpu5:/data/spgpu2_lnk/data/Users/Anamika/eBIC_bi28576-21_m02_28_04_2023/CS-ebic-bi28576-21-appol$ cryosparcm cli "get_job('$csprojectid', '$csjobid', 'job_type', 'version', 'input_slot_groups.connections', 'params_spec', 'status')"

{'\_id': '6a181eac8800c32cbee0d66a', 'input_slot_groups': \[{'connections': \[{'group_name': 'micrographs', 'job_uid': 'J403', 'slots': \[{'group_name': 'micrographs', 'job_uid': 'J403', 'result_name': 'movie_blob', 'result_type': 'exposure.movie_blob', 'slot_name': 'movie_blob', 'version': 'F'}, {'group_name': 'micrographs', 'job_uid': 'J403', 'result_name': 'gain_ref_blob', 'result_type': 'exposure.gain_ref_blob', 'slot_name': 'gain_ref_blob', 'version': 'F'}, {'group_name': 'micrographs', 'job_uid': 'J403', 'result_name': 'mscope_params', 'result_type': 'exposure.mscope_params', 'slot_name': 'mscope_params', 'version': 'F'}, {'group_name': 'micrographs', 'job_uid': 'J403', 'result_name': 'rigid_motion', 'result_type': 'exposure.motion', 'slot_name': 'rigid_motion', 'version': 'F'}, {'group_name': 'micrographs', 'job_uid': 'J403', 'result_name': 'spline_motion', 'result_type': 'exposure.motion', 'slot_name': 'spline_motion', 'version': 'F'}, {'group_name': 'micrographs', 'job_uid': 'J403', 'result_name': 'background_blob', 'result_type': 'exposure.stat_blob', 'slot_name': 'background_blob', 'version': 'F'}, {'group_name': 'micrographs', 'job_uid': 'J403', 'result_name': 'micrograph_blob_non_dw', 'result_type': 'exposure.micrograph_blob', 'slot_name': None, 'version': 'F'}, {'group_name': 'micrographs', 'job_uid': 'J403', 'result_name': 'micrograph_blob_non_dw_AB', 'result_type': 'exposure.micrograph_blob', 'slot_name': None, 'version': 'F'}, {'group_name': 'micrographs', 'job_uid': 'J403', 'result_name': 'micrograph_thumbnail_blob_1x', 'result_type': 'exposure.thumbnail_blob', 'slot_name': None, 'version': 'F'}, {'group_name': 'micrographs', 'job_uid': 'J403', 'result_name': 'micrograph_thumbnail_blob_2x', 'result_type': 'exposure.thumbnail_blob', 'slot_name': None, 'version': 'F'}, {'group_name': 'micrographs', 'job_uid': 'J403', 'result_name': 'micrograph_blob', 'result_type': 'exposure.micrograph_blob', 'slot_name': None, 'version': 'F'}\]}\]}, {'connections': \[\]}, {'connections': \[{'group_name': 'particles', 'job_uid': 'J409', 'slots': \[{'group_name': 'particles', 'job_uid': 'J409', 'result_name': 'blob', 'result_type': 'particle.blob', 'slot_name': 'blob', 'version': 'F'}, {'group_name': 'particles', 'job_uid': 'J409', 'result_name': 'location', 'result_type': 'particle.location', 'slot_name': 'location', 'version': 'F'}, {'group_name': 'particles', 'job_uid': 'J409', 'result_name': 'alignments3D', 'result_type': 'particle.alignments3D', 'slot_name': 'alignments3D', 'version': 'F'}, {'group_name': 'particles', 'job_uid': 'J409', 'result_name': 'ctf', 'result_type': 'particle.ctf', 'slot_name': 'ctf', 'version': 'F'}, {'group_name': 'particles', 'job_uid': 'J409', 'result_name': 'alignments2D', 'result_type': 'particle.alignments2D', 'slot_name': None, 'version': 'F'}, {'group_name': 'particles', 'job_uid': 'J409', 'result_name': 'pick_stats', 'result_type': 'particle.pick_stats', 'slot_name': None, 'version': 'F'}\]}\]}, {'connections': \[{'group_name': 'volume', 'job_uid': 'J409', 'slots': \[{'group_name': 'volume', 'job_uid': 'J409', 'result_name': 'map', 'result_type': 'volume.blob', 'slot_name': 'map', 'version': 'F'}, {'group_name': 'volume', 'job_uid': 'J409', 'result_name': 'map_half_A', 'result_type': 'volume.blob', 'slot_name': 'map_half_A', 'version': 'F'}, {'group_name': 'volume', 'job_uid': 'J409', 'result_name': 'map_half_B', 'result_type': 'volume.blob', 'slot_name': 'map_half_B', 'version': 'F'}, {'group_name': 'volume', 'job_uid': 'J409', 'result_name': 'mask_refine', 'result_type': 'volume.blob', 'slot_name': 'mask_refine', 'version': 'F'}, {'group_name': 'volume', 'job_uid': 'J409', 'result_name': 'map_sharp', 'result_type': 'volume.blob', 'slot_name': None, 'version': 'F'}, {'group_name': 'volume', 'job_uid': 'J409', 'result_name': 'mask_fsc', 'result_type': 'volume.blob', 'slot_name': None, 'version': 'F'}, {'group_name': 'volume', 'job_uid': 'J409', 'result_name': 'mask_fsc_auto', 'result_type': 'volume.blob', 'slot_name': None, 'version': 'F'}, {'group_name': 'volume', 'job_uid': 'J409', 'result_name': 'precision', 'result_type': 'volume.blob', 'slot_name': None, 'version': 'F'}\]}\]}, {'connections': \[{'group_name': 'mask', 'job_uid': 'J409', 'slots': \[{'group_name': 'mask', 'job_uid': 'J409', 'result_name': 'mask_refine', 'result_type': 'volume.blob', 'slot_name': 'mask', 'version': 'F'}\]}\]}\], 'job_type': 'reference_motion_correction', 'params_spec': {}, 'project_uid': 'P14', 'status': 'failed', 'uid': 'J399', 'version': 'v4.7.0'}
4

Thanks @Indrajit. Please can you post the outputs of these commands (after correctly defining the PROJECT_DIR variable):

PROJECT_DIR="/path/to/project_dir" # edit
df -hT ${PROJECT_DIR}/
ls -lhs ${PROJECT_DIR}/J403/motioncorrected/{00877323,00068238208}*_rigid_traj.npy