We are having the exact problem. Could anyone help us out?
Below is the content for job.log:
================= CRYOSPARCW ======= 2023-01-23 17:24:19.055707 =========
Project P9 Job J6
Master login02.rc.byu.edu Port 39002
===========================================================================
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MAINPROCESS PID 30990
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MAIN PID 30990
imports.run cryosparc_compute.jobs.jobregister
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TIFFFetchDirectory: Can not read TIFF directory count.
TIFFReadDirectory: Failed to read directory at offset 160886820.
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TIFFFetchDirectory: Can not read TIFF directory count.
TIFFReadDirectory: Failed to read directory at offset 342883700.
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TIFFFetchDirectory: Can not read TIFF directory count.
TIFFReadDirectory: Failed to read directory at offset 55908204.
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========= main process now complete.
========= monitor process now complete.
Below is the job.json:
{
"project_uid": "P9",
"uid": "J6",
"workspace_uids": [
"W1"
],
"version": "v3.3.2",
"job_type": "import_movies",
"type": "import_movies",
"deleted": false,
"run_as_user": null,
"title": "New Job J6",
"description": "Enter a description.",
"params_secs": {
"import": {
"title": "Movies",
"desc": "Metadata and raw data for movies.",
"order": 0
},
"compute_settings": {
"title": "Compute settings",
"desc": "",
"order": 1
}
},
"params_base": {
"blob_paths": {
"type": "path",
"value": null,
"title": "Movies data path",
"desc": "Absolute path, wildcard-expression (e.g. /mount/data/somewhere/*.mrcs) that will be imported. MRC (mrc, mrcs, stk) and TIFF format supported.",
"order": 0,
"section": "import",
"advanced": false,
"hidden": false,
"path_dir_allowed": false,
"path_file_allowed": true,
"path_glob_allowed": true
},
"gainref_path": {
"type": "path",
"value": null,
"title": "Gain reference path",
"desc": "Absolute path to a single gain reference for all the raw data, in MRC format. Leave blank if data is already gain-corrected.",
"order": 1,
"section": "import",
"advanced": false,
"hidden": false,
"path_dir_allowed": false,
"path_file_allowed": true,
"path_glob_allowed": false
},
"defect_path": {
"type": "path",
"value": null,
"title": "Defect file path",
"desc": "Absolute path to a defect file for all the raw data. This should be a .txt file. Leave blank if not applicable.",
"order": 2,
"section": "import",
"advanced": false,
"hidden": false,
"path_dir_allowed": false,
"path_file_allowed": true,
"path_glob_allowed": false
},
"gainref_flip_x": {
"type": "boolean",
"value": false,
"title": "Flip gain ref & defect file in X?",
"desc": "Flip gain ref and defect file left-to-right (in X axis)",
"order": 3,
"section": "import",
"advanced": false,
"hidden": false
},
"gainref_flip_y": {
"type": "boolean",
"value": false,
"title": "Flip gain ref & defect file in Y?",
"desc": "Flip gain ref and defect file top-to-bottom (in Y axis)",
"order": 4,
"section": "import",
"advanced": false,
"hidden": false
},
"gainref_rotate_num": {
"type": "number",
"value": 0,
"title": "Rotate gain ref?",
"desc": "Rotate gain ref counter-clockwise by 90 degrees this many times",
"order": 5,
"section": "import",
"advanced": false,
"hidden": false
},
"psize_A": {
"type": "number",
"value": null,
"title": "Raw pixel size (A)",
"desc": "Pixel size of the raw movie data in Angstroms",
"order": 6,
"section": "import",
"advanced": false,
"hidden": false
},
"accel_kv": {
"type": "number",
"value": null,
"title": "Accelerating Voltage (kV)",
"desc": "",
"order": 7,
"section": "import",
"advanced": false,
"hidden": false
},
"cs_mm": {
"type": "number",
"value": null,
"title": "Spherical Aberration (mm)",
"desc": "",
"order": 8,
"section": "import",
"advanced": false,
"hidden": false
},
"total_dose_e_per_A2": {
"type": "number",
"value": null,
"title": "Total exposure dose (e/A^2)",
"desc": "",
"order": 9,
"section": "import",
"advanced": false,
"hidden": false
},
"negative_stain_data": {
"type": "boolean",
"value": false,
"title": "Negative Stain Data",
"desc": "If Negative Stain Data is on, this indicates that there are light particles on dark background. If it's off, this indicates the movies have dark particles on light background (cryo-em data).",
"order": 10,
"section": "import",
"advanced": false,
"hidden": false
},
"phase_plate_data": {
"type": "boolean",
"value": false,
"title": "Phase Plate Data",
"desc": "",
"order": 11,
"section": "import",
"advanced": false,
"hidden": false
},
"override_exp_group_id": {
"type": "number",
"value": null,
"title": "Override Exposure Group ID",
"desc": "",
"order": 12,
"section": "import",
"advanced": false,
"hidden": false
},
"skip_header_check": {
"type": "boolean",
"value": false,
"title": "Skip Header Check",
"desc": "Skip reading of every header file to increase import speed. WARNING: this assumes exposure shapes and extensions are consistent across the entire dataset.",
"order": 13,
"section": "import",
"advanced": false,
"hidden": false
},
"eer_num_fractions": {
"type": "number",
"value": 40,
"title": "EER Number of Fractions",
"desc": "Number of fractions to make out of the EER input data.",
"order": 14,
"section": "import",
"advanced": false,
"hidden": false
},
"eer_upsamp_factor": {
"type": "number",
"value": 2,
"title": "EER Upsampling Factor",
"desc": "Upsampling factor when decoding EER input data. Note that the pixel size you provide should be the raw pixel size at the nominal 4k sensor, not the pixel size after EER upsampling. ",
"order": 15,
"section": "import",
"advanced": false,
"hidden": false
},
"compute_num_cpus": {
"type": "number",
"value": 4,
"title": "Number of CPUs to parallelize",
"desc": "Use this many CPUs to read headers in parallel",
"order": 16,
"section": "compute_settings",
"advanced": false,
"hidden": false
}
},
"params_spec": {
"blob_paths": {
"value": "/home/pgajjar/compute/P25/1st/tif/*.tif"
},
"psize_A": {
"value": 0.3115
},
"accel_kv": {
"value": 300
},
"cs_mm": {
"value": 2.7
},
"total_dose_e_per_A2": {
"value": 50
}
},
"input_slot_groups": [],
"output_result_groups": [
{
"uid": "J6-G0",
"type": "exposure",
"name": "imported_movies",
"title": "Imported movies",
"description": "Imported movies.",
"contains": [
{
"uid": "J6-R0",
"type": "exposure.movie_blob",
"group_name": "imported_movies",
"name": "movie_blob",
"passthrough": false
},
{
"uid": "J6-R1",
"type": "exposure.mscope_params",
"group_name": "imported_movies",
"name": "mscope_params",
"passthrough": false
}
],
"passthrough": false,
"num_items": 0,
"summary": {}
},
{
"uid": "J6-G1",
"type": "exposure",
"name": "failed_movies",
"title": "Failed movies",
"description": "Movies that failed to import successfully.",
"contains": [
{
"uid": "J6-R2",
"type": "exposure.movie_blob",
"group_name": "failed_movies",
"name": "movie_blob",
"passthrough": false
}
],
"passthrough": false,
"num_items": 0,
"summary": {}
}
],
"output_results": [
{
"uid": "J6-R0",
"type": "exposure.movie_blob",
"group_name": "imported_movies",
"name": "movie_blob",
"title": "Raw movie data",
"description": "",
"min_fields": [
[
"path",
"O"
],
[
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"3u4"
],
[
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"f4"
],
[
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"u4"
],
[
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"O"
],
[
"has_defect_file",
"u4"
],
[
"import_sig",
"u8"
]
],
"versions": [],
"metafiles": [],
"num_items": [],
"passthrough": false
},
{
"uid": "J6-R1",
"type": "exposure.mscope_params",
"group_name": "imported_movies",
"name": "mscope_params",
"title": "Exposure parameters",
"description": "",
"min_fields": [
[
"accel_kv",
"f4"
],
[
"cs_mm",
"f4"
],
[
"total_dose_e_per_A2",
"f4"
],
[
"phase_plate",
"u4"
],
[
"neg_stain",
"u4"
],
[
"exp_group_id",
"u4"
],
[
"defect_path",
"O"
]
],
"versions": [],
"metafiles": [],
"num_items": [],
"passthrough": false
},
{
"uid": "J6-R2",
"type": "exposure.movie_blob",
"group_name": "failed_movies",
"name": "movie_blob",
"title": "Raw movie data",
"description": "",
"min_fields": [
[
"path",
"O"
],
[
"shape",
"3u4"
],
[
"psize_A",
"f4"
],
[
"is_gain_corrected",
"u4"
],
[
"format",
"O"
],
[
"has_defect_file",
"u4"
],
[
"import_sig",
"u8"
]
],
"versions": [],
"metafiles": [],
"num_items": [],
"passthrough": false
}
],
"output_group_images": {},
"ui_tile_images": [],
"errors_build_params": {},
"errors_build_inputs": {},
"errors_run": [],
"status": "building",
"created_at": {
"$date": 1674519851284
},
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"running_at": null,
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"heartbeat_at": null,
"token_acquired_at": null,
"tokens_requested_at": null,
"last_scheduled_at": null,
"last_accessed": {},
"priority": 0,
"resources_needed": {},
"resources_allocated": {},
"run_on_master_direct": true,
"queued_to_lane": "",
"queue_index": null,
"queue_status": null,
"queue_message": null,
"queued_job_hash": null,
"interactive": false,
"interactive_hostname": "",
"interactive_port": null,
"PID_monitor": null,
"PID_main": null,
"PID_workers": [],
"cluster_job_id": null,
"parents": [],
"children": [],
"created_by_user_id": "62b098d7ca3f1f8c02f197b7",
"created_by_job_uid": null,
"cloned_from": "J3",
"is_experiment": false,
"job_dir": "J6",
"job_dir_size": 0,
"experiment_worker_path": null,
"ui_tile_width": 3,
"ui_tile_height": 1,
"enable_bench": false,
"bench": {},
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"instance_information": {},
"project_uid_num": 9,
"uid_num": 6,
"last_exported": {
"$date": 1674519851304
},
"ui_layouts": {}