TranSPHIRE outputs¶
TranSPHIRE output folder structure¶
The TranSPHIRE output directory looks like this
TranSPHIRE output folders¶
| Output folder | Content |
|---|---|
| Projects | Folder that contains all TranSPHIRE projects. This folder is provided within the TranSPHIRE GUI. |
| Project directory X | TranSPHIRE project directory. Every project is created with the provided Project name. — Every path of the major output files is stored relative to this directory. Therefore it is recommended to use this folder as a project directory for further processing so that problems with for example particle polishing can be avoided. |
| TranSPHIRE_results | Folder containing the actual TranSPHIRE results. |
| 000_Import | Folder containing the incoming movies. If the incoming movies are already tiff files the files will remain in this folder. |
| 000_Import_meta | Folder containing the meta data that comes with the data. This includes xml, jpg, and spot overview mrc files. |
| 000_Session_meta | Folder containing the meta data that is created by the data aquisition software, but is not the meta data for an acquired image but present. in the specified directory. |
| 001_{COMPRESS_NAME} | Folder containing the compressed movies. — If the incoming movies are already tiff files or no compression is specified, the movies remain in the 000_Import folder. The COMPRESS_NAME depends on the specified compression method. |
| 002_{MOTION_NAME} | Folder containing the results of motion correction. — In addition to the outputs produced by the chosen program, TranSPHIRE also creates _meta.star files that can be used to run particle polishing in RELION. The MOTION_NAME depends on the specified motion correction program and version. |
| 003_{CTF_NAME} | Folder containing the results of the CTF estimation. The CTF_NAME depends on the specified ctf estimaion program and version. |
| 004_{PICKING_NAME} | Folder containing the results of the particle picking job. The PICKING_NAME depends on the specified particle picking program and version. |
| 005_{EXTRACT_NAME} | Folder containing the results of particle extraction. The EXTRACT_NAME depends on the specified particle extraction program and version. |
| 006_{2D_CLASSIFICATION_NAME} | Folder containing the results of 2D classification. The 2D_CLASSIFICATION_NAME depends on the specified 2d classification program and version. |
| 007_{2D_CLASS_SELECTION_NAME} | Folder containing the results of 2D class selection. The 2D_CLASS_SELECTION_NAME depends on the specified 2d class selection program and version. |
| 009_{3D_NAME} | Folder containing the results of 3D ab-initio reconstructon and 3D refinement. The 3D_NAME depends on the specified 3D program and version. |
| 000_Feedback_results | Folder containing the results of the feedback loop. — Every feedback round has its own output folder indicated by a _feedback_XX suffix. The XX stands for the respective feedback iteration. Results produced outside the feedback loop will be stored in its respective folders outside the 000_Feedback_results folder. |
| 008_{RETRAIN_NAME}_feedback_XX | Folder containing the results of the training of the used picking model. This folder is only present in the 000_Feedback_results folder. The RETRAIN_NAME depends on the specified retrain program and version. |
| XXX_Error_files | Folder containing the error files of the TranSPHIRE run. |
| XXX_Log_files | Folder containing the log files of the — TranSPHIRE run. Log information like the current feedback loop iteration, the current picking threshold and last used file numbers are stored. |
| XXX_Filtered_Images | Folder containing the filtered images from crYOLO before and after the feedback loop. |
| XXX_Queue_files | Folder containing the queue status of the — TranSPHIRE run. There are 3 queue files per job: NAME, NAME_done, NAME_list. The NAME file contains the information about the to-be-processed files. The NAME_done file contains the information of the already processed files. The NAME_list file is only filled for jobs that have an additional internal queue like particle picking, particle extraction, and 2d classification. The content indicates that files are ready to be processed but still wait for a certain condition to be met. In case of particle picking, the program waits for 30 seconds before starting the actual picking run to reduce the overhead of program initialisation. For particle extraction, the program waits until all the results of motion correction, particle picking, and ctf estimation arrived. 2D classification and 3D waits until a certain number of particles is accumulated. Because multiple files depend on a different number of input files, the provided queue status can be larger than the number of imported movies for the respective jobs. |
| XXX_Restart_Backup | Folder containing the obsolete files due to a restart. |
| XXX_Settings | Folder containing the settings and files for the current session. — Everytime the Start button is pressed, the provided external files and the current setup of TranSPHIRE is saved in a new session folder indicated by the current date and time. Internally, the copied files are used instead of the original ones. |
| XXX_Tar_file_folder | Folder containing the tar files that are created prior to copying when the Tar to work or Tar to backup option is activated. |
| Valid_micrograph_info.txt | File containing the extracted meta data for each movie in a star file format. Only the movies that do not violate the range provided by the user are stored in the Valid version. |
| Discarded_micrograph_info.txt | File containing the extracted meta data for each movie in a star file format. Only the movies that do violate the range provided by the user are stored in the Discarded version. |
| {CTF_NAME}_transphire_ctf_partres.txt | File containing the CTF estimation information in the SPHIRE partres format. This file can be used to skip CTF estimation in a real processing scenario. |
| {CTF_NAME}_transphire_ctf.star | File containing the CTF estimation information in the RELION star file format. This file can be used to skip CTF estimation in a real processing scenario. |
| {MOTION_NAME}_transphire_motion.txt | File containing a list of valid micrograph entries. |
| {MOTION_NAME}_transphire_motion.star | File containing micrograph information like the name and path of the DW and non DW summed image. |
| {MOTION_NAME}_transphire_motion_relion3.star | File containing micrograph information like the name and path of the DW and non DW summed image. Additionally, information to run particle polishing is available. Provide this file to run as input for particle polishing. |