Job: Check for Corrupt Particles
Check each particle stack .mrc file for corruption, including checking the header for length mismatch, NaN values check, and checksum verification.
Last updated
Check each particle stack .mrc file for corruption, including checking the header for length mismatch, NaN values check, and checksum verification.
Last updated
Checks if the particle files on disk are corrupt. The job will read the header of each file and compute the expected file size based on the ny, nx and nz values. If the expected file size of a file doesn't match the actual file size on disk, the job will mark the particle as corrupt. In CryoSPARC v4.6.1+, the job will also by default check for NaN values in the particle stack files, and mark the particles as corrupt if any are found. The job issues a warning for each file that is found corrupt.
The job will produce an output that includes only the non-corrupt particle files. This output can be used for downstream processing. In CryoSPARC v4.6.1+, the job will run through all input particles, produce warnings, and then throw and error fail at the end if any files were found to be corrupt. The job can then either be marked as complete in order to use the filtered output, or it can be run with the "Fail if corruption is detected" flag off.
In CryoSPARC v4.6.1+, the job is also able to check a checksum in the MRC header to ensure that all the data in the file is intact. The checksum is only produced for MRC files written in v4.6.1+. The "verify file checksums" parameter is off by default.
Particles
Particles
You can use the output of the job to carry on processing, since the output only contains files that were found to be intact and not corrupt.
After any corrupt files have been identified, you can then find the files on the filesystem and try to rectify the issue that lead to the corruption.
