From the 24.11 release onwards, if MinKNOW™ ends a run without clearing up correctly, e.g. due to MinKNOW crash or unexpected computer shutdown, raw read data can be left in the /data/queued_reads/complete_reads_xxxx directory. Most queued will be in the .pod5 file format and can be used directly.

Some files that MinKNOW was actively writing to may be in a .pod5.tmp format and can be converted using the pod5_recover tool in the following manner:

pod5 recover broken.pod5

New files are written as siblings to the inputs with the _recovered.pod5 suffix.

On MinKNOW versions prior to 24.11, raw read data will be left in the /data/queued_reads/complete_reads_xxxx directory without being converted to pod5 files.

These raw data files can be converted into .pod5 files using a command line tool that is packaged within the MinKNOW suite:

1. Open up a terminal window
2. Navigate to the directory containing the recover_reads executable, by using the change directory command cd followed by the recover_reads executable location, usually in /opt/ont/minknow/bin for Linux users, and in /Applications/MinKNOW/bin for MacOS users. Newer MacOS users will find this located in /Applications/MinKNOW.app/Contents/Resources/bin/
3. Run the following command to recover your raw reads: ./recover_reads "location of your raw reads" --output-directory "location to output your recovered pod5s

Please Note: The complete_reads_xxx folder should be the one generated during the time of the sequencing run that ended improperly. An example command is shown below: ./recover_reads /data/queued_reads/complete_reads_xxx --output-directory /data/../output Reads will be recovered to the --output-directory specified.

These can then be basecalled using the post-run basecalling option in MinKNOW or stand-alone Dorado.