From the 24.11 release onwards, if MinKNOW™ ends a sequencing run without clearing up correctly, e.g. due to MinKNOW crash or unexpected computer shutdown, raw read data can be left in the C:\data\queued_reads\complete_reads_xxxx directory (more details in this FAQ). Most of these data should 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. They can be manually renamed to .pod5 and 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 in the .raw format will be left in the C:\data\queued_reads\complete_reads_xxxx directory without being converted to .pod5.

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

1. Navigate to the directory containing the recover_reads executable, usually present at this location - C:\Program Files\OxfordNanopore\MinKNOW\bin
2. This directory should contain the binary file: recover_reads
3. Open up a terminal window by clicking on the search bar, typing in “Command prompt”, then right-clicking on “Run as administrator”.
4. Run the command below: cd C:\Program Files\OxfordNanopore\MinKNOW\bin
5. Run the following command to recover your raw reads: recover_reads.exe "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:

C:\Program Files\OxfordNanopore\MinKNOW\bin>recover_reads.exe C:\data\queued_reads\complete_reads_xxx --output-directory C:\..\output

Reads will be recovered to the--output-directory specified. The recovered files can be basecalled using post-run analysis in MinKNOW or Dorado.