Running raw read recovery - Linux, Mac, and Mk1C
(For raw read recovery on Windows please see here).
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 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
followed by the
recover_reads executable location, usually in
/opt/ont/minknow/bin for Linux and Mk1C users, and in
/Applications/MinKNOW/bin for MacOS users. Newer MacOS users will find this located in
An example command for Mk1C is as follows,
minit@MC-100059:~$ cd /opt/ont/minknow/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"
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
These can then be basecalled using the post-run basecalling option in MinKNOW or stand-alone Dorado.