No possibility to change location for tmp & intermediate files generated by MinKnow even with changed data path

[AndriiTarieiev]

Dear developers,

I currently have a serious issue with running the latest version of MinKnow with MinION Mk1D on Ubuntu 24.04LTS. I would like all the data from runs to be stored on a separate dedicated drive and changed the path accordingly. However, even after that MinKnow continues to generate huge temporary and intermediate files in default location /var/lib/minknow/data, overfills the drive, and then forces the run to stop.

I would like to know whether it is possible to address such a problem because it is not feasible to have the OS & software on a huge drive. Instead, the common practice is to store data, logs and tmps in a separate dedicated location.

Thank you in advance for your response,
Best regards,
Andrii Tarieiev

[0x55555555]

Hi @AndriiTarieiev,

Can you please contact Nanopore customer support, they can guide you in configuring MinKNOW as you need.

Thanks,

• George

[AndriiTarieiev]

I already contacted support and hugely disappointed with it because they were unable to provide any meaningful feedback. Instead, they only stated that "it was intended so by design".

[0x55555555]

and changed the path accordingly

Can you confirm what you have actually tried changing?

[AndriiTarieiev]

I followed the instructions provided here https://nanoporetech.com/support/software/MinKNOW/Installation-and-Setup/how-do-i-change-the-directory-for-the-reads-folder and changed the path from /var/lib/minknow/data/ to /media/.../ONT/minknow/data/ in user_conf as described in method 2. In addition, I confirmed this location via MinKnow UI before starting the sequerncing.

Result - it trasferred POD5 & FASTQ to the new location but created a huge .tmp file at original location /var/lib/minknow/data. This tmp was the cause for sequencing abortion due to overfilling the drive with software and system.

[0x55555555]

So to be explicit:

• You edited the user_conf file and changed the base path to be your new drive.
• You then restarted the minknow service?

What is the exact name of the file minknow created in the old location? .tmp? Can you provide any more of the large file's path, or its extension? This isn't a normal file name minknow writes to.

Did MinKNOW seem to write to the new path?

Thanks,

• George

[AndriiTarieiev]

This was a single file located in /var/lib/minknow/data with a long name that includes: PC_name_DATE_Flowcell_ID_Sequencing_run_name_identifier.fast5.tmp
At the moment of interruption it was ca. 500Gb

MinKnow wrote only POD5 & FASTQ files to the new path. All the other folders like reads, reads queued, etc. remain in the old location.

[0x55555555]

I would suggest rechecking the changes to user_conf and confirming you followed the help article exactly. My suspicion from your description is you may have changed reads setting in output_dirs, not base. HOWEVER, its entirely possible I'm not able to determine the issue from the info I have to hand.

It also sounds as if you are configuring the sequencer to write a bulk fast5 output file? Is this deliberate?

To diagnose further I would need access to your config file or logs. You can contact support on the same channel as before and raise a case with these attached, and I can continue to assist.

Thanks,

• George

[AndriiTarieiev]

No, I did not change reads settings. Also, I did not request bulk fast5, only POD5. I am now trying to delete the software completely and reinstall it. Unfortunately, it seems to be impossible to install it in user-defined location either.

[0x55555555]

Ok, if you require further assistance please contact support and pass over some logs - I'll be able to assist in more detail.

Thanks,

• George

[AndriiTarieiev]

After reinstalling it does not recognize the device any more. I have never imagined that this soft is of so poor quality.