MinKNOW folders and log files

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The way The MinKNOW program organises folder, and the makeup of its various log files is complicated.

This page is an attempt to keep track of them


  • The root folder is usually called data.
  • MinKNOW deposits log files in the root folder, but uses a subfolder called reads for the FAST5 files.
  • Generally speaking one read yields one FAST5 files.
  • At this ealy stage FAST5 files contain signal and events, but the bases are not called, so there is no DNA yet.
  • Within reads, MinKNOW separates reads into
- pass
- fail
- skip
- tmp

Log files

Found in:


The log files seem to have prefixes that reflect their type. One set of log files could look like:

  • ws_event_sampler_*
  • control_server_*
  • ws_raw_data_sampler_*
  • read_writer_*
  • ws_longpoll_*
  • analyser_*
  • bulk_writer_*
  • manta_*
  • Script_events_*

These files usually have the date and time added to their name and all have extension txt.