Gotchas

Gotchas - "A common error or misconception that may catch you out..."

These may or may not (!) be mistakes we have made already...

1. If the previous run has not fully completed - i.e is still basecalling or processing raw data, you may connect to the wrong instance and see nothing happening. Always check the previous run has finished completely.
2. If you have forgotten to remove your simulation line from your sequencing toml you will forever be trapped in an inception like resequencing of old data... Don't do this!
3. If basecalling doesn't seem to be working check:
   • your basecalling server is running.
   • the ip of your server is correct.
   • the port of your server is correct.
4. If you are expecting reads to unblock but they do not - check that you have set control=false in your ru_generators toml file. control=true will prevent any unblocks but does otherwise run the full analysis pipeline.
5. Oh no - every single read is being unblocked - I have nothing on target!
   • Double check your reference file is in the correct location.
   • Double check your targets exist in that reference file.
   • Double check your targets are correctly formatted with contig name matching the record names in your reference (Exclude description - i.e the contig name up to the first whitespace).
6. Where has my reference gone? If you are using a _live TOML file - e.g running iter_align or iter_cent, the previous reference MMI file is deleted when a new one is added. This obviosuly saves on disk space use(!) but can lead to unfortunate side effects - i.e you delete yoru MMI file. These can of course be recreated but user beware.
7. My bulkfile isn't generating data. Are you really trying playback from a bulkfile? Users often attempt playback from a standard fast5 file. This will not work. A bulk fast5 must be recorded from a live minKNOW run.