readbouncer cannot connect to minKNOW

[willros]

Hi,

I get the following message when trying to run ReadBouncer:

965 bins were loaded in 0.0445678 seconds from the IBF
29596 bins were loaded in 1.26652 seconds from the IBF
Trying to connect to MinKNOW
Host : localhost
Port : 9502
failed to connect to all addresses
Real time : 4.15342 sec
CPU time  : 4.14012 sec
Peak RSS  : 8896 MByte

I am using the latest ReadBouncer for linux x86. I am using minKNOW 22.10.7 with MinKNOW core: 5.3.1 Guppy: 6.3.8 Bream: 7.3.2 Script Configuration: 5.3.7

The minknow daemon is up and running, controlled by:

systemctl status minknow.service

The config.toml file:

usage               = "target"
output_directory    = '/home/nanopore/setting-up-adaptive-sampling/test-readbouncer'
log_directory       = '/home/nanopore/setting-up-adaptive-sampling/test-readbouncer/log'

[IBF]

kmer_size           = 13                      
fragment_size       = 100000                  
threads             = 3                      
target_files        = ['/home/nanopore/setting-up-adaptive-sampling/test-readbouncer/chm13.v1.1_chr21_22.ibf']
deplete_files       = ['/home/nanopore/setting-up-adaptive-sampling/test-readbouncer/chm13.v1.1_chr1-20_XM.ibf']  
exp_seq_error_rate  = 0.1                      

[MinKNOW]

host                = "localhost"
port                = "9502"       
flowcell            = "MS00000" 

[Basecaller]

caller             = "DeepNano"  
threads            = 3         

Any idea what I can try or what is going on?

Thanks a lot, William

[JensUweUlrich]

Hi @willros

It seems that ReadBouncer cannot connect to the given flowcell port. Did you set up the simulated device MS00000 in MinKNOW?

[willros]

Hi @JensUweUlrich

Yes, I set up the simulated device MS0000 as instructed in your github repo. I also did not change the default value for the ports for guppy and minKNOW.

I can see the simulated the devide in minKNOW and start a dry run inside there, but readbouncer is not able to connect.

[JensUweUlrich]

Just to be sure we don't miss anything: Are you running MinKNOW and ReadBouncer on the same machine? And you have installed the latest ReadBouncer version (version 1.2.2)?

[willros]

Hi,

I was running version 1.1 (from the master branch). I will try to download the latest and see if it works. Thank you!

[JensUweUlrich]

Ah ok, that's probably the issue. ReadBouncer 1.1 is not compatible with MinKNOW 5.x. Using the latest ReadBouncer version should solve your problem.

[JensUweUlrich]

That doesn't depend on the base caller. When the sequencing run has finished or has been stopped by the user via MinKNOW, ReadBouncer will also stop running.

[jamesemery]

Hey I just ran into this same issue. The download link for Linux posted in your Readme.md points to the 1.1 build of ReadBouncer by the way.

[JensUweUlrich]

@jamesemery Which versions of MinKNOW and ReadBouncer are you using?

[jamesemery]

I found that switching to Read bouncer 1.2 fixed this issue, I just fell into the trap of downloading the wrong version from the README. MinKNOW 22.08.9