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JensUweUlrich / ReadBouncer

Fast and scalable nanopore adaptive sampling
GNU General Public License v3.0
33 stars 2 forks source link

Support Minknow Core/API 5.0 #43

Closed Kalior closed 1 year ago

Kalior commented 2 years ago

Hi,

Really fantastic work on this project! Looks like a great alternative to readfish/uncalled/ONT's own adaptive sampling!

I wanted to run this on a fresh install of Minknow, but since march Minknow ships with Minkow core 5.0 (see https://community.nanoporetech.com/posts/software-release-22-03-2-f-9633). As I understand their API, this major update won't be backwards-compatible with the previous API.

Curious if you are planning on supporting the new API or if I'm stuck with the built-in adaptive sampling.

JensUweUlrich commented 2 years ago

Hi @Kalior

Thanks for your interest in ReadBouncer. As you correctly pointed out, MinKNOW core 5.0 and the corresponding API version include some significant changes that are not supported by our latest ReadBouncer version. @lutfia95 is currently working on that and we hope to release a new version solving this issue soon.

Cheers

Kalior commented 2 years ago

Fantastic! Looking forward to it!

trokhym1 commented 2 years ago

Are we there yet?

gchevignon commented 2 years ago

Hello, Would you please share with us install API for Minknow 4.5.0 ? Thanks

gchevignon commented 2 years ago

Hello, It seems that Minknow 5.1 is now supported by ReadBouncer, so I have compiled the last readbouncer 2h ago. However I got an error when I start readbouncer :

/usr/local/ReadBouncer/bin/ReadBouncer /home/userlocal/Bureau/Scripts.dir/ReadBouncer.dir/config_classify_test.toml

Error in command line! Error parsing the toml file: Error in [error] key "log_directory" not found in the top-level table --> | 1 | | the parsed file is empty

Here is my toml file that was working last friday :

usage = "classify" output_directory = '/home/userlocal/work/test_readbouncer_moi.dir' #all generated output files will be stored here log_directory = '/home/userlocal/work/test_readbouncer_moi.dir' #all generated log files will be stored here

[IBF]

threads = 10 #(unsigned integer; default: 3) target_files = ['/home/userlocal/work/test_readbouncer_moi.dir/OsHV-1_microVar-A_KY242785_C.gigas.ibf'] deplete_files = ['/home/userlocal/work/test_readbouncer_moi.dir/cgigas_uk_roslin_v1.ibf'] read_files = ['/home/userlocal/Bureau/Data_test.dir/all_01_1.fastq']
exp_seq_error_rate = 0.07 #(unsigned float between 0 and 1; default: 0.1) chunk_length = 150 #(unsigned integer; default: 250) max_chunks = 5

Best, Germain

lutfia95 commented 2 years ago

Hey @gchevignon,

we also updated the command line, to add the config.toml file you have also to use the flag --config. In your case will be: /usr/local/ReadBouncer/bin/ReadBouncer --config /home/userlocal/Bureau/Scripts.dir/ReadBouncer.dir/config_classify_test.toml

Best, Ahmad

JensUweUlrich commented 2 years ago

Hi Germain

We are currently utilizing the last tests with MinKNOW 5.1 and will Release ReadBouncer 1.2.0 today. However, you could try to call ReadBouncer using the --config parameter. In your case that would be /usr/local/ReadBouncer/bin/ReadBouncer --config /home/userlocal/Bureau/Scripts.dir/ReadBouncer.dir/config_classify_test.toml

JensUweUlrich commented 2 years ago

@lutfia95

could we please add a meaningful error message for the missing --config parameter? Thanks

gchevignon commented 2 years ago

Sorry I did not pay attention to the --config parameter .... I'm a little too excited to get readbouncer working! Thanks a lot

gchevignon commented 2 years ago

Me again ... I have succeeded to setup the simulated device in Minknow and readbouncer is connecting it but I got an error with guppy:

/usr/local/ReadBouncer/bin/ReadBouncer --config /home/userlocal/Bureau/Scripts.dir/ReadBouncer.dir/config_target_test.toml 59192 bins were loaded in 2.20847 seconds from the IBF 1930 bins were loaded in 0.0754784 seconds from the IBF Trying to connect to MinKNOW Host : localhost Port : 9502 Connecting to MinKNOW using the token: c17017a7-eb85-4140-b6bd-8721bc9a3f17 Connection successfully established! Waiting for device to start sequencing! Please start the sequencing run now! Sequencing has begun. Starting live signal processing! Connecting to Guppy basecall server on address : 127.0.0.1:5555 [guppy/error] basecall_service::BasecallClient::worker_loop: Connection error. [timed_out] Timeout waiting for reply to request: LOAD_CONFIG [timed_out] Timeout waiting for reply to request: LOAD_CONFIG Real time : 136.666 sec CPU time : 7.94097 sec Peak RSS : 17459 MByte

Guppy seems to work properly because it produce basecalled fastq file.... Best Germain

Here is my toml file:

usage = "target" output_directory = '/home/userlocal/work/test_readbouncer_bulk.dir/' log_directory = '/home/userlocal/work/test_readbouncer_bulk.dir/'

[IBF]

kmer_size = 13
fragment_size = 100000
threads = 3
target_files = ['/home/userlocal/work/test_readbouncer_bulk.dir/chm13.v1.1_chr21_22.ibf'] deplete_files = ['/home/userlocal/work/test_readbouncer_bulk.dir/chm13.v1.1_chr1-20_XM.ibf']
exp_seq_error_rate = 0.1

[MinKNOW]

host = "localhost" port = "9502"
flowcell = "MS00000" token_path = "test/tmp/minknow-auth-token.json" #path to authentication token file (if not localhost)

[Basecaller]

caller = "Guppy"

JensUweUlrich commented 2 years ago

Can you give us some more information on how you use Guppy:

  1. Which Guppy version are you using?
  2. Do Guppy and ReadBouncer run on the same machine?
  3. Are you using the default Guppy parameters provided with MinKNOW or did you start Guppy separately?

Thanks Jens

gchevignon commented 2 years ago

I have installed guppy-gpu following this protocol : https://community.nanoporetech.com/docs/prepare/library_prep_protocols/experiment-companion-minknow/v/mke_1013_v1_revch_11apr2016/installing-gpu-version-of-guppy-with-minknow-for-minion

So I have installed ont-guppy_6.1.5_linux64.tar.gz

Yes they run on the same machine

I probably run Guppy with MinKNOW but not sure ...

Thanks

Germain

JensUweUlrich commented 2 years ago

Ok. Than you will probably use the default settings of Guppy, which means that the basecall_server uses IPC. You will need to add the following line to the config.toml file:

[Basecaller]

caller = "Guppy"
host   = "ipc:///tmp/.guppy"

I hope this fixes the problem.

Best Jens

gchevignon commented 2 years ago

Hey, sorry for the late reply ... this did not fix the problem. Best Germain

JensUweUlrich commented 2 years ago

Ok. Could you please check if there is a /lib/systemd/system/guppyd.service file on your system and post the content of that file?

gchevignon commented 2 years ago

[Unit] Description=Service to manage the guppy basecall server. Documentation=https://community.nanoporetech.com/protocols/Guppy-protocol/v/GPB_2003_v1_revQ_14Dec2018

Disable start rate limiting -- the service will try and restart itself forever.

StartLimitIntervalSec=0

[Service] Type=simple Environment="LD_LIBRARY_PATH=/usr/lib/nvidia-current-ont:$LD_LIBRARY_PATH" ExecStart=/opt/ont/guppy/bin/guppy_basecall_server --log_path /var/log/guppy --config dna_r9.4.1_450bps_fast.cfg --num_callers 1 --cpu_threads_per_caller 2 --port /tmp/.guppy/5555 --ipc_threads 3 Restart=always

Wait ten seconds in-between restarts, to avoid spam if the service starts crashing frequently.

RestartSec=10 User=minknow MemoryLimit=8G MemoryHigh=8G CPUQuota=200%

[Install] Alias=guppyd.service WantedBy=multi-user.target

JensUweUlrich commented 2 years ago

Thanks You would need to change the ExecStart line and add some parameters to make live-basecalling with Guppy use GPUs, which is needed for adaptive sampling. I also assume that there is a problem with the permissions on the /tmp/.guppy/5555 file. Thus you could try to change the line to ExecStart=/opt/ont/guppy/bin/guppy_basecall_server --log_path /var/log/guppy --config dna_r9.4.1_450bps_fast.cfg --num_callers 1 --cpu_threads_per_caller 2 --port 5555 --ipc_threads 3 --gpu_runners_per_device 2 --chunks_per_runner 64 --device cuda:all --use_tcp

After changing these lines, you need to restart the guppy service with the following commands sudo systemctl daemon-reload sudo service guppyd restart

Now you can use the following settings in the ReadBouncer config TOML file for connection to the basecaller

[Basecaller]

caller = "Guppy"
host   = "localhost"
port   = "5555"
gchevignon commented 2 years ago

I have modified the /lib/systemd/system/guppyd.service and ReadBouncer config TOML file accordingly but I still have the same error. I have also played around with /etc/systemd/system/guppyd.service file and /opt/ont/minknow/conf/app_conf file but I am unable to get this working. I have changed permission on the /tmp/.guppy/5555 with sudo chmod a+w /tmp/.guppy/5555 (from this discussion : https://community.nanoporetech.com/posts/can-anyone-solve-it-super). Still no success ...

Thanks Germain

moisann commented 2 years ago

Hi there, I am trying to run a simulation test, but I have the same problem here...


$ /home/work/ReadBouncer-1.2.0-Linux/bin/ReadBouncer --config /home/work/ReadBouncer-1.2.0-Linux/config.toml
965 bins were loaded in 0.0401868 seconds from the IBF
29596 bins were loaded in 1.09497 seconds from the IBF
Trying to connect to MinKNOW
Host : localhost
Port : 9502
Connecting to MinKNOW using the token: 710eb963-babe-4740-bdef-854b9af4a3d1
Connection successfully established!
Waiting for device to start sequencing!
Please start the sequencing run now!
Sequencing has begun. Starting live signal processing!
Connecting to Guppy basecall server on address : localhost:5555
[guppy/error] basecall_service::BasecallClient::worker_loop: Connection error. [timed_out] Timeout waiting for reply to request: LOAD_CONFIG
[timed_out] Timeout waiting for reply to request: LOAD_CONFIG
Real time : 212.296 sec
CPU time  : 3.87901 sec
Peak RSS  : 8896 MByte

Thanks

JensUweUlrich commented 2 years ago

Just for comparison, this is the Service entry of my guppyd.service file on my Nvidia Xavier

[Service]
Type=simple
Environment="LD_LIBRARY_PATH=/usr/lib/nvidia-current-ont:$LD_LIBRARY_PATH"
ExecStart=/usr/bin/guppy_basecall_server --log_path /media/jens/xavierSSD/guppy_logs --config dna_r9.4.1_450bps_fast.cfg --num_callers 4 --gpu_runners_per_device 3 --chunks_per_runner 64 --device cuda:all --port 5555 --ipc_threads 4 --cpu_threads_per_caller 4 --allow_non_local --use_tcp
Restart=always
# Wait ten seconds in-between restarts, to avoid spam if the service starts crashing frequently.
RestartSec=10
User=jens
MemoryLimit=28G
MemoryHigh=28G
CPUQuota=400%

and this is my ReadBouncer config.toml from a remote laptop

Basecaller]
caller              = "Guppy"             #(default: DeepNano)
host                = "xavier"                       #(ip address or name of the computer hosting Guppy Basecall Server; default: 127.0.0.1)
port                = 5555                                 #(port number on which the basecall server is running on the host; default: 5555)
config              = "dna_r9.4.1_450bps_fast"

I guess the problem is that you did not provide the config file. Please also check whether the basecaller service is working by

sudo service guppyd status

moisann commented 2 years ago

I still haven't solved the problem...(I can complete testing with DeepNano) Here is my toml file:


usage               = "target"
output_directory    = '/home/myname/ReadBouncer-1.2.0-Linux/results/'
log_directory       = '/home/myname/ReadBouncer-1.2.0-Linux/log/'

[IBF]

kmer_size           = 13                      
fragment_size       = 100000                  
threads             = 3                      
target_files        = ['/home/myname/ReadBouncer-1.2.0-Linux/results/chm13.v1.1_chr21_22.ibf']
deplete_files       = ['/home/myname/ReadBouncer-1.2.0-Linux/results/chm13.v1.1_chr1-20_XM.ibf']  
exp_seq_error_rate  = 0.1                      

[MinKNOW]

host                = "localhost"
port                = "9502"       
flowcell            = "MS00000" 
token_path         = "test/tmp/minknow-auth-token.json"  #path to authentication token file (if not localhost)

[Basecaller]

caller = "Guppy"
host   = "ipc:///tmp/.guppy"
config = "dna_r9.4.1_450bps_fast"

and minknow/guppyd status:

~$ sudo service minknow status
● minknow.service - MinKNOW Instrument Software for MinION (daemon)
     Loaded: loaded (/etc/systemd/system/minknow.service; enabled; vendor preset: enabled)
     Active: active (running) since Mon 2022-08-29 13:19:19 JST; 2min 3s ago
    Process: 21394 ExecStartPre=/bin/sleep 15 (code=exited, status=0/SUCCESS)
   Main PID: 21395 (mk_manager_svc)
      Tasks: 275 (limit: 154228)
     Memory: 276.5M
     CGroup: /system.slice/minknow.service
             ├─21395 /opt/ont/minknow/bin/mk_manager_svc --simulated-integrated-devices 1
             ├─21397 /opt/ont/minknow/bin/crashpad_handler --database=/var/lib/minknow/data/core-dump-db --metrics-dir=/var/lib/minknow/data/core-dump-db --url=https://submit.backtrace.io/nanoporetech/6e3c4958cfd996b7000dadb02a931ff700986aa48b33903b5902dff716c95809/minidump --annotation=cmd_line=/o>
             ├─21448 /opt/ont/minknow/bin/grpcwebproxy --server_tls_cert_file=/opt/ont/minknow/conf/rpc-certs/localhost.crt --server_tls_key_file=/opt/ont/minknow/conf/rpc-certs/localhost.key --backend_addr=127.0.0.1:33667 --backend_tls_noverify --backend_tls=true --server_bind_address=0.0.0.0 --se>
             ├─21449 /opt/ont/minknow/bin/basecall_manager --guppy-address ipc:///tmp/.guppy/5555 --conf /opt/ont/minknow/conf --system-info /tmp/minknow_9fd0bf68-c06f-4dd7-9486-854c3ecc0eaa/system_info.pb --secure 127.0.0.1:0 --queued-command-count 2
             ├─21450 /opt/ont/minknow/bin/control_server --config /tmp/minknow_9fd0bf68-c06f-4dd7-9486-854c3ecc0eaa/conf-MS00000 --system-info /tmp/minknow_9fd0bf68-c06f-4dd7-9486-854c3ecc0eaa/system_info.pb --queued-command-count 2
             ├─21458 /opt/ont/minknow/bin/crashpad_handler --database=/var/lib/minknow/data/core-dump-db --metrics-dir=/var/lib/minknow/data/core-dump-db --url=https://submit.backtrace.io/nanoporetech/6e3c4958cfd996b7000dadb02a931ff700986aa48b33903b5902dff716c95809/minidump --annotation=cmd_line=/o>
             ├─21472 /opt/ont/minknow/bin/crashpad_handler --database=/var/lib/minknow/data/core-dump-db --metrics-dir=/var/lib/minknow/data/core-dump-db --url=https://submit.backtrace.io/nanoporetech/6e3c4958cfd996b7000dadb02a931ff700986aa48b33903b5902dff716c95809/minidump --annotation=cmd_line=/o>
             ├─21510 /opt/ont/minknow/bin/grpcwebproxy --server_tls_cert_file=/opt/ont/minknow/conf/rpc-certs/localhost.crt --server_tls_key_file=/opt/ont/minknow/conf/rpc-certs/localhost.key --backend_addr=127.0.0.1:39227 --backend_tls_noverify --backend_tls=true --server_bind_address=0.0.0.0 --se>
             ├─21621 /opt/ont/minknow/bin/analyser --config /tmp/minknow_9fd0bf68-c06f-4dd7-9486-854c3ecc0eaa/conf-MS00000 --system-info /tmp/minknow_9fd0bf68-c06f-4dd7-9486-854c3ecc0eaa/system_info.pb
             ├─21622 /opt/ont/minknow/bin/grpcwebproxy --server_tls_cert_file=/opt/ont/minknow/conf/rpc-certs/localhost.crt --server_tls_key_file=/opt/ont/minknow/conf/rpc-certs/localhost.key --backend_addr=127.0.0.1:8000 --backend_tls_noverify --backend_tls=true --server_bind_address=0.0.0.0 --ser>
             └─21630 /opt/ont/minknow/bin/crashpad_handler --database=/var/lib/minknow/data/core-dump-db --metrics-dir=/var/lib/minknow/data/core-dump-db --url=https://submit.backtrace.io/nanoporetech/6e3c4958cfd996b7000dadb02a931ff700986aa48b33903b5902dff716c95809/minidump --annotation=cmd_line=/o>

 Aug 29 13:19:04 myname-ZA9C-R39 systemd[1]: Starting MinKNOW Instrument Software for MinION (daemon)...
 Aug 29 13:19:19 myname-ZA9C-R39 systemd[1]: Started MinKNOW Instrument Software for MinION (daemon).
~$ sudo service guppyd status
● guppyd.service - Service to manage the guppy basecall server.
     Loaded: loaded (/etc/systemd/system/guppyd.service; enabled; vendor preset: enabled)
     Active: active (running) since Mon 2022-08-29 13:18:57 JST; 2min 52s ago
       Docs: https://community.nanoporetech.com/protocols/Guppy-protocol/v/GPB_2003_v1_revQ_14Dec2018
   Main PID: 21306 (guppy_basecall_)
      Tasks: 80 (limit: 154228)
     Memory: 838.5M (high: 20.0G limit: 20.0G)
     CGroup: /system.slice/guppyd.service
             └─21306 /home/myname/ont-guppy/ont-guppy/bin/guppy_basecall_server --log_path /var/log/guppy --config dna_r9.4.1_450bps_fast.cfg --num_callers 1 --cpu_threads_per_caller 2 --gpu_runners_per_device 2 --chunks_per_runner 64 --port /tmp/.guppy/5555 --ipc_threads 3 -x cuda:all

 Aug 29 13:18:57 myname-ZA9C-R39 guppy_basecall_server[21306]: kernel path:
 Aug 29 13:18:57 myname-ZA9C-R39 guppy_basecall_server[21306]: runners per device:  2
 Aug 29 13:18:57 myname-ZA9C-R39 guppy_basecall_server[21306]: Use of this software is permitted solely under the terms of the end user license agreement (EULA).By running, copying or accessing this software, you are demonstrating your acceptance of the EULA.
 Aug 29 13:18:57 myname-ZA9C-R39 guppy_basecall_server[21306]: The EULA may be found in /home/myname/ont-guppy/ont-guppy/bin
 Aug 29 13:18:57 myname-ZA9C-R39 guppy_basecall_server[21306]: Config loaded:
 Aug 29 13:18:57 myname-ZA9C-R39 guppy_basecall_server[21306]: config file:               /home/myname/ont-guppy/ont-guppy/data/dna_r9.4.1_450bps_fast.cfg
 Aug 29 13:18:57 myname-ZA9C-R39 guppy_basecall_server[21306]: model file:                /home/myname/ont-guppy/ont-guppy/data/template_r9.4.1_450bps_fast.jsn
 Aug 29 13:18:57 myname-ZA9C-R39 guppy_basecall_server[21306]: model version id           2021-05-17_dna_r9.4.1_minion_96_29d8704b
 Aug 29 13:18:57 myname-ZA9C-R39 guppy_basecall_server[21306]: adapter scaler model file: None
 Aug 29 13:18:57 myname-ZA9C-R39 guppy_basecall_server[21306]: Starting server on port: ipc:///tmp/.guppy/5555

Was I not able to provide the config file?

JensUweUlrich commented 2 years ago

@moisann

That's strange. I used excatly the same parameter settings for the basecaller as you did and it works for me. Can you also make sure that you have installed the Guppy-GPU version. The output from your service guppyd status command does not tell anything about using CUDA. Mine looks like this

● guppyd.service - Service to manage the guppy basecall server.
   Loaded: loaded (/lib/systemd/system/guppyd.service; enabled; vendor preset: enabled)
   Active: active (running) since Mon 2022-08-29 11:35:42 CEST; 24min ago
     Docs: https://community.nanoporetech.com/protocols/Guppy-protocol/v/GPB_2003_v1_revQ_14Dec2018
 Main PID: 6567 (guppy_basecall_)
    Tasks: 76 (limit: 4915)
   CGroup: /system.slice/guppyd.service
           └─6567 /usr/bin/guppy_basecall_server --log_path /media/jens/xavierSSD/guppy_logs --config dna_r9.4.1_450bps_fast.cfg --num_callers 4 --gpu_runners_per_device 3 --chunks_p

Aug 29 11:35:43 xavier guppy_basecall_server[6567]: max returned events: 50000
Aug 29 11:35:43 xavier guppy_basecall_server[6567]: gpu device:          cuda:all
Aug 29 11:35:43 xavier guppy_basecall_server[6567]: kernel path:
Aug 29 11:35:43 xavier guppy_basecall_server[6567]: runners per device:  3
Aug 29 11:35:45 xavier guppy_basecall_server[6567]: Config loaded:
Aug 29 11:35:45 xavier guppy_basecall_server[6567]: config file:               /opt/ont/ont-guppy/data/dna_r9.4.1_450bps_fast.cfg
Aug 29 11:35:45 xavier guppy_basecall_server[6567]: model file:                /opt/ont/ont-guppy/data/template_r9.4.1_450bps_fast.jsn
Aug 29 11:35:45 xavier guppy_basecall_server[6567]: model version id           2021-05-17_dna_r9.4.1_minion_96_29d8704b
Aug 29 11:35:45 xavier guppy_basecall_server[6567]: adapter scaler model file: None
Aug 29 11:35:45 xavier guppy_basecall_server[6567]: Starting server on port: ipc:///tmp/.guppy/5555

It also seems to me that you are starting Guppy with the user minknow and when you start ReadBouncer with another user, you may have no access to the file tmp/.guppy/5555. You could change this as well, or use TCP/IP for communication with Guppy as I recommended above.

gchevignon commented 2 years ago

Hello, Because I have modified so much different file I have decided to reinstall minknow and guppy ... and I have eventually reformated my computer to restart on clean base ... Unfortunatly the new install of minknow did not install guppyd.service file ... So I am stuck and I can't even install guppy-gpu so I made a ticket to Nanopore support regarding this missing guppyd.service file. Best

JensUweUlrich commented 2 years ago

You can easily create the guppyd service file on your own because it is a simple text file. I also recommend you to read the repository from Miles Benton where he provides a guppyd.service file as well.

gchevignon commented 2 years ago

Just for comparison, this is the Service entry of my guppyd.service file on my Nvidia Xavier

[Service]
Type=simple
Environment="LD_LIBRARY_PATH=/usr/lib/nvidia-current-ont:$LD_LIBRARY_PATH"
ExecStart=/usr/bin/guppy_basecall_server --log_path /media/jens/xavierSSD/guppy_logs --config dna_r9.4.1_450bps_fast.cfg --num_callers 4 --gpu_runners_per_device 3 --chunks_per_runner 64 --device cuda:all --port 5555 --ipc_threads 4 --cpu_threads_per_caller 4 --allow_non_local --use_tcp
Restart=always
# Wait ten seconds in-between restarts, to avoid spam if the service starts crashing frequently.
RestartSec=10
User=jens
MemoryLimit=28G
MemoryHigh=28G
CPUQuota=400%

and this is my ReadBouncer config.toml from a remote laptop

Basecaller]
caller              = "Guppy"             #(default: DeepNano)
host                = "xavier"                       #(ip address or name of the computer hosting Guppy Basecall Server; default: 127.0.0.1)
port                = 5555                                 #(port number on which the basecall server is running on the host; default: 5555)
config              = "dna_r9.4.1_450bps_fast"

I guess the problem is that you did not provide the config file. Please also check whether the basecaller service is working by

sudo service guppyd status

Hi, still not working on my side ... the simulation run get stuck in "starting run" and I think this is because my /lib/systemd/system/guppyd.service is not OK ... Can you please share your two Service entry from /lib/systemd/system/guppyd.service and /etc/systemd/system/guppyd.service Thanks Germain

gchevignon commented 1 year ago

Hey ! Nanopore just released a patch to fix the guppyd.service problem with last version of Minknow : https://community.nanoporetech.com/posts/minknow-22-08-8-patch-rele

I hope readbouncer will work with this new release ...?

I will not be able to test it before next tuesday. Best Germain

gchevignon commented 1 year ago

Hello, this patch indeed fixed the problem with guppyd.service which is now guppyd-cpu.service .... So i was able to restart simulation run but readbouncer still produce the same error as before :

/usr/local/ReadBouncer/bin/ReadBouncer --config /home/userlocal/Desktop/Scripts.dir/ReadBouncer.dir/config_target_test-V2.toml 965 bins were loaded in 0.0415536 seconds from the IBF 29596 bins were loaded in 1.18629 seconds from the IBF Trying to connect to MinKNOW Host : localhost Port : 9502 Connecting to MinKNOW using the token: 5ca149dd-ba11-4d30-ab77-540ec7f59302 Connection successfully established! Waiting for device to start sequencing! Please start the sequencing run now! Sequencing has begun. Starting live signal processing! Connecting to Guppy basecall server on address : ipc:///tmp/.guppy/5555 [guppy/error] basecall_service::BasecallClient::worker_loop: Connection error. [timed_out] Timeout waiting for reply to request: LOAD_CONFIG [timed_out] Timeout waiting for reply to request: LOAD_CONFIG Real time : 144.397 sec CPU time : 4.53437 sec Peak RSS : 8896 MByte

So sadly I am still stuck on this ...

JensUweUlrich commented 1 year ago

@gchevignon

ONT did break the ReadBouncer-Guppy-Interface with their latest changes, as also reported in issue #54. This should be fixed in release 1.2.2

gchevignon commented 1 year ago

Great Thanks a lot !