setup help on minion

[looselab]

setup help on minion

[brentp]

Hi Alex, thanks for the reply. I did have a newer guppy installed, and I'm pretty sure that's what was running. I won't be able to get back to this until quarantine is over, but I'll check then and get back to you.
-B

[alexomics]

Could you paste your TOML file here? You can remove IP addresses/paths/ports

[alexomics]

Also, when terminating Read Until what’s the error/trace back?

[brentp]

Here is the toml:

[caller_settings]
config_name = "dna_r9.4.1_450bps_hac"
host = "127.0.0.1"
port = 5555

[conditions]
reference = "/data/human_g1k_v38_decoy_phix.fasta.mmi"

[conditions.0]
name = "select_chr_21_22"
control = false
min_chunks = 0
max_chunks = inf
targets = ["chr21", "chr22"]
single_on = "stop_receiving"
multi_on = "stop_receiving"
single_off = "unblock"
multi_off = "unblock"
no_seq = "proceed"
no_map = "proceed"

and here is the traceback when pressing ctrl+c on the process that was running ru_generators:

2020-03-10 15:33:15,340 read_until_api_v2.main Sending init command, channels:1-512, min_chunk:0


^C2020-03-11 08:50:15,198 Manager Caught ctrl-c, terminating workflow.
2020-03-11 08:50:15,203 read_until_api_v2.main Reset request received, shutting down...
2020-03-11 08:50:15,210 read_until_api_v2.main Reset signal received by action handler.
2020-03-11 08:50:15,252 read_until_api_v2.main Stopping processing of reads due to reset.
SIGINT received. Terminating server.
2020-03-11 08:50:15,397 read_until_api_v2.main Stream handler exited successfully.
2020-03-11 08:50:15,405 Manager EXCEPT
Traceback (most recent call last):
  File "/home/quinlan/.local/lib/python3.6/site-packages/ru/ru_gen.py", line 408, in run_workflow
    res = result.get(3)
  File "/usr/lib/python3.6/multiprocessing/pool.py", line 644, in get
    raise self._value
  File "/usr/lib/python3.6/multiprocessing/pool.py", line 119, in worker
    result = (True, func(*args, **kwds))
  File "/home/quinlan/.local/lib/python3.6/site-packages/ru/ru_gen.py", line 125, in simple_analysis
    caller = Caller(**caller_kwargs)
  File "/home/quinlan/.local/lib/python3.6/site-packages/ru/basecall.py", line 65, in __init__
    self.connect()
  File "/home/quinlan/.local/lib/python3.6/site-packages/pyguppyclient/client.py", line 73, in connect
    config = self._load_config(self.config_name)
  File "/home/quinlan/.local/lib/python3.6/site-packages/pyguppyclient/client.py", line 95, in _load_config
    loaded_configs = {Config(c).name: Config(c) for c in self.get_configs()}
  File "/home/quinlan/.local/lib/python3.6/site-packages/pyguppyclient/client.py", line 91, in get_configs
    res = self.send(SimpleRequestType.GET_CONFIGS)
  File "/home/quinlan/.local/lib/python3.6/site-packages/pyguppyclient/client.py", line 55, in send
    return simple_response(self.recv())
  File "/home/quinlan/.local/lib/python3.6/site-packages/pyguppyclient/client.py", line 65, in recv
    raise Again()
zmq.error.Again: Resource temporarily unavailable
[guppy/warning] main: The basecall server has been terminated.

[alexomics]

Brent,

Very sorry for the slow response! I think that this issue is due to a guppy server incompatibility. We require guppy >=3.4

If you are able to test with a newer guppy version (not one that ships with MinKNOW) and let me know, that would really help!

Alex

[tchrisboles]

Alex and Matt,
If one has a linux box running new Minion-nc, AND new guppy (version 3.5.x) in a different directory (say home/local/bin), one could run basecalling "remote" using the local/bin copy in server mode as long as the toml file is properly configured (port other than 5555). Is that correct? I think that Alex had a diagram for some thing close to this in an earlier reply to someone setting up ru on a gridion. I want to set this up for a minion, and was wondering if running basecalling server on the same machine (but different installation directory) would work. Any advice on setting up basecalling server or toml file for this case?

[alexomics]

@tchrisboles I have split this into another issue here: #39