Handshake failed with fatal error SSL_ERROR_SSL: error:1000007d:SSL routines:OPENSSL_internal:CERTIFICATE_VERIFY_FAILED

[daanishmahajan]

Hi @Adoni5,

I am facing the above mentioned error while running readfish in MacOS with apple silicon. Also I am connecting via wifi using my mobile hotspot. I have verified the readfish toml file and PyBasecallClient connection using:

python -c 'from pybasecall_client_lib.pyclient import PyBasecallClient as PGC; c = PGC("ipc:///tmp/.guppy/5555", "dna_r10.4.1_e8.2_400bps_fast.cfg"); c.connect(); print(c)'

Also I have implemented the steps for Apple silicon chip mentioned here: https://github.com/LooseLab/readfish?tab=readme-ov-file#apple-silicon

Other important files and commands:

1. readfish toml file:

[caller_settings.dorado]
config = "dna_r10.4.1_e8.2_400bps_fast.cfg"
address = "ipc:///tmp/.guppy/5555"

[mapper_settings.mappy_rs]
fn_idx_in = "/Users/daanishmahajan/Projects/AdaptiveSampling/Icarust/experiments/data/readfish_simulation/data/reduced_ref.mmi"

[[regions]]
name = "Human_sub Enrichment"
control = false
min_chunks = 1
max_chunks = 6
targets = ["chr21_MATERNAL", "chr22_PATERNAL"]
single_on = "stop_receiving"
multi_on = "stop_receiving"
single_off = "unblock"
multi_off = "unblock"
no_seq = "proceed"
no_map = "proceed"

2. Icarust toml file

output_path = "/Users/daanishmahajan/Projects/AdaptiveSampling/Icarust/experiments/data/readfish_simulation/output"
random_seed = 10
target_yield = 100000000000
working_pore_percent = 85
pore_type = "R10"

[parameters]
sample_name = "human_sub_enrichment"
experiment_name = "readfish_simulation"
flowcell_name = "FAQ1234"
experiment_duration_set = 7200
device_id = "Bantersaurus"
position = "FenceSitter"
break_read_ms = 400

[[sample]]
name = "HG002_sub"
input_genome = "/Users/daanishmahajan/Projects/AdaptiveSampling/Icarust/experiments/data/readfish_simulation/data/reduced_21_22.fasta"
mean_read_length = 15000
weight = 1

3. config.ini

[TLS]
cert-dir = ./static/tls_certs
; cert-dir = /opt/ont/minknow/conf/rpc-certs
[PORTS]
manager = 10000
position = 10001

[SEQUENCER]
channels = 3000

4. Dorado command

/Users/daanishmahajan/Projects/AdaptiveSampling/Icarust/dorado/ont-dorado-server/bin/dorado_basecall_server \
--log_path /Users/daanishmahajan/Projects/AdaptiveSampling/Icarust/dorado/dorado/log \
--config /Users/daanishmahajan/Projects/AdaptiveSampling/Icarust/dorado/ont-dorado-server/data/dna_r10.4.1_e8.2_400bps_fast.cfg \
--ipc_threads 3 \
--port /tmp/.guppy/5555 \
--dorado_download_path /Users/daanishmahajan/Projects/AdaptiveSampling/Icarust/dorado/dorado/models

5. Readfish command

sudo /opt/anaconda3/envs/readfish/bin/readfish targets --device Bantersaurus \
--experiment-name test_connect \
--log-level info \
--toml /Users/daanishmahajan/Projects/AdaptiveSampling/Icarust/Profile_tomls/readfish.toml \
--port 10000 \
--chunk-log /Users/daanishmahajan/Projects/AdaptiveSampling/Icarust/experiments/data/readfish_simulation/log/control_icarust_R10_chunks.tsv

6. Icarust command

cargo run -r -- -s Profile_tomls/test.toml -v 

7. Full error log

E0516 11:07:55.535760000 7950916672 ssl_transport_security.cc:1653]    Handshake failed with fatal error SSL_ERROR_SSL: error:1000007d:SSL routines:OPENSSL_internal:CERTIFICATE_VERIFY_FAILED.
E0516 11:07:55.540749000 7950916672 ssl_transport_security.cc:1653]    Handshake failed with fatal error SSL_ERROR_SSL: error:1000007d:SSL routines:OPENSSL_internal:CERTIFICATE_VERIFY_FAILED.
Traceback (most recent call last):
  File "/opt/anaconda3/envs/readfish/bin/readfish", line 8, in <module>
    sys.exit(main())
  File "/opt/anaconda3/envs/readfish/lib/python3.10/site-packages/readfish/_cli_base.py", line 61, in main
    raise SystemExit(args.func(parser, args, extras))
  File "/opt/anaconda3/envs/readfish/lib/python3.10/site-packages/readfish/entry_points/targets.py", line 587, in run
    minknow_version = _get_minknow_version(host=args.host, port=args.port)
  File "/opt/anaconda3/envs/readfish/lib/python3.10/site-packages/readfish/_compatibility.py", line 58, in _get_minknow_version
    manager = Manager(host=host, port=port)
  File "/opt/anaconda3/envs/readfish/lib/python3.10/site-packages/minknow_api/manager.py", line 355, in __init__
    version_info = self.rpc.get_version_info()
  File "/opt/anaconda3/envs/readfish/lib/python3.10/site-packages/minknow_api/manager_service.py", line 476, in get_version_info
    return run_with_retry(self._stub.get_version_info,
  File "/opt/anaconda3/envs/readfish/lib/python3.10/site-packages/minknow_api/manager_service.py", line 99, in run_with_retry
    result = MessageWrapper(method(message, timeout=timeout), unwraps=unwraps)
  File "/opt/anaconda3/envs/readfish/lib/python3.10/site-packages/grpc/_channel.py", line 1181, in __call__
    return _end_unary_response_blocking(state, call, False, None)
  File "/opt/anaconda3/envs/readfish/lib/python3.10/site-packages/grpc/_channel.py", line 1006, in _end_unary_response_blocking
    raise _InactiveRpcError(state)  # pytype: disable=not-instantiable
grpc._channel._InactiveRpcError: <_InactiveRpcError of RPC that terminated with:
        status = StatusCode.UNAVAILABLE
        details = "failed to connect to all addresses; last error: UNKNOWN: ipv4:127.0.0.1:10000: Ssl handshake failed: SSL_ERROR_SSL: error:1000007d:SSL routines:OPENSSL_internal:CERTIFICATE_VERIFY_FAILED"
        debug_error_string = "UNKNOWN:Error received from peer  {created_time:"2024-05-16T11:07:55.540956+05:30", grpc_status:14, grpc_message:"failed to connect to all addresses; last error: UNKNOWN: ipv4:127.0.0.1:10000: Ssl handshake failed: SSL_ERROR_SSL: error:1000007d:SSL routines:OPENSSL_internal:CERTIFICATE_VERIFY_FAILED"}"