Handshake failed with fatal error SSL_ERROR_SSL: error:1000007d: #370

adbeggs · 2024-08-05T14:00:46Z

Hello

Thanks in advance for looking at our query. I am trying to get Readfish working on a Gridion with attached P2 Solo.

Getting fine through the simulation bit etc but when I try and do an unblock all I get the following below. It seems to want import of a TLS certificate but I can't see how to achieve this from the ReadFish documentation:

2024-08-05 14:00:03,929 readfish /data/software/condaenvs/readfish/bin/readfish unblock-all --device PS2-00952-B --experiment-name Bas
2024-08-05 14:00:03,929 readfish chemistry=<Chemistry.SIMPLEX: 'simplex'>
2024-08-05 14:00:03,929 readfish command='unblock-all'
2024-08-05 14:00:03,929 readfish debug_log=True
2024-08-05 14:00:03,929 readfish device='PS2-00952-B'
2024-08-05 14:00:03,929 readfish dry_run=False
2024-08-05 14:00:03,929 readfish experiment_name='Bastard'
2024-08-05 14:00:03,929 readfish host='127.0.0.1'
2024-08-05 14:00:03,929 readfish log_file=None
2024-08-05 14:00:03,930 readfish log_format='%(asctime)s %(name)s %(message)s'
2024-08-05 14:00:03,930 readfish log_level='info'
2024-08-05 14:00:03,930 readfish max_unblock_read_length_seconds=5
2024-08-05 14:00:03,930 readfish port=None
2024-08-05 14:00:03,930 readfish throttle=0.4
2024-08-05 14:00:03,930 readfish unblock_duration=0.1
2024-08-05 14:00:03,930 readfish wait_for_ready=120
2024-08-05 14:00:03,930 readfish Version=2024.2.0
WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
E0000 00:00:1722866403.952401  337256 ssl_transport_security.cc:1650] Handshake failed with fatal error SSL_ERROR_SSL: error:1000007d:SSL routines:OPENSSL_internal:CERTIFICATE_VERIFY_FAILED.
E0000 00:00:1722866403.968253  337256 ssl_transport_security.cc:1650] Handshake failed with fatal error SSL_ERROR_SSL: error:1000007d:SSL routines:OPENSSL_internal:CERTIFICATE_VERIFY_FAILED.
Traceback (most recent call last):
  File "/data/software/condaenvs/readfish/bin/readfish", line 8, in <module>
    sys.exit(main())
  File "/data/software/condaenvs/readfish/lib/python3.10/site-packages/readfish/_cli_base.py", line 61, in main
    raise SystemExit(args.func(parser, args, extras))
  File "/data/software/condaenvs/readfish/lib/python3.10/site-packages/readfish/entry_points/unblock_all.py", line 66, in run
    ret = targets.run(parser, args, extras)
  File "/data/software/condaenvs/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 "/data/software/condaenvs/readfish/lib/python3.10/site-packages/readfish/_compatibility.py", line 58, in _get_minknow_version
    manager = Manager(host=host, port=port)
  File "/data/software/condaenvs/readfish/lib/python3.10/site-packages/minknow_api/manager.py", line 361, in __init__
    version_info = self.rpc.get_version_info()
  File "/data/software/condaenvs/readfish/lib/python3.10/site-packages/minknow_api/manager_service.py", line 478, in get_version_info
    return run_with_retry(self._stub.get_version_info,
  File "/data/software/condaenvs/readfish/lib/python3.10/site-packages/minknow_api/manager_service.py", line 101, in run_with_retry
    result = MessageWrapper(method(message, timeout=timeout), unwraps=unwraps)
  File "/data/software/condaenvs/readfish/lib/python3.10/site-packages/grpc/_channel.py", line 1181, in __call__
    return _end_unary_response_blocking(state, call, False, None)
  File "/data/software/condaenvs/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: ipv4:127.0.0.1:9502: Ssl handshake failed (TSI_PROTOCOL_FAILURE): SSL_ERROR_SSL: error:1000007d:SSL routines:OPENSSL_internal:CERTIFICATE_VERIFY_FAILED"
	debug_error_string = "UNKNOWN:Error received from peer  {grpc_message:"failed to connect to all addresses; last error: UNKNOWN: ipv4:127.0.0.1:9502: Ssl handshake failed (TSI_PROTOCOL_FAILURE): SSL_ERROR_SSL: error:1000007d:SSL routines:OPENSSL_internal:CERTIFICATE_VERIFY_FAILED", grpc_status:14, created_time:"2024-08-05T14:00:03.968470271+00:00"}"

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github-actions · 2024-08-05T14:01:05Z

Thank you for your issue. Give us a little time to review it.

PS. You might want to check the FAQ if you haven't done so already.

This is an automated reply, generated by FAQtory

mattloose · 2024-08-05T14:04:39Z

Interesting choice of experiment name.

Are you using the latest version of minKNOW by any chance?

adbeggs · 2024-08-05T14:07:20Z

Might be one or two behind - thanks - I'll try it and see.

mattloose · 2024-08-05T14:10:02Z

Before you update.

I suspect that your version of MinKNOW has not had the option checked to allow "guest" logins and that you need an account to log into it remotely. A quick fix woudl be to enable guest login on the GUI.

adbeggs · 2024-08-05T14:19:14Z

It's currently 24.02.10, upgraded to 24.02.16, guest access has been on... still same error

adbeggs · 2024-08-05T14:20:14Z

Here's the output of pip list:

(/data/software/condaenvs/readfish) grid@grid0001:/data/software/condaenvs$ pip list
Package Version

about-time 4.2.1
alive-progress 3.1.5
attrs 24.1.0
Bottleneck 1.3.8
cattrs 23.2.3
click 8.1.7
exceptiongroup 1.2.2
grapheme 0.6.0
grpcio 1.65.4
iniconfig 2.0.0
llvmlite 0.42.0
mappy 2.28
mappy-rs 0.0.7
minknow_api 6.0.4
more-itertools 10.3.0
numba 0.59.1
numpy 1.26.4
ont-pybasecall-client-lib 7.4.12
packaging 24.1
pip 24.2
pluggy 1.5.0
protobuf 4.25.4
pyRFC3339 1.1
pytest 8.3.2
pytz 2024.1
readfish 2024.2.0
readfish_summarise 0.2.6
rtoml 0.11.0
scipy 1.12.0
setuptools 72.1.0
tomli 2.0.1
typing_extensions 4.12.2
wheel 0.44.0

mattloose · 2024-08-05T14:23:18Z

Can you check if you can remotely access minKnow on the p2solo from a different computer via minkow itself (if that makes sense...)

adbeggs · 2024-08-05T14:25:56Z

Yes tried that and yes I can Sent from Outlook for iOS<https://aka.ms/o0ukef>

…

________________________________ From: mattloose ***@***.***> Sent: Monday, August 5, 2024 3:23:40 PM To: LooseLab/readfish ***@***.***> Cc: Andrew Beggs (Cancer and Genomic Sciences) ***@***.***>; Author ***@***.***> Subject: Re: [LooseLab/readfish] Handshake failed with fatal error SSL_ERROR_SSL: error:1000007d: (Issue #370) CAUTION: This email originated from outside the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe. Can you check if you can remotely access minKnow on the p2solo from a different computer via minkow itself (if that makes sense...) — Reply to this email directly, view it on GitHub<#370 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AC7KTDDVKA3TE4HROF5MD5DZP6DGZAVCNFSM6AAAAABMAL5GQWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRZGIYDIOBRG4>. You are receiving this because you authored the thread.Message ID: ***@***.***>

mattloose · 2024-08-05T14:30:11Z

You are ahead of me then – I can’t connect remotely to my P2solo on minknow 6.0 Will look into this and come back to you. From: Andrew Beggs ***@***.***> Date: Monday, 5 August 2024 at 15:26 To: LooseLab/readfish ***@***.***> Cc: Matthew Loose (staff) ***@***.***>, Comment ***@***.***> Subject: Re: [LooseLab/readfish] Handshake failed with fatal error SSL_ERROR_SSL: error:1000007d: (Issue #370) Yes tried that and yes I can Sent from Outlook for iOS<https://aka.ms/o0ukef>

…

________________________________ From: mattloose ***@***.***> Sent: Monday, August 5, 2024 3:23:40 PM To: LooseLab/readfish ***@***.***> Cc: Andrew Beggs (Cancer and Genomic Sciences) ***@***.***>; Author ***@***.***> Subject: Re: [LooseLab/readfish] Handshake failed with fatal error SSL_ERROR_SSL: error:1000007d: (Issue #370) CAUTION: This email originated from outside the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe. Can you check if you can remotely access minKnow on the p2solo from a different computer via minkow itself (if that makes sense...) — Reply to this email directly, view it on GitHub<#370 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AC7KTDDVKA3TE4HROF5MD5DZP6DGZAVCNFSM6AAAAABMAL5GQWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRZGIYDIOBRG4>. You are receiving this because you authored the thread.Message ID: ***@***.***> — Reply to this email directly, view it on GitHub<#370 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AB6SR5EZ3N5DTHMZR2NGHOLZP6DQXAVCNFSM6AAAAABMAL5GQWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRZGIYTANRSHE>. You are receiving this because you commented.Message ID: ***@***.***> This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please contact the sender and delete the email and attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. Email communications with the University of Nottingham may be monitored where permitted by law.

mattloose · 2024-08-05T14:58:41Z

You might want to look at:

#356

presuming you are on a linux machine running this then the path to the certificate is:

/opt/ont/minknow/conf/rpc-certs/ca.crt

adbeggs · 2024-08-05T15:03:39Z

Interesting… this seems to have made a difference A From: mattloose ***@***.***> Sent: Monday, August 5, 2024 3:59 PM To: LooseLab/readfish ***@***.***> Cc: Andrew Beggs (Cancer and Genomic Sciences) ***@***.***>; Author ***@***.***> Subject: Re: [LooseLab/readfish] Handshake failed with fatal error SSL_ERROR_SSL: error:1000007d: (Issue #370) CAUTION: This email originated from outside the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe. You might want to look at: #356<#356> presuming you are on a linux machine running this then the path to the certificate is: /opt/ont/minknow/conf/rpc-certs/ca.crt — Reply to this email directly, view it on GitHub<#370 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AC7KTDAQFUE73CIXXJPSZCLZP6HLPAVCNFSM6AAAAABMAL5GQWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRZGI4DGMZUGQ>. You are receiving this because you authored the thread.Message ID: ***@***.***>

mattloose · 2024-08-05T15:05:31Z

Great! From: Andrew Beggs ***@***.***> Date: Monday, 5 August 2024 at 16:04 To: LooseLab/readfish ***@***.***> Cc: Matthew Loose (staff) ***@***.***>, Comment ***@***.***> Subject: Re: [LooseLab/readfish] Handshake failed with fatal error SSL_ERROR_SSL: error:1000007d: (Issue #370) Interesting… this seems to have made a difference A From: mattloose ***@***.***> Sent: Monday, August 5, 2024 3:59 PM To: LooseLab/readfish ***@***.***> Cc: Andrew Beggs (Cancer and Genomic Sciences) ***@***.***>; Author ***@***.***> Subject: Re: [LooseLab/readfish] Handshake failed with fatal error SSL_ERROR_SSL: error:1000007d: (Issue #370) CAUTION: This email originated from outside the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe. You might want to look at: #356<#356> presuming you are on a linux machine running this then the path to the certificate is: /opt/ont/minknow/conf/rpc-certs/ca.crt — Reply to this email directly, view it on GitHub<#370 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AC7KTDAQFUE73CIXXJPSZCLZP6HLPAVCNFSM6AAAAABMAL5GQWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRZGI4DGMZUGQ>. You are receiving this because you authored the thread.Message ID: ***@***.***> — Reply to this email directly, view it on GitHub<#370 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AB6SR5CM2KDBEC67GTEW4LDZP6H6FAVCNFSM6AAAAABMAL5GQWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRZGI4TINRUGI>. You are receiving this because you commented.Message ID: ***@***.***> This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please contact the sender and delete the email and attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. Email communications with the University of Nottingham may be monitored where permitted by law.

adbeggs · 2024-08-05T15:09:17Z

More joy but then:

2024-08-05 15:06:57,364 readfish chemistry=<Chemistry.SIMPLEX: 'simplex'>
2024-08-05 15:06:57,364 readfish command='unblock-all'
2024-08-05 15:06:57,364 readfish debug_log=True
2024-08-05 15:06:57,364 readfish device='P2S-00952-B'
2024-08-05 15:06:57,364 readfish dry_run=False
2024-08-05 15:06:57,364 readfish experiment_name='Bastard'
2024-08-05 15:06:57,364 readfish host='127.0.0.1'
2024-08-05 15:06:57,364 readfish log_file=None
2024-08-05 15:06:57,364 readfish log_format='%(asctime)s %(name)s %(message)s'
2024-08-05 15:06:57,364 readfish log_level='info'
2024-08-05 15:06:57,364 readfish max_unblock_read_length_seconds=5
2024-08-05 15:06:57,364 readfish port=None
2024-08-05 15:06:57,364 readfish throttle=0.4
2024-08-05 15:06:57,364 readfish unblock_duration=0.1
2024-08-05 15:06:57,364 readfish wait_for_ready=120
2024-08-05 15:06:57,364 readfish Version=2024.2.0
2024-08-05 15:06:57,392 readfish.unblock-all This readfish version (2024.2.0) is tested for compatibility with MinKNOW v5.0.0 to v5.9.7.
This version of minknow is 5.9.12.
If readfish fails please try to upgrade readfish.
If there isn't a newer version of readfish and readfish is failing, please open an issue:
    https://github.com/LooseLab/readfish/issues
2024-08-05 15:06:57,427 readfish._read_until_client Protocol phase changed to PHASE_SEQUENCING
2024-08-05 15:06:57,427 readfish._read_until_client Protocol state changed to PROTOCOL_RUNNING
2024-08-05 15:06:57,429 readfish.unblock-all eJxtj1EKwjAQRP9zitADCPrvSUIIadjW0M1uzaba4xtBrAn+7b4ZhhkTPCJkJ1BKpFlOxI5Xq0zy6/qPmwxzZBJrFfkE+qqHjUbksOiaNKgUyYXbRotU6ayS34/3oorPM5T3baySGozgmH5Chi+dpganDUvsvR/YWWtVgXuP6qAG+ZEf4Jp+hzgC8tM1Ww7xBaW9au4=
2024-08-05 15:06:57,450 readfish.unblock-all Configuration description:
Region unblock all (control=False).
Region applies to section of flow cell (# = applied, . = not applied):

    ########################################################################################################################
    ########################################################################################################################
    ########################################################################################################################
    ########################################################################################################################
    ########################################################################################################################
    ########################################################################################################################
    ########################################################################################################################
    ########################################################################################################################
    ########################################################################################################################
    ########################################################################################################################
    ########################################################################################################################
    ########################################################################################################################
    ########################################################################################################################

2024-08-05 15:06:57,452 readfish.unblock-all Fetching Run Configuration
2024-08-05 15:06:57,453 readfish.unblock-all Run Configuration Received
2024-08-05 15:06:57,453 readfish.unblock-all run_id=b750e3e5-c154-4a96-a24a-5a88ff61e253
2024-08-05 15:06:57,453 readfish.unblock-all break_reads_after_seconds=1.0
2024-08-05 15:06:57,453 readfish.unblock-all sample_rate=5000
2024-08-05 15:06:57,467 readfish.unblock-all Initialising Caller
2024-08-05 15:06:57,467 readfish.unblock-all Caller initialised
2024-08-05 15:06:57,467 readfish.unblock-all Using the `no_op` Caller. No base-calling will be performed, and minimum viable results will be yielded back for each read provided.
2024-08-05 15:06:57,469 readfish.unblock-all Initialising Aligner
2024-08-05 15:06:57,469 readfish.unblock-all Aligner initialised
2024-08-05 15:06:57,472 readfish.unblock-all Starting main loop
2024-08-05 15:06:57,472 readfish.unblock-all Using the `no_op` Aligner. No alignments will be performed, and all Results will be passed through.
2024-08-05 15:06:57,475 readfish.unblock-all readfish started in PHASE_SEQUENCING. Fully sequencing first read from each channel.
Traceback (most recent call last):
  File "/data/software/condaenvs/readfish/bin/readfish", line 8, in <module>
    sys.exit(main())
  File "/data/software/condaenvs/readfish/lib/python3.10/site-packages/readfish/_cli_base.py", line 61, in main
    raise SystemExit(args.func(parser, args, extras))
  File "/data/software/condaenvs/readfish/lib/python3.10/site-packages/readfish/entry_points/unblock_all.py", line 66, in run
    ret = targets.run(parser, args, extras)
  File "/data/software/condaenvs/readfish/lib/python3.10/site-packages/readfish/entry_points/targets.py", line 653, in run
    worker.run()
  File "/data/software/condaenvs/readfish/lib/python3.10/site-packages/readfish/entry_points/targets.py", line 483, in run
    chunks = self.client.get_read_chunks(self.client.channel_count, last=True)
  File "/data/software/condaenvs/readfish/lib/python3.10/site-packages/readfish/read_until/base.py", line 349, in get_read_chunks
    data = [
  File "/data/software/condaenvs/readfish/lib/python3.10/site-packages/readfish/read_until/base.py", line 352, in <listcomp>
    if read.number > self.channel_read_latest_decision[channel]
AttributeError: number

mattloose · 2024-08-05T15:11:22Z

https://github.com/LooseLab/readfish/tree/feature/minknow6-compatibility

This will be your fix....

We were hoping it would be out now but it should work. Sorry for the hassle - it's a major minknow release!

adbeggs · 2024-08-06T10:00:45Z

Hi @mattloose

Still getting the AttributeError: number error with simulation.
Using Minknow 5.9.12 not 6, have downloaded the right version of readfish for this...
The Readfish for v6 won't run (although I have installed this) as it expects Minknow 6

mattloose · 2024-08-06T10:32:39Z

Can you try restarting your system? 5.9.12 should be working with readfish 2024.2.0 as the issue causing the number error is minkno 6.0 specific.

github-actions · 2024-09-06T02:26:12Z

This issue is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 5 days.

github-actions · 2024-09-11T02:26:19Z

This issue was closed because there has been no response for 5 days after becoming stale.

ahfitzpa mentioned this issue Aug 16, 2024

readfish unblock-all Command Fails with AttributeError: number with MinKNOW v6.0.8 #373

Closed

github-actions bot added the Stale label Sep 6, 2024

github-actions bot closed this as not planned Won't fix, can't repro, duplicate, stale Sep 11, 2024

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Handshake failed with fatal error SSL_ERROR_SSL: error:1000007d: #370

Handshake failed with fatal error SSL_ERROR_SSL: error:1000007d: #370

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Handshake failed with fatal error SSL_ERROR_SSL: error:1000007d: #370

Handshake failed with fatal error SSL_ERROR_SSL: error:1000007d: #370

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