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LooseLab / readfish

CLI tool for flexible and fast adaptive sampling on ONT sequencers
https://looselab.github.io/readfish/
GNU General Public License v3.0
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TLS error when running unblock-all #204

Closed melkramer closed 11 months ago

melkramer commented 2 years ago

Hello,

We are getting an error when trying to test unblocking as per the protocol instructions. The process seems to start running but always errors with the same message (I've tried changing the host IP, the port, and re-creating the conda environment). Could you please advise on what the issue might be?

Thank you, Melissa

$ readfish unblock-all --device X1 --experiment-name "Testing ReadFish Unblock All"

2022-06-29 16:41:51,196 Manager /data/.miniconda/envs/readfish/bin/readfish unblock-all --device X1 --experiment-name Testing ReadFish Unblock All INFO 2022-06-29 16:41:51,196 Manager batch_size=512 2022-06-29 16:41:51,196 Manager batch_size=512 INFO 2022-06-29 16:41:51,196 Manager cache_size=512 2022-06-29 16:41:51,196 Manager cache_size=512 INFO 2022-06-29 16:41:51,196 Manager channels=[1, 512] 2022-06-29 16:41:51,196 Manager channels=[1, 512] INFO 2022-06-29 16:41:51,196 Manager command=unblock-all 2022-06-29 16:41:51,196 Manager command=unblock-all INFO 2022-06-29 16:41:51,196 Manager device=X1 2022-06-29 16:41:51,196 Manager device=X1 INFO 2022-06-29 16:41:51,196 Manager dry_run=False 2022-06-29 16:41:51,196 Manager dry_run=False INFO 2022-06-29 16:41:51,196 Manager experiment_name=Testing ReadFish Unblock All 2022-06-29 16:41:51,196 Manager experiment_name=Testing ReadFish Unblock All INFO 2022-06-29 16:41:51,196 Manager func=<function run at 0x7fe6413efdc0> 2022-06-29 16:41:51,196 Manager func=<function run at 0x7fe6413efdc0> INFO 2022-06-29 16:41:51,196 Manager host=127.0.0.1 2022-06-29 16:41:51,196 Manager host=127.0.0.1 INFO 2022-06-29 16:41:51,196 Manager log_file=None 2022-06-29 16:41:51,196 Manager log_file=None INFO 2022-06-29 16:41:51,196 Manager log_format=%(asctime)s %(name)s %(message)s 2022-06-29 16:41:51,196 Manager log_format=%(asctime)s %(name)s %(message)s INFO 2022-06-29 16:41:51,196 Manager log_level=info 2022-06-29 16:41:51,196 Manager log_level=info INFO 2022-06-29 16:41:51,196 Manager port=9501 2022-06-29 16:41:51,196 Manager port=9501 INFO 2022-06-29 16:41:51,196 Manager run_time=172800 2022-06-29 16:41:51,196 Manager run_time=172800 INFO 2022-06-29 16:41:51,196 Manager throttle=0.4 2022-06-29 16:41:51,196 Manager throttle=0.4 INFO 2022-06-29 16:41:51,196 Manager unblock_duration=0.1 2022-06-29 16:41:51,196 Manager unblock_duration=0.1 INFO 2022-06-29 16:41:51,196 Manager workers=1 2022-06-29 16:41:51,196 Manager workers=1 Traceback (most recent call last): File "/data/.miniconda/envs/readfish/bin/readfish", line 8, in sys.exit(main()) File "/data/.miniconda/envs/readfish/lib/python3.8/site-packages/ru/cli.py", line 43, in main args.func(parser, args) File "/data/.miniconda/envs/readfish/lib/python3.8/site-packages/ru/unblock_all.py", line 127, in run position = get_device(args.device) File "/data/.miniconda/envs/readfish/lib/python3.8/site-packages/ru/utils.py", line 918, in get_device manager = Manager(host=host, port=port, use_tls=use_tls) TypeError: init() got an unexpected keyword argument 'use_tls'

alexomics commented 2 years ago

Hi Melissa, Are you running using MinKNOW v5? I think that you need to use the issue187 branch.

Your conda environment should look something like this, don't forget to set your Guppy version: 

name: readfish
channels:
  - bioconda
  - conda-forge
  - defaults
dependencies:
  - python=3.7
  - pip
  - pip:
    - git+https://github.com/nanoporetech/read_until_api@v3.0.0
    - git+https://github.com/LooseLab/readfish@issue187
    - ont-pyguppy-client-lib==6.0.6

Please let me know if you run into any other issues.

melkramer commented 2 years ago

Apologies to bother you again, but actually we are running MinKnow 4.5. I tried setting up the environment as follows:

I am able to do the unblocking with no problem, and I have validated the toml file, but when I try to test basecalling it just hangs at this point:

2022-07-22 14:03:27,646 ru.ru_gen /home/grid/.conda/envs/readfish/bin/readfish targets --device X1 --experiment-name RU Test basecall and map --toml /

data/human_chr_selection.toml --log-file ru_test.log --port 9502

2022-07-22 14:03:27,646 ru.ru_gen batch_size=512

2022-07-22 14:03:27,646 ru.ru_gen cache_size=512

2022-07-22 14:03:27,646 ru.ru_gen channels=[1, 512]

2022-07-22 14:03:27,646 ru.ru_gen chunk_log=None

2022-07-22 14:03:27,646 ru.ru_gen command=targets

2022-07-22 14:03:27,646 ru.ru_gen device=X1

2022-07-22 14:03:27,647 ru.ru_gen dry_run=False

2022-07-22 14:03:27,647 ru.ru_gen experiment_name=RU Test basecall and map

2022-07-22 14:03:27,647 ru.ru_gen func=<function run at 0x7fcd653eaf70>

2022-07-22 14:03:27,647 ru.ru_gen host=127.0.0.1

2022-07-22 14:03:27,647 ru.ru_gen log_file=ru_test.log

2022-07-22 14:03:27,647 ru.ru_gen log_format=%(asctime)s %(name)s %(message)s

2022-07-22 14:03:27,647 ru.ru_gen log_level=info

2022-07-22 14:03:27,647 ru.ru_gen paf_log=None

2022-07-22 14:03:27,647 ru.ru_gen port=9502

2022-07-22 14:03:27,647 ru.ru_gen run_time=172800

2022-07-22 14:03:27,647 ru.ru_gen throttle=0.4

2022-07-22 14:03:27,647 ru.ru_gen toml=/data/human_chr_selection.toml

2022-07-22 14:03:27,647 ru.ru_gen unblock_duration=0.1

2022-07-22 14:03:27,647 ru.ru_gen workers=1

2022-07-22 14:03:27,653 ru.ru_gen Initialising minimap2 mapper

2022-07-22 14:03:33,871 ru.ru_gen Mapper initialised

2022-07-22 14:03:33,879 ru.ru_gen This experiment has 1 region on the flowcell

2022-07-22 14:03:33,879 ru.ru_gen Using reference: /data/isilon_mount/hg38.mmi

2022-07-22 14:03:41,122 ru.ru_gen Region 'select_chr_21_22' (control=False) has 2 contigs of which 2 are in the reference. There are 4 targets (includ

ing +/- strand) representing 3.04% of the reference. Reads will be unblocked when classed as single_off or multi_off; sequenced when classed as single

_on or multi_on; and polled for more data when classed as no_map or no_seq.

It does not generate any errors or write other messages to the log. Can you please advise what might be happening?

Thank you so much, Melissa

From: alex @.***> Sent: Thursday, June 30, 2022 9:50:21 AM To: LooseLab/readfish Cc: delaBastide, Melissa; Author Subject: Re: [LooseLab/readfish] TLS error when running unblock-all (Issue #204)

Hi Melissa, Are you running using MinKNOW v5? I think that you need to use the issue187 branch.

Your conda environment should look something like this, don't forget to set your Guppy version:

name: readfish channels:

Please let me know if you run into any other issues.

— Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_LooseLab_readfish_issues_204-23issuecomment-2D1171245102&d=DwMCaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=YkQFpFMc1TX4EpPMAcLbOFRrB-GWTkBhuseQ_TTscv4&m=LSCyi8LvH1mPw2qpTmXCN9drM4QkUiDNszwkzLPG-qoALkzwkCdFqXwFRt6aZivW&s=nw1WXLdZul2EPG0hzdKRu23HIjQA8Ru3_IpOLljFmms&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ATP2RALPQGSGNBLOHNV7S4TVRWQZ3ANCNFSM52JNIWOQ&d=DwMCaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=YkQFpFMc1TX4EpPMAcLbOFRrB-GWTkBhuseQ_TTscv4&m=LSCyi8LvH1mPw2qpTmXCN9drM4QkUiDNszwkzLPG-qoALkzwkCdFqXwFRt6aZivW&s=YluiUVJd45s9NjCIBAOsPbBUpypO0ozsgHob8A82YOE&e=. You are receiving this because you authored the thread.Message ID: @.***>

melkramer commented 2 years ago

Hi Matt,

Just wanted to follow up on this to see if you knew why the software hangs on basecalling?

Thanks very much, Melissa

From: delaBastide, Melissa Sent: Monday, July 25, 2022 10:51:20 AM To: LooseLab/readfish; LooseLab/readfish Cc: Author Subject: Re: [LooseLab/readfish] TLS error when running unblock-all (Issue #204)

Apologies to bother you again, but actually we are running MinKnow 4.5. I tried setting up the environment as follows:

I am able to do the unblocking with no problem, and I have validated the toml file, but when I try to test basecalling it just hangs at this point:

2022-07-22 14:03:27,646 ru.ru_gen /home/grid/.conda/envs/readfish/bin/readfish targets --device X1 --experiment-name RU Test basecall and map --toml /

data/human_chr_selection.toml --log-file ru_test.log --port 9502

2022-07-22 14:03:27,646 ru.ru_gen batch_size=512

2022-07-22 14:03:27,646 ru.ru_gen cache_size=512

2022-07-22 14:03:27,646 ru.ru_gen channels=[1, 512]

2022-07-22 14:03:27,646 ru.ru_gen chunk_log=None

2022-07-22 14:03:27,646 ru.ru_gen command=targets

2022-07-22 14:03:27,646 ru.ru_gen device=X1

2022-07-22 14:03:27,647 ru.ru_gen dry_run=False

2022-07-22 14:03:27,647 ru.ru_gen experiment_name=RU Test basecall and map

2022-07-22 14:03:27,647 ru.ru_gen func=<function run at 0x7fcd653eaf70>

2022-07-22 14:03:27,647 ru.ru_gen host=127.0.0.1

2022-07-22 14:03:27,647 ru.ru_gen log_file=ru_test.log

2022-07-22 14:03:27,647 ru.ru_gen log_format=%(asctime)s %(name)s %(message)s

2022-07-22 14:03:27,647 ru.ru_gen log_level=info

2022-07-22 14:03:27,647 ru.ru_gen paf_log=None

2022-07-22 14:03:27,647 ru.ru_gen port=9502

2022-07-22 14:03:27,647 ru.ru_gen run_time=172800

2022-07-22 14:03:27,647 ru.ru_gen throttle=0.4

2022-07-22 14:03:27,647 ru.ru_gen toml=/data/human_chr_selection.toml

2022-07-22 14:03:27,647 ru.ru_gen unblock_duration=0.1

2022-07-22 14:03:27,647 ru.ru_gen workers=1

2022-07-22 14:03:27,653 ru.ru_gen Initialising minimap2 mapper

2022-07-22 14:03:33,871 ru.ru_gen Mapper initialised

2022-07-22 14:03:33,879 ru.ru_gen This experiment has 1 region on the flowcell

2022-07-22 14:03:33,879 ru.ru_gen Using reference: /data/isilon_mount/hg38.mmi

2022-07-22 14:03:41,122 ru.ru_gen Region 'select_chr_21_22' (control=False) has 2 contigs of which 2 are in the reference. There are 4 targets (includ

ing +/- strand) representing 3.04% of the reference. Reads will be unblocked when classed as single_off or multi_off; sequenced when classed as single

_on or multi_on; and polled for more data when classed as no_map or no_seq.

It does not generate any errors or write other messages to the log. Can you please advise what might be happening?

Thank you so much, Melissa

From: alex @.***> Sent: Thursday, June 30, 2022 9:50:21 AM To: LooseLab/readfish Cc: delaBastide, Melissa; Author Subject: Re: [LooseLab/readfish] TLS error when running unblock-all (Issue #204)

Hi Melissa, Are you running using MinKNOW v5? I think that you need to use the issue187 branch.

Your conda environment should look something like this, don't forget to set your Guppy version:

name: readfish channels:

Please let me know if you run into any other issues.

— Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_LooseLab_readfish_issues_204-23issuecomment-2D1171245102&d=DwMCaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=YkQFpFMc1TX4EpPMAcLbOFRrB-GWTkBhuseQ_TTscv4&m=LSCyi8LvH1mPw2qpTmXCN9drM4QkUiDNszwkzLPG-qoALkzwkCdFqXwFRt6aZivW&s=nw1WXLdZul2EPG0hzdKRu23HIjQA8Ru3_IpOLljFmms&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ATP2RALPQGSGNBLOHNV7S4TVRWQZ3ANCNFSM52JNIWOQ&d=DwMCaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=YkQFpFMc1TX4EpPMAcLbOFRrB-GWTkBhuseQ_TTscv4&m=LSCyi8LvH1mPw2qpTmXCN9drM4QkUiDNszwkzLPG-qoALkzwkCdFqXwFRt6aZivW&s=YluiUVJd45s9NjCIBAOsPbBUpypO0ozsgHob8A82YOE&e=. You are receiving this because you authored the thread.Message ID: @.***>

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