Skip to content

Readfish not rejecting reads #406

Closed
Closed
Readfish not rejecting reads#406
Labels
Stale

Description

@hiruna72
hiruna72
opened on Sep 29, 2025

Hello authors,

It's me again. This issue might be related to the Issue as well .

For one of our runs we saw that readfish is not rejecting anymore (but readfish kept running without crashing).
What could be the reason for this behaviour?
I have pasted the last part of the log for your reference.

Thank you!

2025-09-17 19:19:02,009 readfish.targets 0195R/0.4422s; Avg: 0206R/0.4539s; Seq:1,301,924; Unb:49,253,555; Pro:21,294,053; Slow batches (>0.80s): 2261/347126
2025-09-17 19:19:02,453 readfish.targets 0110R/0.4412s; Avg: 0206R/0.4539s; Seq:1,301,925; Unb:49,253,620; Pro:21,294,097; Slow batches (>0.80s): 2261/347127
2025-09-17 19:19:02,899 readfish.targets 0204R/0.4435s; Avg: 0206R/0.4539s; Seq:1,301,928; Unb:49,253,747; Pro:21,294,171; Slow batches (>0.80s): 2261/347128
2025-09-17 19:19:03,340 readfish.targets 0108R/0.4362s; Avg: 0206R/0.4539s; Seq:1,301,931; Unb:49,253,824; Pro:21,294,199; Slow batches (>0.80s): 2261/347129
2025-09-17 19:19:03,780 readfish.targets 0168R/0.4381s; Avg: 0206R/0.4539s; Seq:1,301,937; Unb:49,253,934; Pro:21,294,251; Slow batches (>0.80s): 2261/347130
2025-09-17 19:19:04,230 readfish.targets 0121R/0.4470s; Avg: 0206R/0.4539s; Seq:1,301,939; Unb:49,254,013; Pro:21,294,291; Slow batches (>0.80s): 2261/347131
2025-09-17 19:19:04,679 readfish.targets 0084R/0.4468s; Avg: 0206R/0.4539s; Seq:1,301,939; Unb:49,254,060; Pro:21,294,328; Slow batches (>0.80s): 2261/347132
2025-09-17 19:19:05,125 readfish.targets 0187R/0.4436s; Avg: 0206R/0.4539s; Seq:1,301,943; Unb:49,254,192; Pro:21,294,379; Slow batches (>0.80s): 2261/347133
2025-09-17 19:19:05,565 readfish.targets 0110R/0.4367s; Avg: 0206R/0.4539s; Seq:1,301,946; Unb:49,254,270; Pro:21,294,408; Slow batches (>0.80s): 2261/347134
2025-09-17 19:19:06,027 readfish.targets 0215R/0.4587s; Avg: 0206R/0.4539s; Seq:1,301,950; Unb:49,254,415; Pro:21,294,474; Slow batches (>0.80s): 2261/347135
2025-09-17 19:19:06,471 readfish.targets 0084R/0.4414s; Avg: 0206R/0.4539s; Seq:1,301,953; Unb:49,254,472; Pro:21,294,498; Slow batches (>0.80s): 2261/347136
2025-09-17 19:19:06,912 readfish.targets 0161R/0.4384s; Avg: 0206R/0.4539s; Seq:1,301,957; Unb:49,254,566; Pro:21,294,561; Slow batches (>0.80s): 2261/347137
2025-09-17 19:19:07,338 readfish.targets 0102R/0.4229s; Avg: 0206R/0.4539s; Seq:1,301,958; Unb:49,254,634; Pro:21,294,594; Slow batches (>0.80s): 2261/347138
2025-09-17 19:19:07,788 readfish.targets 0179R/0.4473s; Avg: 0206R/0.4539s; Seq:1,301,961; Unb:49,254,749; Pro:21,294,655; Slow batches (>0.80s): 2261/347139
2025-09-17 19:19:08,228 readfish.targets 0106R/0.4375s; Avg: 0206R/0.4539s; Seq:1,301,964; Unb:49,254,821; Pro:21,294,686; Slow batches (>0.80s): 2261/347140
2025-09-17 19:19:08,672 readfish.targets 0178R/0.4421s; Avg: 0206R/0.4539s; Seq:1,301,966; Unb:49,254,937; Pro:21,294,746; Slow batches (>0.80s): 2261/347141
2025-09-17 19:19:09,123 readfish.targets 0116R/0.4473s; Avg: 0206R/0.4539s; Seq:1,301,969; Unb:49,255,008; Pro:21,294,788; Slow batches (>0.80s): 2261/347142
2025-09-17 19:19:09,563 readfish.targets 0182R/0.4380s; Avg: 0206R/0.4539s; Seq:1,301,975; Unb:49,255,124; Pro:21,294,848; Slow batches (>0.80s): 2261/347143
2025-09-17 19:19:10,002 readfish.targets 0086R/0.4367s; Avg: 0206R/0.4539s; Seq:1,301,977; Unb:49,255,185; Pro:21,294,871; Slow batches (>0.80s): 2261/347144
2025-09-17 19:19:10,447 readfish.targets 0179R/0.4428s; Avg: 0206R/0.4539s; Seq:1,301,980; Unb:49,255,304; Pro:21,294,928; Slow batches (>0.80s): 2261/347145
2025-09-17 19:19:10,885 readfish.targets 0096R/0.4325s; Avg: 0206R/0.4539s; Seq:1,301,983; Unb:49,255,359; Pro:21,294,966; Slow batches (>0.80s): 2261/347146
2025-09-17 19:19:11,334 readfish.targets 0180R/0.4472s; Avg: 0206R/0.4539s; Seq:1,301,992; Unb:49,255,472; Pro:21,295,024; Slow batches (>0.80s): 2261/347147
2025-09-17 19:19:11,778 readfish.targets 0094R/0.4415s; Avg: 0206R/0.4539s; Seq:1,301,994; Unb:49,255,528; Pro:21,295,060; Slow batches (>0.80s): 2261/347148
2025-09-17 19:19:12,212 readfish.targets 0090R/0.4311s; Avg: 0206R/0.4539s; Seq:1,301,996; Unb:49,255,578; Pro:21,295,098; Slow batches (>0.80s): 2261/347149
2025-09-17 19:19:14,229 readfish.targets 0235R/2.0153s; Avg: 0206R/0.4539s; Seq:1,301,999; Unb:49,255,735; Pro:21,295,173; Slow batches (>0.80s): 2262/347150
2025-09-17 19:19:14,679 readfish.targets 0100R/0.4370s; Avg: 0206R/0.4539s; Seq:1,302,000; Unb:49,255,810; Pro:21,295,197; Slow batches (>0.80s): 2262/347151
2025-09-17 19:29:31,052 readfish._read_until_client Protocol phase changed to PHASE_MUX_SCAN                                                                                   
2025-09-17 19:29:31,053 readfish.targets MinKNOW is reporting PHASE_MUX_SCAN, waiting for PHASE_SEQUENCING to begin.                                                           
2025-09-17 19:33:31,300 readfish._read_until_client Protocol phase changed to PHASE_SEQUENCING                                                                                 
2025-09-17 21:04:35,486 readfish._read_until_client Protocol phase changed to PHASE_MUX_SCAN                                                                                   
2025-09-17 21:04:35,487 readfish.targets MinKNOW is reporting PHASE_MUX_SCAN, waiting for PHASE_SEQUENCING to begin.                                                           
2025-09-17 21:08:35,774 readfish._read_until_client Protocol phase changed to PHASE_SEQUENCING                                                                                 
2025-09-17 22:39:39,750 readfish._read_until_client Protocol phase changed to PHASE_MUX_SCAN                                                                                   
2025-09-17 22:39:39,751 readfish.targets MinKNOW is reporting PHASE_MUX_SCAN, waiting for PHASE_SEQUENCING to begin.                                                           
2025-09-17 22:43:42,024 readfish._read_until_client Protocol phase changed to PHASE_SEQUENCING                                                                                 
2025-09-18 00:14:46,226 readfish._read_until_client Protocol phase changed to PHASE_MUX_SCAN                                                                                   
2025-09-18 00:14:46,226 readfish.targets MinKNOW is reporting PHASE_MUX_SCAN, waiting for PHASE_SEQUENCING to begin.                                                           
2025-09-18 00:18:47,720 readfish._read_until_client Protocol phase changed to PHASE_SEQUENCING                                                                                 
2025-09-18 01:49:51,034 readfish._read_until_client Protocol phase changed to PHASE_MUX_SCAN                                                                                   
2025-09-18 01:49:51,034 readfish.targets MinKNOW is reporting PHASE_MUX_SCAN, waiting for PHASE_SEQUENCING to begin.                                                           
2025-09-18 01:53:51,753 readfish._read_until_client Protocol phase changed to PHASE_SEQUENCING                                                                                 
2025-09-18 03:24:55,590 readfish._read_until_client Protocol phase changed to PHASE_MUX_SCAN                                                                                   
2025-09-18 03:24:55,591 readfish.targets MinKNOW is reporting PHASE_MUX_SCAN, waiting for PHASE_SEQUENCING to begin.                                                           
2025-09-18 03:28:56,646 readfish._read_until_client Protocol phase changed to PHASE_SEQUENCING                                                                                 
2025-09-18 05:00:00,073 readfish._read_until_client Protocol phase changed to PHASE_MUX_SCAN                                                                                   
2025-09-18 05:00:00,073 readfish.targets MinKNOW is reporting PHASE_MUX_SCAN, waiting for PHASE_SEQUENCING to begin.                                                           
2025-09-18 05:04:01,922 readfish._read_until_client Protocol phase changed to PHASE_SEQUENCING                                                                                 
2025-09-18 06:35:05,687 readfish._read_until_client Protocol phase changed to PHASE_MUX_SCAN                                                                                   
2025-09-18 06:35:05,687 readfish.targets MinKNOW is reporting PHASE_MUX_SCAN, waiting for PHASE_SEQUENCING to begin.                                                           
2025-09-18 06:39:06,782 readfish._read_until_client Protocol phase changed to PHASE_SEQUENCING                                                                                 
2025-09-18 08:10:10,333 readfish._read_until_client Protocol phase changed to PHASE_MUX_SCAN                                                                                   
2025-09-18 08:10:10,333 readfish.targets MinKNOW is reporting PHASE_MUX_SCAN, waiting for PHASE_SEQUENCING to begin.

Activity

  1. github-actions commented on Sep 29, 2025

    @github-actions
    github-actionsbot
    on Sep 29, 2025 – with GitHub Actions

    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

  2. github-actions commented on Oct 29, 2025

    @github-actions
    github-actionsbot
    on Oct 29, 2025 – with GitHub Actions

    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.

  3. github-actions
    added
    Stale
    on Oct 29, 2025

  4. mattloose commented on Oct 29, 2025

    @mattloose
    mattloose
    on Oct 29, 2025
    Contributor

    Apologies that no one has responded to this - let me look at the alternate issue #405 and comment there.

  5. mattloose
    closed this as completedon Oct 29, 2025
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Metadata

Assignees

No one assigned

    Labels

    Stale

    Type

    No type

    Projects

    No projects

      Milestone

      No milestone

      Relationships

      None yet

      Development

      No branches or pull requests

      Issue actions