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POA panics on some sets of sequences #572

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davidlougheed opened this issue Feb 7, 2024 · 8 comments · May be fixed by #575
Open

POA panics on some sets of sequences #572

davidlougheed opened this issue Feb 7, 2024 · 8 comments · May be fixed by #575

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@davidlougheed
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I've written a wrapper function to calculate consensus sequences from POA alignments using rust-bio. Some sets of sequences panic where I wouldn't expect them too; for example, see the following:

>>> seqs = ('GTGTGTGTGTGTATATGTTGTAGAA', 'GTGTGTGTGTGTGTGTGTTGT', 'GTGTGTGTGTGTGTGTGTTGT', 'GTGTGTGTGTGTGTGTTGTG', 'GTGTGTGTGTGTGTGTTGTG', 'GTGTGTGTGTGTGTTGTG', 'TGTGAGTGTGTGTGTGTGTGTGTTGT', 'TGTGGTGTGTGTGTGTTGT')
>>> seqs
('GTGTGTGTGTGTATATGTTGTAGAA', 'GTGTGTGTGTGTGTGTGTTGT', 'GTGTGTGTGTGTGTGTGTTGT', 'GTGTGTGTGTGTGTGTTGTG', 'GTGTGTGTGTGTGTGTTGTG', 'GTGTGTGTGTGTGTTGTG', 'TGTGAGTGTGTGTGTGTGTGTGTTGT', 'TGTGGTGTGTGTGTGTTGT')
>>> strkit_rust_ext.consensus_seq(seqs)
thread '<unnamed>' panicked at /Users/davidlougheed/.cargo/registry/src/index.crates.io-6f17d22bba15001f/bio-1.5.0/src/alignment/poa.rs:439:28:
index out of bounds: the len is 31 but the index is 31
stack backtrace:
   0: rust_begin_unwind
             at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/std/src/panicking.rs:645:5
   1: core::panicking::panic_fmt
             at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/core/src/panicking.rs:72:14
   2: core::panicking::panic_bounds_check
             at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/core/src/panicking.rs:190:5
   3: bio::alignment::poa::Aligner<F>::consensus
   4: std::panicking::try
   5: strkit_rust_ext::strkit::consensus::_::<impl strkit_rust_ext::strkit::consensus::consensus_seq::MakeDef>::DEF::trampoline
   6: _cfunction_vectorcall_FASTCALL_KEYWORDS
   7: _call_function
   8: __PyEval_EvalFrameDefault
   9: __PyEval_Vector
  10: _PyEval_EvalCode
  11: _run_eval_code_obj
  12: _run_mod
  13: _PyRun_InteractiveOneObjectEx
  14: __PyRun_InteractiveLoopObject
  15: __PyRun_AnyFileObject
  16: _PyRun_AnyFileExFlags
  17: _pymain_run_stdin
  18: _Py_RunMain
  19: _Py_BytesMain
note: Some details are omitted, run with `RUST_BACKTRACE=full` for a verbose backtrace.
@davidlougheed
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this might be a duplicate of #549 ... any chance of the PR open for that being merged soon?

@lorewar2
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lorewar2 commented Feb 7, 2024

The PR with the fix has been merged, is this issue fixed now?

@davidlougheed
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I'll test when there's a new version released, thanks for the update!

@davidlougheed
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davidlougheed commented Feb 8, 2024 •
edited

@lorewar2 ok I tested - the latest PR does not fix all forms of this problem. For example, the following sequences still cause a panic with rust_bio https://github.com/rust-bio/rust-bio.git?rev=440cb1c#440cb1ce:

('ACACACACACACACACACACACACACACACACACACACACACAC', 'ACACACACACACACACACACACACACACACACACACACACACACACACACAC', 'ACACACACACACACACACACACACACACACACACACACACACACACACACACTT', 'ACACACACACACACATTACTGCACACACACACACACACACACACACACACAC', 'CACACACACACACACACACACACACACACACACACACACACACACACACACAC', 'CATACACACACACACACACACACACACACACACACACACACACACACAC')

results in:

thread '<unnamed>' panicked at /Users/davidlougheed/.cargo/git/checkouts/rust-bio-d51470571d61aed1/440cb1c/src/alignment/poa.rs:550:28:
index out of bounds: the len is 59 but the index is 59
stack backtrace:
   0:        0x100b43110 - std::backtrace_rs::backtrace::libunwind::trace::h2966c6fbfac9d426
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/std/src/../../backtrace/src/backtrace/libunwind.rs:104:5
   1:        0x100b43110 - std::backtrace_rs::backtrace::trace_unsynchronized::h8a5f4aefe890b7c5
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/std/src/../../backtrace/src/backtrace/mod.rs:66:5
   2:        0x100b43110 - std::sys_common::backtrace::_print_fmt::h7574dd98fd39c257
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/std/src/sys_common/backtrace.rs:67:5
   3:        0x100b43110 - <std::sys_common::backtrace::_print::DisplayBacktrace as core::fmt::Display>::fmt::h298c9ab285ff3934
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/std/src/sys_common/backtrace.rs:44:22
   4:        0x100b57b64 - core::fmt::rt::Argument::fmt::hf9661447f7b99899
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/core/src/fmt/rt.rs:142:9
   5:        0x100b57b64 - core::fmt::write::h4e276abdb6d0c2a1
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/core/src/fmt/mod.rs:1120:17
   6:        0x100b41b84 - std::io::Write::write_fmt::hd421848f5f0bf9d0
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/std/src/io/mod.rs:1762:15
   7:        0x100b42f4c - std::sys_common::backtrace::_print::h09e653c6686dbd70
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/std/src/sys_common/backtrace.rs:47:5
   8:        0x100b42f4c - std::sys_common::backtrace::print::hd8bd9ecab1f94b94
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/std/src/sys_common/backtrace.rs:34:9
   9:        0x100b44148 - std::panicking::default_hook::{{closure}}::h520eeb743fc98fb4
  10:        0x100b43e90 - std::panicking::default_hook::ha6550ffe49b63df1
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/std/src/panicking.rs:292:9
  11:        0x100b44570 - std::panicking::rust_panic_with_hook::hddb0e884a202de7c
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/std/src/panicking.rs:779:13
  12:        0x100b44470 - std::panicking::begin_panic_handler::{{closure}}::hd2798398a2fd9077
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/std/src/panicking.rs:657:13
  13:        0x100b43578 - std::sys_common::backtrace::__rust_end_short_backtrace::h9201cc364dbb8a23
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/std/src/sys_common/backtrace.rs:170:18
  14:        0x100b4420c - rust_begin_unwind
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/std/src/panicking.rs:645:5
  15:        0x100b64e98 - core::panicking::panic_fmt::h4d5168028d4c43c7
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/core/src/panicking.rs:72:14
  16:        0x100b64fdc - core::panicking::panic_bounds_check::h17fa693e54374598
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/core/src/panicking.rs:190:5
  17:        0x100ac7244 - bio::alignment::poa::Aligner<F>::consensus::hde9245f33981f8bd
                               at /Users/davidlougheed/.cargo/git/checkouts/rust-bio-d51470571d61aed1/440cb1c/src/alignment/poa.rs:550:28
  18:        0x100ac1a70 - strkit_rust_ext::strkit::consensus::consensus_seq::{{closure}}::{{closure}}::he58e26ad547fc66c
...

@lorewar2
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lorewar2 commented Feb 8, 2024

I ran the same sequences and worked fine for me, this could be the same issue mentioned in #549
Is it possible to provide the graph for this?
e.g
let graph = aligner.graph(); println!("{:?}", Dot::new(&graph.map(|_, n| (*n) as char, |_, e| *e)));
Thank you for your help in debugging.

@davidlougheed
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here is the output:

digraph {
    0 [ label = "'C'" ]
    1 [ label = "'A'" ]
    2 [ label = "'T'" ]
    3 [ label = "'A'" ]
    4 [ label = "'C'" ]
    5 [ label = "'A'" ]
    6 [ label = "'C'" ]
    7 [ label = "'A'" ]
    8 [ label = "'C'" ]
    9 [ label = "'A'" ]
    10 [ label = "'C'" ]
    11 [ label = "'A'" ]
    12 [ label = "'C'" ]
    13 [ label = "'A'" ]
    14 [ label = "'C'" ]
    15 [ label = "'A'" ]
    16 [ label = "'C'" ]
    17 [ label = "'A'" ]
    18 [ label = "'C'" ]
    19 [ label = "'A'" ]
    20 [ label = "'C'" ]
    21 [ label = "'A'" ]
    22 [ label = "'C'" ]
    23 [ label = "'A'" ]
    24 [ label = "'C'" ]
    25 [ label = "'A'" ]
    26 [ label = "'C'" ]
    27 [ label = "'A'" ]
    28 [ label = "'C'" ]
    29 [ label = "'A'" ]
    30 [ label = "'C'" ]
    31 [ label = "'A'" ]
    32 [ label = "'C'" ]
    33 [ label = "'A'" ]
    34 [ label = "'C'" ]
    35 [ label = "'A'" ]
    36 [ label = "'C'" ]
    37 [ label = "'A'" ]
    38 [ label = "'C'" ]
    39 [ label = "'A'" ]
    40 [ label = "'C'" ]
    41 [ label = "'A'" ]
    42 [ label = "'C'" ]
    43 [ label = "'A'" ]
    44 [ label = "'C'" ]
    45 [ label = "'A'" ]
    46 [ label = "'C'" ]
    47 [ label = "'A'" ]
    48 [ label = "'C'" ]
    49 [ label = "'A'" ]
    50 [ label = "'C'" ]
    51 [ label = "'A'" ]
    52 [ label = "'C'" ]
    53 [ label = "'T'" ]
    54 [ label = "'T'" ]
    55 [ label = "'T'" ]
    56 [ label = "'T'" ]
    57 [ label = "'T'" ]
    58 [ label = "'G'" ]
    0 -> 1 [ label = "6" ]
    1 -> 2 [ label = "1" ]
    2 -> 3 [ label = "1" ]
    3 -> 4 [ label = "4" ]
    4 -> 5 [ label = "6" ]
    5 -> 6 [ label = "6" ]
    6 -> 7 [ label = "6" ]
    7 -> 8 [ label = "6" ]
    8 -> 9 [ label = "6" ]
    9 -> 10 [ label = "6" ]
    10 -> 11 [ label = "6" ]
    11 -> 12 [ label = "6" ]
    12 -> 13 [ label = "6" ]
    13 -> 14 [ label = "6" ]
    14 -> 15 [ label = "6" ]
    15 -> 16 [ label = "5" ]
    16 -> 17 [ label = "5" ]
    17 -> 18 [ label = "6" ]
    18 -> 19 [ label = "5" ]
    19 -> 20 [ label = "5" ]
    20 -> 21 [ label = "6" ]
    21 -> 22 [ label = "6" ]
    22 -> 23 [ label = "6" ]
    23 -> 24 [ label = "6" ]
    24 -> 25 [ label = "6" ]
    25 -> 26 [ label = "6" ]
    26 -> 27 [ label = "6" ]
    27 -> 28 [ label = "6" ]
    28 -> 29 [ label = "6" ]
    29 -> 30 [ label = "6" ]
    30 -> 31 [ label = "6" ]
    31 -> 32 [ label = "6" ]
    32 -> 33 [ label = "6" ]
    33 -> 34 [ label = "6" ]
    34 -> 35 [ label = "6" ]
    35 -> 36 [ label = "6" ]
    36 -> 37 [ label = "6" ]
    37 -> 38 [ label = "6" ]
    38 -> 39 [ label = "6" ]
    39 -> 40 [ label = "6" ]
    40 -> 41 [ label = "6" ]
    41 -> 42 [ label = "6" ]
    42 -> 43 [ label = "6" ]
    43 -> 44 [ label = "6" ]
    44 -> 45 [ label = "6" ]
    45 -> 46 [ label = "6" ]
    46 -> 47 [ label = "5" ]
    47 -> 48 [ label = "5" ]
    1 -> 4 [ label = "2" ]
    49 -> 0 [ label = "3" ]
    1 -> 50 [ label = "3" ]
    50 -> 3 [ label = "3" ]
    48 -> 51 [ label = "4" ]
    51 -> 52 [ label = "4" ]
    52 -> 53 [ label = "1" ]
    53 -> 54 [ label = "1" ]
    15 -> 55 [ label = "1" ]
    55 -> 56 [ label = "1" ]
    56 -> 17 [ label = "1" ]
    18 -> 57 [ label = "1" ]
    57 -> 58 [ label = "1" ]
    58 -> 20 [ label = "1" ]
    4 -> 0 [ label = "1" ]
}

I'm pretty sure I'm using master since I specified bio = { git = "https://github.com/rust-bio/rust-bio.git", rev = "440cb1c" } in my Cargo.toml

@lorewar2
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lorewar2 commented Feb 8, 2024

Okay, I see a reverse edge on the graph, this is the same as the #549, I need to debug this.

@davidlougheed
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in both cases it involves short tandem repeats too, interesting...

@lorewar2 lorewar2 linked a pull request Feb 17, 2024 that will close this issue
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fix: POA reverse edge fix lorewar2/rust-bio
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@davidlougheed @lorewar2