lbcb-sci / herro

HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or R9.4.1 reads (read length of >= 10 kbps is recommended).
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herro inference error #14

Open Mar10L opened 3 months ago

Mar10L commented 3 months ago

Dear, I encountered some issues in the final step of the herro pipeline. In the last command (herro inference), the following error emerges:

[00:00:01] Parsed 2313 reads.                                                                                                                                                                              
[00:00:05] Processing 1/? batch ⢀
[>---------------------------------------] 4/698                                                                                                                                                           
thread '<unnamed>' panicked at src/inference.rs:172:64:
called `Result::unwrap()` on an `Err` value: Torch("Expected at most 4 argument(s) for operator 'forward', but received 5 argument(s). Declaration: forward(__torch__.model.PositionClassifier self, Tensor bases, Tensor qualities, Tensor[] target_positions) -> Tensor\nException raised from checkAndNormalizeInputs at /libtorch/include/ATen/core/function_schema_inl.h:383 (most recent call first):\nframe #0: c10::Error::Error(c10::SourceLocation, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) + 0x6b (0x7fc7aa65a6bb in /libs/libtorch/lib/libc10.so)\nframe #1: c10::detail::torchCheckFail(char const*, char const*, unsigned int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) + 0xbf (0x7fc7aa6555ef in /libs/libtorch/lib/libc10.so)\nframe #2: void c10::FunctionSchema::checkAndNormalizeInputs<c10::Type>(std::vector<c10::IValue, std::allocator<c10::IValue> >&, std::unordered_map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, c10::IValue, std::hash<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::equal_to<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, c10::IValue> > > const&) const + 0x45b (0x55f489b0f2eb in herro)\nframe #3: torch::jit::Method::operator()(std::vector<c10::IValue, std::allocator<c10::IValue> >, std::unordered_map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, c10::IValue, std::hash<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::equal_to<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, c10::IValue> > > const&) const + 0x173 (0x7fc7af01b663 in /libs/libtorch/lib/libtorch_cpu.so)\nframe #4: <unknown function> + 0x1ea9cd (0x55f489b0f9cd in herro)\nframe #5: <unknown function> + 0xaadaa (0x55f4899cfdaa in herro)\nframe #6: <unknown function> + 0xa9133 (0x55f4899ce133 in herro)\nframe #7: <unknown function> + 0xd2a11 (0x55f4899f7a11 in herro)\nframe #8: <unknown function> + 0xd9d0c (0x55f4899fed0c in herro)\nframe #9: <unknown function> + 0xf4a96 (0x55f489a19a96 in herro)\nframe #10: <unknown function> + 0x145375 (0x55f489a6a375 in herro)\nframe #11: <unknown function> + 0x94ac3 (0x7fc7aa46bac3 in /lib/x86_64-linux-gnu/libc.so.6)\nframe #12: <unknown function> + 0x126850 (0x7fc7aa4fd850 in /lib/x86_64-linux-gnu/libc.so.6)\n")
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
Aborted (core dumped)

I was wondering if anybody can help me.

Best Mario

bpanda-dev commented 2 months ago

Hey @Mar10L , were you able to find a solution to this?

Edit: I was able to solve my problem by creating the docker image(please check the Dockerfile in repo) and running Herro inside the container.

Best, Bikram Panda