Created
August 11, 2023 20:06
-
-
Save stepwise-ai-dev/f23a79faaedd006bf51d486259440dd5 to your computer and use it in GitHub Desktop.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| $ conda activate myenv | |
| $ RUST_BACKTRACE=full tokenise_bio -i /data/ncbi_dataset/GCF_000001405.39_GRCh38.p13_genomic.fasta -t '/data/generated/ncbi_tokenisers/tokeniser_39_GRCh38.json' | |
| COMMAND LINE ARGUMENTS FOR REPRODUCIBILITY: | |
| /home/ec2-user/mambaforge/envs/myenv/bin/tokenise_bio -i /data/ncbi_dataset/GCF_000001405.39_GRCh38.p13_genomic.fasta -t /data/generated/ncbi_tokenisers/tokeniser_39_GRCh38.json | |
| [00:01:25] Pre-processing sequences ███████████████████████████████████████████████████████████████████████████████████████████████ 0 / 0 | |
| [00:00:00] Suffix array seeds ███████████████████████████████████████████████████████████████████████████████████████████████ 0 / 0 | |
| thread '<unnamed>' panicked at 'called `Result::unwrap()` on an `Err` value: Internal', tokenizers-lib/src/models/unigram/trainer.rs:212:53 | |
| stack backtrace: | |
| 0: 0x7f08eb392d2d - std::backtrace_rs::backtrace::libunwind::trace::h22893a5306c091b4 | |
| at /rustc/fe5b13d681f25ee6474be29d748c65adcd91f69e/library/std/src/../../backtrace/src/backtrace/libunwind.rs:93:5 | |
| 1: 0x7f08eb392d2d - std::backtrace_rs::backtrace::trace_unsynchronized::h29c3bc6f9e91819d | |
| at /rustc/fe5b13d681f25ee6474be29d748c65adcd91f69e/library/std/src/../../backtrace/src/backtrace/mod.rs:66:5 | |
| 2: 0x7f08eb392d2d - std::sys_common::backtrace::_print_fmt::he497d8a0ec903793 | |
| at /rustc/fe5b13d681f25ee6474be29d748c65adcd91f69e/library/std/src/sys_common/backtrace.rs:66:5 | |
| 3: 0x7f08eb392d2d - <std::sys_common::backtrace::_print::DisplayBacktrace as core::fmt::Display>::fmt::h9c2a9d2774d81873 | |
| at /rustc/fe5b13d681f25ee6474be29d748c65adcd91f69e/library/std/src/sys_common/backtrace.rs:45:22 | |
| 4: 0x7f08eb3b4a0c - core::fmt::write::hba4337c43d992f49 | |
| at /rustc/fe5b13d681f25ee6474be29d748c65adcd91f69e/library/core/src/fmt/mod.rs:1194:17 | |
| 5: 0x7f08eb38d7b1 - std::io::Write::write_fmt::heb73de6e02cfabed | |
| at /rustc/fe5b13d681f25ee6474be29d748c65adcd91f69e/library/std/src/io/mod.rs:1655:15 | |
| 6: 0x7f08eb394855 - std::sys_common::backtrace::_print::h63c8b24acdd8e8ce | |
| at /rustc/fe5b13d681f25ee6474be29d748c65adcd91f69e/library/std/src/sys_common/backtrace.rs:48:5 | |
| 7: 0x7f08eb394855 - std::sys_common::backtrace::print::h426700d6240cdcc2 | |
| at /rustc/fe5b13d681f25ee6474be29d748c65adcd91f69e/library/std/src/sys_common/backtrace.rs:35:9 | |
| 8: 0x7f08eb394855 - std::panicking::default_hook::{{closure}}::hc9a76eed0b18f82b | |
| at /rustc/fe5b13d681f25ee6474be29d748c65adcd91f69e/library/std/src/panicking.rs:295:22 | |
| 9: 0x7f08eb394509 - std::panicking::default_hook::h2e88d02087fae196 | |
| at /rustc/fe5b13d681f25ee6474be29d748c65adcd91f69e/library/std/src/panicking.rs:314:9 | |
| 10: 0x7f08eb394da2 - std::panicking::rust_panic_with_hook::habfdcc2e90f9fd4c | |
| at /rustc/fe5b13d681f25ee6474be29d748c65adcd91f69e/library/std/src/panicking.rs:698:17 | |
| 11: 0x7f08eb394c87 - std::panicking::begin_panic_handler::{{closure}}::he054b2a83a51d2cd | |
| at /rustc/fe5b13d681f25ee6474be29d748c65adcd91f69e/library/std/src/panicking.rs:588:13 | |
| 12: 0x7f08eb3931e4 - std::sys_common::backtrace::__rust_end_short_backtrace::ha48b94ab49b30915 | |
| at /rustc/fe5b13d681f25ee6474be29d748c65adcd91f69e/library/std/src/sys_common/backtrace.rs:138:18 | |
| 13: 0x7f08eb3949b9 - rust_begin_unwind | |
| at /rustc/fe5b13d681f25ee6474be29d748c65adcd91f69e/library/std/src/panicking.rs:584:5 | |
| 14: 0x7f08eae40153 - core::panicking::panic_fmt::h366d3a309ae17c94 | |
| at /rustc/fe5b13d681f25ee6474be29d748c65adcd91f69e/library/core/src/panicking.rs:143:14 | |
| 15: 0x7f08eae40243 - core::result::unwrap_failed::hddd78f4658ac7d0f | |
| at /rustc/fe5b13d681f25ee6474be29d748c65adcd91f69e/library/core/src/result.rs:1785:5 | |
| 16: 0x7f08eb0a5748 - tokenizers::models::unigram::trainer::UnigramTrainer::do_train::h82b421a34bd7ad59 | |
| 17: 0x7f08eb02c81f - <tokenizers::models::TrainerWrapper as tokenizers::tokenizer::Trainer>::train::hf338d3868b92a1a9 | |
| 18: 0x7f08eaecb3f1 - <tokenizers::trainers::PyTrainer as tokenizers::tokenizer::Trainer>::train::h797d6fbe1484d439 | |
| 19: 0x7f08eaeeeabe - tokenizers::tokenizer::TokenizerImpl<M,N,PT,PP,D>::train::hc262ae02e631cc04 | |
| 20: 0x7f08eaf55ca3 - tokenizers::utils::iter::ResultShunt<I,E>::process::h9b0c24be256be1db | |
| 21: 0x7f08eafefc00 - <core::panic::unwind_safe::AssertUnwindSafe<F> as core::ops::function::FnOnce<()>>::call_once::hf2eb4b8dad41f8fc | |
| 22: 0x7f08eafb0517 - pyo3::python::Python::allow_threads::hfe4597fb821e57cf | |
| 23: 0x7f08eaf43e85 - tokenizers::tokenizer::PyTokenizer::train_from_iterator::h0d94a2269a130013 | |
| 24: 0x7f08eae9432a - std::panicking::try::h37eed0e7d72cc93a | |
| 25: 0x7f08eaf4c3ca - tokenizers::tokenizer::__init4851609660326938678::__wrap::h19ece55281e9215f | |
| 26: 0x55afd68ee79c - cfunction_call | |
| at /usr/local/src/conda/python-3.9.15/Objects/methodobject.c:543:19 | |
| 27: 0x55afd68d4db7 - _PyObject_MakeTpCall | |
| at /usr/local/src/conda/python-3.9.15/Objects/call.c:191:18 | |
| 28: 0x55afd68d0e62 - _PyObject_VectorcallTstate | |
| at /usr/local/src/conda/python-3.9.15/Include/cpython/abstract.h:116:16 | |
| 29: 0x55afd68d0e62 - _PyObject_VectorcallTstate | |
| at /usr/local/src/conda/python-3.9.15/Include/cpython/abstract.h:103:1 | |
| 30: 0x55afd68d0e62 - PyObject_Vectorcall | |
| at /usr/local/src/conda/python-3.9.15/Include/cpython/abstract.h:127:12 | |
| 31: 0x55afd68d0e62 - call_function | |
| at /usr/local/src/conda/python-3.9.15/Python/ceval.c:5077:13 | |
| 32: 0x55afd68d0e62 - _PyEval_EvalFrameDefault | |
| at /usr/local/src/conda/python-3.9.15/Python/ceval.c:3537:19 | |
| 33: 0x55afd68ca8b7 - _PyEval_EvalFrame | |
| at /usr/local/src/conda/python-3.9.15/Include/internal/pycore_ceval.h:40:12 | |
| 34: 0x55afd68ca8b7 - _PyEval_EvalCode | |
| at /usr/local/src/conda/python-3.9.15/Python/ceval.c:4329:14 | |
| 35: 0x55afd68ec198 - _PyFunction_Vectorcall | |
| at /usr/local/src/conda/python-3.9.15/Objects/call.c:396:12 | |
| 36: 0x55afd68ec198 - _PyObject_VectorcallTstate | |
| at /usr/local/src/conda/python-3.9.15/Include/cpython/abstract.h:118:11 | |
| 37: 0x55afd68ec198 - method_vectorcall | |
| at /usr/local/src/conda/python-3.9.15/Objects/classobject.c:53:18 | |
| 38: 0x55afd68cca70 - _PyObject_VectorcallTstate | |
| at /usr/local/src/conda/python-3.9.15/Include/cpython/abstract.h:118:11 | |
| 39: 0x55afd68cca70 - PyObject_Vectorcall | |
| at /usr/local/src/conda/python-3.9.15/Include/cpython/abstract.h:127:12 | |
| 40: 0x55afd68cca70 - call_function | |
| at /usr/local/src/conda/python-3.9.15/Python/ceval.c:5077:13 | |
| 41: 0x55afd68cca70 - _PyEval_EvalFrameDefault | |
| at /usr/local/src/conda/python-3.9.15/Python/ceval.c:3537:19 | |
| 42: 0x55afd68dd113 - _PyEval_EvalFrame | |
| at /usr/local/src/conda/python-3.9.15/Include/internal/pycore_ceval.h:40:12 | |
| 43: 0x55afd68dd113 - function_code_fastcall | |
| at /usr/local/src/conda/python-3.9.15/Objects/call.c:330:24 | |
| 44: 0x55afd68cbc4f - _PyObject_VectorcallTstate | |
| at /usr/local/src/conda/python-3.9.15/Include/cpython/abstract.h:118:11 | |
| 45: 0x55afd68cbc4f - PyObject_Vectorcall | |
| at /usr/local/src/conda/python-3.9.15/Include/cpython/abstract.h:127:12 | |
| 46: 0x55afd68cbc4f - call_function | |
| at /usr/local/src/conda/python-3.9.15/Python/ceval.c:5077:13 | |
| 47: 0x55afd68cbc4f - _PyEval_EvalFrameDefault | |
| at /usr/local/src/conda/python-3.9.15/Python/ceval.c:3520:19 | |
| 48: 0x55afd68ca8b7 - _PyEval_EvalFrame | |
| at /usr/local/src/conda/python-3.9.15/Include/internal/pycore_ceval.h:40:12 | |
| 49: 0x55afd68ca8b7 - _PyEval_EvalCode | |
| at /usr/local/src/conda/python-3.9.15/Python/ceval.c:4329:14 | |
| 50: 0x55afd68ca577 - _PyEval_EvalCodeWithName | |
| at /usr/local/src/conda/python-3.9.15/Python/ceval.c:4361:12 | |
| 51: 0x55afd68ca529 - PyEval_EvalCodeEx | |
| at /usr/local/src/conda/python-3.9.15/Python/ceval.c:4377:12 | |
| 52: 0x55afd6985cdb - PyEval_EvalCode | |
| at /usr/local/src/conda/python-3.9.15/Python/ceval.c:828:12 | |
| 53: 0x55afd69b4229 - run_eval_code_obj | |
| at /usr/local/src/conda/python-3.9.15/Python/pythonrun.c:1221:9 | |
| 54: 0x55afd69b03c4 - run_mod | |
| at /usr/local/src/conda/python-3.9.15/Python/pythonrun.c:1242:19 | |
| 55: 0x55afd6835673 - pyrun_file | |
| at /usr/local/src/conda/python-3.9.15/Python/pythonrun.c:1140:15 | |
| 56: 0x55afd69a9f02 - pyrun_simple_file | |
| at /usr/local/src/conda/python-3.9.15/Python/pythonrun.c:450:13 | |
| 57: 0x55afd69a9f02 - PyRun_SimpleFileExFlags | |
| at /usr/local/src/conda/python-3.9.15/Python/pythonrun.c:483:15 | |
| 58: 0x55afd69a7263 - pymain_run_file | |
| at /usr/local/src/conda/python-3.9.15/Modules/main.c:377:15 | |
| 59: 0x55afd69a7263 - pymain_run_python | |
| at /usr/local/src/conda/python-3.9.15/Modules/main.c:602:21 | |
| 60: 0x55afd69a7263 - Py_RunMain | |
| at /usr/local/src/conda/python-3.9.15/Modules/main.c:681:5 | |
| 61: 0x55afd6979979 - Py_BytesMain | |
| at /usr/local/src/conda/python-3.9.15/Modules/main.c:1101:12 | |
| 62: 0x7f08f2bde13a - __libc_start_main | |
| 63: 0x55afd6979881 - <unknown> | |
| Traceback (most recent call last): | |
| File "/home/ec2-user/mambaforge/envs/myenv/bin/tokenise_bio", line 11, in <module> | |
| sys.exit(main()) | |
| File "/home/ec2-user/mambaforge/envs/myenv/lib/python3.9/site-packages/genomenlp/tokenise_bio.py", line 62, in main | |
| tokeniser.train_from_iterator( | |
| File "/home/ec2-user/mambaforge/envs/myenv/lib/python3.9/site-packages/tokenizers/implementations/sentencepiece_unigram.py", line 142, in train_from_ite | |
| rator | |
| self._tokenizer.train_from_iterator( | |
| pyo3_runtime.PanicException: called `Result::unwrap()` on an `Err` value: Internal |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment