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"thread '<unnamed>' panicked at /herro/herro/src/mm2.rs:37:10" running demo sequence #73

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runujhkj opened this issue Dec 9, 2024 · 0 comments

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@runujhkj
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runujhkj commented Dec 9, 2024

Hi, I don't have the best understanding of what this software is doing, I'm just an admin. I got it compiled via Rust, I think, and followed the environment setup (LIBTORCH and LD_LIBRARY_PATH), but running the demo sequence given in the github repo at demo/README causes a panic and fails:

herro inference -t 4 -m model_R10_v0.1.pt -d 2 -b 32 HG002.chr19_10M_12M.fastq.gz output.fasta 
[00:00:00] Parsed 1177 reads.                                                                             [00:00:00] Processing 1/? batch ⠂                                                                         thread '<unnamed>' panicked at /opt/apps/herro/herro/src/mm2.rs:37:10:
Failed to start echo process: Os { code: 2, kind: NotFound, message: "No such file or directory" }
stack backtrace:
   0: rust_begin_unwind
   1: core::panicking::panic_fmt
   2: core::result::unwrap_failed
   3: herro::mm2::call_mm2
   4: <core::iter::adapters::map::Map<I,F> as core::iter::traits::iterator::Iterator>::next
   5: herro::overlaps::alignment_reader
note: Some details are omitted, run with `RUST_BACKTRACE=full` for a verbose backtrace.
Aborted (core dumped)

Here's the full backtrace:

stack backtrace:
   0:     0x5638e8320b0c - <std::sys::backtrace::BacktraceLock::print::DisplayBacktrace as core::fmt::Display>::fmt::h5b6bd5631a6d1f6b
   1:     0x5638e8259dc3 - core::fmt::write::h7550c97b06c86515
   2:     0x5638e831e333 - std::io::Write::write_fmt::h7b09c64fe0be9c84
   3:     0x5638e8320942 - std::sys::backtrace::BacktraceLock::print::h2395ccd2c84ba3aa
   4:     0x5638e83215cd - std::panicking::default_hook::{{closure}}::he19d4c7230e07961
   5:     0x5638e8321417 - std::panicking::default_hook::hf614597d3c67bbdb
   6:     0x5638e8321b6e - std::panicking::rust_panic_with_hook::h8942133a8b252070
   7:     0x5638e8321a1a - std::panicking::begin_panic_handler::{{closure}}::hb5f5963570096b29
   8:     0x5638e8320ff9 - std::sys::backtrace::__rust_end_short_backtrace::h6208cedc1922feda
   9:     0x5638e83216bc - rust_begin_unwind
  10:     0x5638e81e9e00 - core::panicking::panic_fmt::h0c3082644d1bf418
  11:     0x5638e81ea1a6 - core::result::unwrap_failed::hd20b4aa073bda1e2
  12:     0x5638e828fedb - herro::mm2::call_mm2::hde9788a16770a2fb
  13:     0x5638e82a4d44 - <core::iter::adapters::map::Map<I,F> as core::iter::traits::iterator::Iterator>::next::h289f7c13e5cb9cb7
  14:     0x5638e82a9459 - herro::overlaps::alignment_reader::h447af5fad27b476f
  15:     0x5638e82b978e - std::sys::backtrace::__rust_begin_short_backtrace::h3626b87bb092c76e
  16:     0x5638e82b61b2 - core::ops::function::FnOnce::call_once{{vtable.shim}}::h440980e63baa94de
  17:     0x5638e832466b - std::sys::pal::unix::thread::Thread::new::thread_start::hcc78f3943333fa94
  18:     0x7fd4ce46bac3 - start_thread
                               at ./nptl/pthread_create.c:442:8
  19:     0x7fd4ce4fd850 - __GI___clone3
                               at ./misc/../sysdeps/unix/sysv/linux/x86_64/clone3.S:81
  20:                0x0 - <unknown>
Aborted (core dumped)

I'm still looking into what's going on, as I'm assuming the issue is with my own lack of knowledge on herro, Rust, every part of this really. Figured I'd post it here as well.

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