Out of bounds for 2-bit sequence decoding.

[jguhlin]

Getting the following error:

❯ nice nice singularity run --nv herro.sif inference -m model_R9_v0.1.pt -b 64 --read-alns batched_alignments out.fastq.gz corrected
[00:44:38] Parsed 9283361 reads.
[00:03:06] Processing 1/? batch ⠠
[>---------------------------------------] 3/68175
[W graph_fuser.cpp:108] Warning: operator() profile_node %1243 : int[] = prim::profile_ivalue(%1241)
[00:04:51] Processing 1/? batch ⢀
[>---------------------------------------] 844/68175
thread '<unnamed>' panicked at /herro/src/haec_io.rs:144:9:
Out of bounds for 2-bit sequence decoding.
[00:04:51] Processing 1/? batch ⠐
[>---------------------------------------] 844/68175                                                                                      0:     0x5567db11c2b1 - std::backtrace_rs::backtrace::libunwind::trace::ha637c64ce894333a
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/std/src/../../backtrace/src/backtrace/libunwind.rs:104:5
   1:     0x5567db11c2b1 - std::backtrace_rs::backtrace::trace_unsynchronized::h47f62dea28e0c88d
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/std/src/../../backtrace/src/backtrace/mod.rs:66:5
   2:     0x5567db11c2b1 - std::sys_common::backtrace::_print_fmt::h9eef0abe20ede486
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/std/src/sys_common/backtrace.rs:67:5
   3:     0x5567db11c2b1 - <std::sys_common::backtrace::_print::DisplayBacktrace as core::fmt::Display>::fmt::hed7f999df88cc644
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/std/src/sys_common/backtrace.rs:44:22
   4:     0x5567db067390 - core::fmt::rt::Argument::fmt::h1539a9308b8d058d
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/core/src/fmt/rt.rs:142:9
   5:     0x5567db067390 - core::fmt::write::h3a39390d8560d9c9
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/core/src/fmt/mod.rs:1120:17
   6:     0x5567db11a3ff - std::io::Write::write_fmt::h5fc9997dfe05f882
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/std/src/io/mod.rs:1762:15
   7:     0x5567db11c094 - std::sys_common::backtrace::_print::h894006fb5c6f3d45
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/std/src/sys_common/backtrace.rs:47:5
   8:     0x5567db11c094 - std::sys_common::backtrace::print::h23a2d212c6fff936
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/std/src/sys_common/backtrace.rs:34:9
   9:     0x5567db11d4a7 - std::panicking::default_hook::{{closure}}::h8a1d2ee00185001a
  10:     0x5567db11d205 - std::panicking::default_hook::h6038f2eba384e475
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/std/src/panicking.rs:292:9
  11:     0x5567db11da40 - std::panicking::rust_panic_with_hook::h2b5517d590cab22e
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/std/src/panicking.rs:779:13
  12:     0x5567db11d7b9 - std::panicking::begin_panic_handler::{{closure}}::h233112c06e0ef43e
13:     0x5567db11c776 - std::sys_common::backtrace::__rust_end_short_backtrace::h6e893f24d7ebbff8
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/std/src/sys_common/backtrace.rs:170:18
  14:     0x5567db11d572 - rust_begin_unwind
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/std/src/panicking.rs:645:5
  15:     0x5567dafff975 - core::panicking::panic_fmt::hbf0e066aabfa482c
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/core/src/panicking.rs:72:14
  16:     0x5567db094cd6 - herro::features::extract_features::{{closure}}::h3588956aabde7bf6
  17:     0x5567db0944a4 - core::slice::sort::insertion_sort_shift_left::h6a8cb7ba2acaadd2
  18:     0x5567db093da6 - core::slice::sort::merge_sort::ha0f0096f1486e1d5
  19:     0x5567db0ac7b8 - herro::features::extract_features::h00ea577d98be430b
  20:     0x5567db0b5a6d - std::sys_common::backtrace::__rust_begin_short_backtrace::hd2c9f1af20faea53
  21:     0x5567db0d0be6 - core::ops::function::FnOnce::call_once{{vtable.shim}}::h44881a552781c61d
  22:     0x5567db121375 - <alloc::boxed::Box<F,A> as core::ops::function::FnOnce<Args>>::call_once::hc7eafaff61e32df9
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/alloc/src/boxed.rs:2007:9
  23:     0x5567db121375 - <alloc::boxed::Box<F,A> as core::ops::function::FnOnce<Args>>::call_once::h6ba4a5de48dd2304
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/alloc/src/boxed.rs:2007:9
  24:     0x5567db121375 - std::sys::unix::thread::Thread::new::thread_start::he469335aef763e45
                               at /rustc/82e1608dfa6e0b5569232559e3d385fea5a93112/library/std/src/sys/unix/thread.rs:108:17
  25:     0x7f0a5d66bac3 - <unknown>
  26:     0x7f0a5d6fca04 - __clone
  27:                0x0 - <unknown>
Aborted (core dumped)

[dominikstanojevic]

Hello Joseph,

interesting. Can you please check for me if your input data (fastq) file contains only canonical (A, C, G, T) bases? Thanks.

Best regards, Dominik

[peterdfields]

I see this same error. There does not appear to be non-canonical bases in the fastq file which resulted from the preprocess.sh script. Would any additional info be helpful to troubleshoot the error?

I can also share reads if that would be helpful.