cdarby
commented
4 years ago From the traceback, the error is occurring in the external code we call for read pseudoalignment. It fails to extract a substring of a read (kmer). I can't tell exactly what the issue is without knowing what read in your dataset caused the error. But based on the error, I have one guess of what could be going wrong. Among the reads scHLAcount uses for input (reads aligned to the HLA region), are there any reads that are very short (less than 20 bases, which is the kmer length used in the pseudoalignment algorithm)?
rrydbirk
I've successfully run 31 samples, but the last one crashes. Can you tell me what's wrong? All samples have been treated the same way.
name = 'sc_hla_count' operating_system = 'unix:Ubuntu' crate_version = '0.1.0' explanation = ''' Cause: assertion failed: self.len() - pos >= K::k(). Panic occurred in file '/home/travis/.c$ ''' method = 'Panic' backtrace = ''' stack backtrace: 0: backtrace::backtrace::libunwind::trace::haf40a01432d42c61 (0x562018522ce7) at /home/travis/.cargo/registry/src/github.com-1ecc6299db9ec823/backtrace-0.3.3$ backtrace::backtrace::trace_unsynchronized::h86bb21cca35f9927 at /home/travis/.cargo/registry/src/github.com-1ecc6299db9ec823/backtrace-0.3.3$ backtrace::backtrace::trace::h53026d916847a4e2 at /home/travis/.cargo/registry/src/github.com-1ecc6299db9ec823/backtrace-0.3.3$ 1: backtrace::capture::Backtrace::create::h15ee241c08d3314e (0x562018522243) at /home/travis/.cargo/registry/src/github.com-1ecc6299db9ec823/backtrace-0.3.3$ backtrace::capture::Backtrace::new::hfa537f24b00fbd81 at /home/travis/.cargo/registry/src/github.com-1ecc6299db9ec823/backtrace-0.3.3$ 2: human_panic::report::Report::new::hdcc2fe1769a7e55b (0x5620185111d7) at /home/travis/.cargo/registry/src/github.com-1ecc6299db9ec823/human-panic-1.0$ 3: human_panic::handle_dump::h319213eee1e267f2 (0x5620185108c7) at /home/travis/.cargo/registry/src/github.com-1ecc6299db9ec823/human-panic-1.0$ 4: sc_hla_count::main::{{closure}}::h93cf456556fa5fbd (0x562018459179) at /home/travis/build/10XGenomics/scHLAcount/<::human_panic::setup_panic macros$ 5: std::panicking::rust_panic_with_hook::hffcefc09751839d1 (0x562018648ec9) at src/libstd/panicking.rs:481 6: std::panicking::begin_panic::h51328ca360700b9a (0x5620184a3615) at /rustc/eae3437dfe991621e8afdc82734f4a172d7ddf9b/src/libstd/panicking.rs:411 7:::get_kmer::h1b9ad17a9842b113 (0x56$
at /home/travis/build/10XGenomics/scHLAcount/<::std::macros::panic macros>:4
8: debruijn_mapping::pseudoaligner::Pseudoaligner::map_read::{{closure}}::h155fc7e3bad$
at /home/travis/.cargo/git/checkouts/rust-pseudoaligner-435331298a1cadf6/ae4aad$
9: debruijn_mapping::pseudoaligner::Pseudoaligner::map_read::hd33cd425a0e12f0a (0x5620$
at /home/travis/.cargo/git/checkouts/rust-pseudoaligner-435331298a1cadf6/ae4aad$
10: sc_hla_count::mapping::mapping_wrapper::h8e687a93e926ae64 (0x562018425bd2)
at src/mapping.rs:336
11: sc_hla_count::_main::h623a028a6a6d278a (0x56201845ee13)
at src/main.rs:198
12: sc_hla_count::main::h9607481a7611a730 (0x562018458fd3)
at src/main.rs:139
13: std::rt::lang_start::{{closure}}::h194d0e8b51bf9c2b (0x56201844fb03)
at /rustc/eae3437dfe991621e8afdc82734f4a172d7ddf9b/src/libstd/rt.rs:64
14: std::rt::lang_start_internal::{{closure}}::h447d8812e3ee306d (0x5620186487e3)
at src/libstd/rt.rs:49
std::panicking::try::do_call::h4a61cb372364c745
at src/libstd/panicking.rs:296
15: __rust_maybe_catch_panic (0x56201864fd6a)
at src/libpanic_unwind/lib.rs:82
16: std::panicking::try::hdf71f938885bca42 (0x5620186493ad)
at src/libstd/panicking.rs:275
std::panic::catch_unwind::h7e85dbf162b1611a
at src/libstd/panic.rs:394
std::rt::lang_start_internal::h1e06cc26b9fc25ea
at src/libstd/rt.rs:48
17: main (0x5620184607d8)
18: __libc_start_main (0x7f694b32ab97)
19: _start (0x56201840c7b9)
20: (0x0)'''