`ska map` fails with some fragmented reference sequences
Closed this issue · 3 comments
tmaklin commented
- ska version: v0.3.2
- installed with cargo
I ran into an issue with ska map where it fails with some fragmented reference sequences (but not all, I also had some cases with fragmented references that ran just fine). This seems to have something to do with the reference assembly being fragmented because manually concatenating the contigs with something like
cat reference.fa | grep -v "^>" | tr -d '\n' | awk '{print ">concatenated_ref\n" $0}' > concatenated.fa
produces a reference assembly that is okay. I've included instructions and data for how to reproduce this on my x86_64 Linux laptop below.
Reproducing
Data that fails: https://urly.fi/3fm0
Commands that fail:
ska build -f SKA_input_list.tsv -o assemblies -k 31 --threads 1
ska map -o assemblies.aln --ambig-mask --threads 1 assemblies/LA069.fa.gz assemblies.skf
Commands that work (reference concatenated):
ska build -f SKA_input_list.tsv -o assemblies -k 31 --threads 1
gzip -dc assemblies/LA069.fa.gz | grep -v "^>" | tr -d '\n' | awk '{print ">LA069\n" $0}' > ref.fa
ska map -o assemblies.aln --ambig-mask --threads 1 ref.fa assemblies.skf
Errors from failed commands with `RUST_BACKTRACE=1` (click to expand):
SKA: Split K-mer Analysis (the alignment-free aligner)
2023-10-11T18:44:07.178Z WARN [ska::ska_ref] Reference contained multiple contigs, in the output they will be concatenated
thread '<unnamed>' panicked at 'range end index 1988 out of range for slice of length 1283', src/ska_ref/aln_writer.rs:148:35
stack backtrace:
0: rust_begin_unwind
1: core::panicking::panic_fmt
2: core::slice::index::slice_end_index_len_fail
3: ska::ska_ref::aln_writer::AlnWriter::write_split_kmer
4: rayon::iter::plumbing::Producer::fold_with
5: rayon::iter::plumbing::bridge_producer_consumer::helper
6: rayon_core::join::join_context::{{closure}}
7: rayon_core::registry::in_worker
8: rayon::iter::plumbing::bridge_producer_consumer::helper
9: rayon_core::join::join_context::{{closure}}
10: rayon_core::registry::in_worker
11: rayon::iter::plumbing::bridge_producer_consumer::helper
12: rayon_core::join::join_context::{{closure}}
13: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
14: rayon_core::registry::WorkerThread::wait_until_cold
15: rayon_core::registry::ThreadBuilder::run
note: Some details are omitted, run with `RUST_BACKTRACE=full` for a verbose backtrace.
thread '<unnamed>' panicked at 'range end index 12660 out of range for slice of length 4873', src/ska_ref/aln_writer.rs:148:35
stack backtrace:
0: rust_begin_unwind
1: core::panicking::panic_fmt
2: core::slice::index::slice_end_index_len_fail
3: ska::ska_ref::aln_writer::AlnWriter::write_split_kmer
4: rayon::iter::plumbing::Producer::fold_with
5: rayon::iter::plumbing::bridge_producer_consumer::helper
6: rayon_core::join::join_context::{{closure}}
7: rayon_core::registry::in_worker
8: rayon::iter::plumbing::bridge_producer_consumer::helper
9: rayon_core::join::join_context::{{closure}}
10: rayon_core::registry::in_worker
11: rayon::iter::plumbing::bridge_producer_consumer::helper
12: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
13: rayon_core::registry::WorkerThread::wait_until_cold
14: rayon_core::join::join_recover_from_panic
15: rayon_core::join::join_context::{{closure}}
16: rayon_core::registry::in_worker
17: rayon::iter::plumbing::bridge_producer_consumer::helper
18: rayon_core::join::join_context::{{closure}}
19: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
20: rayon_core::registry::WorkerThread::wait_until_cold
21: rayon_core::registry::ThreadBuilder::run
note: Some details are omitted, run with `RUST_BACKTRACE=full` for a verbose backtrace.
thread '<unnamed>' panicked at 'range end index 17466 out of range for slice of length 4873', src/ska_ref/aln_writer.rs:148:35
stack backtrace:
0: rust_begin_unwind
1: core::panicking::panic_fmt
2: core::slice::index::slice_end_index_len_fail
3: ska::ska_ref::aln_writer::AlnWriter::write_split_kmer
4: rayon::iter::plumbing::Producer::fold_with
5: rayon::iter::plumbing::bridge_producer_consumer::helper
6: rayon_core::join::join_context::{{closure}}
7: rayon_core::registry::in_worker
8: rayon::iter::plumbing::bridge_producer_consumer::helper
9: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
10: rayon_core::registry::WorkerThread::wait_until_cold
11: rayon_core::join::join_recover_from_panic
12: rayon_core::join::join_context::{{closure}}
13: rayon_core::registry::in_worker
14: rayon::iter::plumbing::bridge_producer_consumer::helper
15: rayon_core::join::join_context::{{closure}}
16: rayon_core::registry::in_worker
17: rayon::iter::plumbing::bridge_producer_consumer::helper
18: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
19: rayon_core::registry::WorkerThread::wait_until_cold
20: rayon_core::join::join_recover_from_panic
21: rayon_core::join::join_context::{{closure}}
22: rayon_core::registry::in_worker
23: rayon::iter::plumbing::bridge_producer_consumer::helper
24: rayon_core::join::join_context::{{closure}}
25: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
26: rayon_core::registry::WorkerThread::wait_until_cold
27: rayon_core::registry::ThreadBuilder::run
note: Some details are omitted, run with `RUST_BACKTRACE=full` for a verbose backtrace.
thread '<unnamed>' panicked at 'range end index 2974 out of range for slice of length 595', src/ska_ref/aln_writer.rs:148:35
stack backtrace:
0: rust_begin_unwind
1: core::panicking::panic_fmt
2: core::slice::index::slice_end_index_len_fail
3: ska::ska_ref::aln_writer::AlnWriter::write_split_kmer
4: rayon::iter::plumbing::Producer::fold_with
5: rayon::iter::plumbing::bridge_producer_consumer::helper
6: rayon_core::join::join_context::{{closure}}
7: rayon_core::registry::in_worker
8: rayon::iter::plumbing::bridge_producer_consumer::helper
9: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
10: rayon_core::registry::WorkerThread::wait_until_cold
11: rayon_core::join::join_recover_from_panic
12: rayon_core::join::join_context::{{closure}}
13: rayon_core::registry::in_worker
14: rayon::iter::plumbing::bridge_producer_consumer::helper
15: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
16: rayon_core::registry::WorkerThread::wait_until_cold
17: rayon_core::join::join_recover_from_panic
18: rayon_core::join::join_context::{{closure}}
19: rayon_core::registry::in_worker
20: rayon::iter::plumbing::bridge_producer_consumer::helper
21: rayon_core::join::join_context::{{closure}}
22: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
23: rayon_core::registry::WorkerThread::wait_until_cold
24: rayon_core::registry::ThreadBuilder::run
note: Some details are omitted, run with `RUST_BACKTRACE=full` for a verbose backtrace.
thread '<unnamed>' panicked at 'range end index 12706 out of range for slice of length 4873', src/ska_ref/aln_writer.rs:148:35
stack backtrace:
0: rust_begin_unwind
1: core::panicking::panic_fmt
2: core::slice::index::slice_end_index_len_fail
3: ska::ska_ref::aln_writer::AlnWriter::write_split_kmer
4: rayon::iter::plumbing::Producer::fold_with
5: rayon::iter::plumbing::bridge_producer_consumer::helper
6: rayon_core::job::StackJob<L,F,R>::run_inline
7: rayon_core::join::join_context::{{closure}}
8: rayon_core::registry::in_worker
9: rayon::iter::plumbing::bridge_producer_consumer::helper
10: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
11: rayon_core::registry::WorkerThread::wait_until_cold
12: rayon_core::join::join_recover_from_panic
13: rayon_core::join::join_context::{{closure}}
14: rayon_core::registry::in_worker
15: rayon::iter::plumbing::bridge_producer_consumer::helper
16: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
17: rayon_core::registry::WorkerThread::wait_until_cold
18: rayon_core::join::join_recover_from_panic
19: rayon_core::join::join_context::{{closure}}
20: rayon_core::registry::in_worker
21: rayon::iter::plumbing::bridge_producer_consumer::helper
22: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
23: rayon_core::registry::WorkerThread::wait_until_cold
24: rayon_core::join::join_recover_from_panic
25: rayon_core::join::join_context::{{closure}}
26: rayon_core::registry::in_worker
27: rayon::iter::plumbing::bridge_producer_consumer::helper
28: rayon_core::join::join_context::{{closure}}
29: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
30: rayon_core::registry::WorkerThread::wait_until_cold
31: rayon_core::registry::ThreadBuilder::run
note: Some details are omitted, run with `RUST_BACKTRACE=full` for a verbose backtrace.
thread '<unnamed>' panicked at 'range end index 17647 out of range for slice of length 4873', src/ska_ref/aln_writer.rs:148:35
stack backtrace:
0: rust_begin_unwind
1: core::panicking::panic_fmt
2: core::slice::index::slice_end_index_len_fail
3: ska::ska_ref::aln_writer::AlnWriter::write_split_kmer
4: rayon::iter::plumbing::Producer::fold_with
5: rayon::iter::plumbing::bridge_producer_consumer::helper
6: rayon_core::join::join_context::{{closure}}
7: rayon_core::registry::in_worker
8: rayon::iter::plumbing::bridge_producer_consumer::helper
9: rayon_core::join::join_context::{{closure}}
10: rayon_core::registry::in_worker
11: rayon::iter::plumbing::bridge_producer_consumer::helper
12: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
13: rayon_core::registry::WorkerThread::wait_until_cold
14: rayon_core::join::join_recover_from_panic
15: rayon_core::join::join_context::{{closure}}
16: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
17: rayon_core::registry::WorkerThread::wait_until_cold
18: rayon_core::registry::ThreadBuilder::run
note: Some details are omitted, run with `RUST_BACKTRACE=full` for a verbose backtrace.
thread '<unnamed>' panicked at 'range end index 2955 out of range for slice of length 595', src/ska_ref/aln_writer.rs:148:35
stack backtrace:
0: rust_begin_unwind
1: core::panicking::panic_fmt
2: core::slice::index::slice_end_index_len_fail
3: ska::ska_ref::aln_writer::AlnWriter::write_split_kmer
4: rayon::iter::plumbing::Producer::fold_with
5: rayon::iter::plumbing::bridge_producer_consumer::helper
6: rayon_core::join::join_context::{{closure}}
7: rayon_core::registry::in_worker
8: rayon::iter::plumbing::bridge_producer_consumer::helper
9: rayon_core::job::StackJob<L,F,R>::run_inline
10: rayon_core::join::join_context::{{closure}}
11: rayon_core::registry::in_worker
12: rayon::iter::plumbing::bridge_producer_consumer::helper
13: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
14: rayon_core::registry::WorkerThread::wait_until_cold
15: rayon_core::join::join_recover_from_panic
16: rayon_core::join::join_context::{{closure}}
17: rayon_core::registry::in_worker
18: rayon::iter::plumbing::bridge_producer_consumer::helper
19: rayon_core::join::join_context::{{closure}}
20: rayon_core::registry::in_worker
21: rayon::iter::plumbing::bridge_producer_consumer::helper
22: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
23: rayon_core::registry::WorkerThread::wait_until_cold
24: rayon_core::join::join_recover_from_panic
25: rayon_core::join::join_context::{{closure}}
26: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
27: rayon_core::registry::WorkerThread::wait_until_cold
28: rayon_core::registry::ThreadBuilder::run
note: Some details are omitted, run with `RUST_BACKTRACE=full` for a verbose backtrace.
thread '<unnamed>' panicked at 'range end index 2955 out of range for slice of length 595', src/ska_ref/aln_writer.rs:148:35
stack backtrace:
0: rust_begin_unwind
1: core::panicking::panic_fmt
2: core::slice::index::slice_end_index_len_fail
3: ska::ska_ref::aln_writer::AlnWriter::write_split_kmer
4: rayon::iter::plumbing::Producer::fold_with
5: rayon::iter::plumbing::bridge_producer_consumer::helper
6: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
7: rayon_core::registry::WorkerThread::wait_until_cold
8: rayon_core::join::join_recover_from_panic
9: rayon_core::join::join_context::{{closure}}
10: rayon_core::registry::in_worker
11: rayon::iter::plumbing::bridge_producer_consumer::helper
12: rayon_core::job::StackJob<L,F,R>::run_inline
13: rayon_core::join::join_context::{{closure}}
14: rayon_core::registry::in_worker
15: rayon::iter::plumbing::bridge_producer_consumer::helper
16: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
17: rayon_core::registry::WorkerThread::wait_until_cold
18: rayon_core::join::join_recover_from_panic
19: rayon_core::join::join_context::{{closure}}
20: rayon_core::registry::in_worker
21: rayon::iter::plumbing::bridge_producer_consumer::helper
22: rayon_core::join::join_context::{{closure}}
23: rayon_core::registry::in_worker
24: rayon::iter::plumbing::bridge_producer_consumer::helper
25: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
26: rayon_core::registry::WorkerThread::wait_until_cold
27: rayon_core::join::join_recover_from_panic
28: rayon_core::join::join_context::{{closure}}
29: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
30: rayon_core::registry::WorkerThread::wait_until_cold
31: rayon_core::registry::ThreadBuilder::run
note: Some details are omitted, run with `RUST_BACKTRACE=full` for a verbose backtrace.
thread '<unnamed>' panicked at 'range end index 2955 out of range for slice of length 595', src/ska_ref/aln_writer.rs:148:35
stack backtrace:
0: rust_begin_unwind
1: core::panicking::panic_fmt
2: core::slice::index::slice_end_index_len_fail
3: ska::ska_ref::aln_writer::AlnWriter::write_split_kmer
4: rayon::iter::plumbing::Producer::fold_with
5: rayon::iter::plumbing::bridge_producer_consumer::helper
6: rayon_core::join::join_context::{{closure}}
7: rayon_core::registry::in_worker
8: rayon::iter::plumbing::bridge_producer_consumer::helper
9: rayon_core::join::join_context::{{closure}}
10: rayon_core::registry::in_worker
11: rayon::iter::plumbing::bridge_producer_consumer::helper
12: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
13: rayon_core::registry::WorkerThread::wait_until_cold
14: rayon_core::join::join_recover_from_panic
15: rayon_core::join::join_context::{{closure}}
16: rayon_core::registry::in_worker
17: rayon::iter::plumbing::bridge_producer_consumer::helper
18: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
19: rayon_core::registry::WorkerThread::wait_until_cold
20: rayon_core::join::join_recover_from_panic
21: rayon_core::join::join_context::{{closure}}
22: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
23: rayon_core::registry::WorkerThread::wait_until_cold
24: rayon_core::registry::ThreadBuilder::run
note: Some details are omitted, run with `RUST_BACKTRACE=full` for a verbose backtrace.
thread '<unnamed>' panicked at 'range end index 2955 out of range for slice of length 595', src/ska_ref/aln_writer.rs:148:35
stack backtrace:
0: rust_begin_unwind
1: core::panicking::panic_fmt
2: core::slice::index::slice_end_index_len_fail
3: ska::ska_ref::aln_writer::AlnWriter::write_split_kmer
4: rayon::iter::plumbing::Producer::fold_with
5: rayon::iter::plumbing::bridge_producer_consumer::helper
6: rayon_core::join::join_context::{{closure}}
7: rayon_core::registry::in_worker
8: rayon::iter::plumbing::bridge_producer_consumer::helper
9: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
10: rayon_core::registry::WorkerThread::wait_until_cold
11: rayon_core::join::join_recover_from_panic
12: rayon_core::join::join_context::{{closure}}
13: rayon_core::registry::in_worker
14: rayon::iter::plumbing::bridge_producer_consumer::helper
15: rayon_core::join::join_context::{{closure}}
16: rayon_core::registry::in_worker
17: rayon::iter::plumbing::bridge_producer_consumer::helper
18: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
19: rayon_core::registry::WorkerThread::wait_until_cold
20: rayon_core::join::join_recover_from_panic
21: rayon_core::join::join_context::{{closure}}
22: rayon_core::registry::in_worker
23: rayon::iter::plumbing::bridge_producer_consumer::helper
24: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
25: rayon_core::registry::WorkerThread::wait_until_cold
26: rayon_core::join::join_recover_from_panic
27: rayon_core::join::join_context::{{closure}}
28: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
29: rayon_core::registry::WorkerThread::wait_until_cold
30: rayon_core::registry::ThreadBuilder::run
note: Some details are omitted, run with `RUST_BACKTRACE=full` for a verbose backtrace.
thread '<unnamed>' panicked at 'range end index 1988 out of range for slice of length 1283', src/ska_ref/aln_writer.rs:148:35
stack backtrace:
0: rust_begin_unwind
1: core::panicking::panic_fmt
2: core::slice::index::slice_end_index_len_fail
3: ska::ska_ref::aln_writer::AlnWriter::write_split_kmer
4: rayon::iter::plumbing::Producer::fold_with
5: rayon::iter::plumbing::bridge_producer_consumer::helper
6: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
7: rayon_core::registry::WorkerThread::wait_until_cold
8: rayon_core::join::join_recover_from_panic
9: rayon_core::join::join_context::{{closure}}
10: rayon_core::registry::in_worker
11: rayon::iter::plumbing::bridge_producer_consumer::helper
12: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
13: rayon_core::registry::WorkerThread::wait_until_cold
14: rayon_core::join::join_recover_from_panic
15: rayon_core::join::join_context::{{closure}}
16: rayon_core::registry::in_worker
17: rayon::iter::plumbing::bridge_producer_consumer::helper
18: rayon_core::join::join_context::{{closure}}
19: rayon_core::registry::in_worker
20: rayon::iter::plumbing::bridge_producer_consumer::helper
21: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
22: rayon_core::registry::WorkerThread::wait_until_cold
23: rayon_core::join::join_recover_from_panic
24: rayon_core::join::join_context::{{closure}}
25: rayon_core::registry::in_worker
26: rayon::iter::plumbing::bridge_producer_consumer::helper
27: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
28: rayon_core::registry::WorkerThread::wait_until_cold
29: rayon_core::join::join_recover_from_panic
30: rayon_core::join::join_context::{{closure}}
31: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
32: rayon_core::registry::WorkerThread::wait_until_cold
33: rayon_core::registry::ThreadBuilder::run
note: Some details are omitted, run with `RUST_BACKTRACE=full` for a verbose backtrace.
thread '<unnamed>' panicked at 'range end index 2955 out of range for slice of length 595', src/ska_ref/aln_writer.rs:148:35
stack backtrace:
0: rust_begin_unwind
1: core::panicking::panic_fmt
2: core::slice::index::slice_end_index_len_fail
3: ska::ska_ref::aln_writer::AlnWriter::write_split_kmer
4: rayon::iter::plumbing::Producer::fold_with
5: rayon::iter::plumbing::bridge_producer_consumer::helper
6: rayon_core::join::join_context::{{closure}}
7: rayon_core::registry::in_worker
8: rayon::iter::plumbing::bridge_producer_consumer::helper
9: rayon_core::join::join_context::{{closure}}
10: rayon_core::registry::in_worker
11: rayon::iter::plumbing::bridge_producer_consumer::helper
12: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
13: rayon_core::registry::WorkerThread::wait_until_cold
14: rayon_core::join::join_recover_from_panic
15: rayon_core::join::join_context::{{closure}}
16: rayon_core::registry::in_worker
17: rayon::iter::plumbing::bridge_producer_consumer::helper
18: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
19: rayon_core::registry::WorkerThread::wait_until_cold
20: rayon_core::join::join_recover_from_panic
21: rayon_core::join::join_context::{{closure}}
22: rayon_core::registry::in_worker
23: rayon::iter::plumbing::bridge_producer_consumer::helper
24: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
25: rayon_core::registry::WorkerThread::wait_until_cold
26: rayon_core::join::join_recover_from_panic
27: rayon_core::join::join_context::{{closure}}
28: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
29: rayon_core::registry::WorkerThread::wait_until_cold
30: rayon_core::registry::ThreadBuilder::run
note: Some details are omitted, run with `RUST_BACKTRACE=full` for a verbose backtrace.
thread '<unnamed>' panicked at 'range end index 2955 out of range for slice of length 595', src/ska_ref/aln_writer.rs:148:35
stack backtrace:
0: rust_begin_unwind
1: core::panicking::panic_fmt
2: core::slice::index::slice_end_index_len_fail
3: ska::ska_ref::aln_writer::AlnWriter::write_split_kmer
4: rayon::iter::plumbing::Producer::fold_with
5: rayon::iter::plumbing::bridge_producer_consumer::helper
6: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
7: rayon_core::registry::WorkerThread::wait_until_cold
8: rayon_core::join::join_recover_from_panic
9: rayon_core::join::join_context::{{closure}}
10: rayon_core::registry::in_worker
11: rayon::iter::plumbing::bridge_producer_consumer::helper
12: rayon_core::join::join_context::{{closure}}
13: rayon_core::registry::in_worker
14: rayon::iter::plumbing::bridge_producer_consumer::helper
15: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
16: rayon_core::registry::WorkerThread::wait_until_cold
17: rayon_core::join::join_recover_from_panic
18: rayon_core::join::join_context::{{closure}}
19: rayon_core::registry::in_worker
20: rayon::iter::plumbing::bridge_producer_consumer::helper
21: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
22: rayon_core::registry::WorkerThread::wait_until_cold
23: rayon_core::join::join_recover_from_panic
24: rayon_core::join::join_context::{{closure}}
25: rayon_core::registry::in_worker
26: rayon::iter::plumbing::bridge_producer_consumer::helper
27: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
28: rayon_core::registry::WorkerThread::wait_until_cold
29: rayon_core::join::join_recover_from_panic
30: rayon_core::join::join_context::{{closure}}
31: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
32: rayon_core::registry::WorkerThread::wait_until_cold
33: rayon_core::registry::ThreadBuilder::run
note: Some details are omitted, run with `RUST_BACKTRACE=full` for a verbose backtrace.
thread '<unnamed>' panicked at 'range end index 2955 out of range for slice of length 595', src/ska_ref/aln_writer.rs:148:35
stack backtrace:
0: rust_begin_unwind
1: core::panicking::panic_fmt
2: core::slice::index::slice_end_index_len_fail
3: ska::ska_ref::aln_writer::AlnWriter::write_split_kmer
4: rayon::iter::plumbing::Producer::fold_with
5: rayon::iter::plumbing::bridge_producer_consumer::helper
6: rayon_core::join::join_context::{{closure}}
7: rayon_core::registry::in_worker
8: rayon::iter::plumbing::bridge_producer_consumer::helper
9: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
10: rayon_core::registry::WorkerThread::wait_until_cold
11: rayon_core::join::join_recover_from_panic
12: rayon_core::join::join_context::{{closure}}
13: rayon_core::registry::in_worker
14: rayon::iter::plumbing::bridge_producer_consumer::helper
15: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
16: rayon_core::registry::WorkerThread::wait_until_cold
17: rayon_core::join::join_recover_from_panic
18: rayon_core::join::join_context::{{closure}}
19: rayon_core::registry::in_worker
20: rayon::iter::plumbing::bridge_producer_consumer::helper
21: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
22: rayon_core::registry::WorkerThread::wait_until_cold
23: rayon_core::join::join_recover_from_panic
24: rayon_core::join::join_context::{{closure}}
25: rayon_core::registry::in_worker
26: rayon::iter::plumbing::bridge_producer_consumer::helper
27: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
28: rayon_core::registry::WorkerThread::wait_until_cold
29: rayon_core::join::join_recover_from_panic
30: rayon_core::join::join_context::{{closure}}
31: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
32: rayon_core::registry::WorkerThread::wait_until_cold
33: rayon_core::registry::ThreadBuilder::run
note: Some details are omitted, run with `RUST_BACKTRACE=full` for a verbose backtrace.
thread '<unnamed>' panicked at 'range end index 2955 out of range for slice of length 595', src/ska_ref/aln_writer.rs:148:35
stack backtrace:
0: rust_begin_unwind
1: core::panicking::panic_fmt
2: core::slice::index::slice_end_index_len_fail
3: ska::ska_ref::aln_writer::AlnWriter::write_split_kmer
4: rayon::iter::plumbing::Producer::fold_with
5: rayon::iter::plumbing::bridge_producer_consumer::helper
6: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
7: rayon_core::registry::WorkerThread::wait_until_cold
8: rayon_core::join::join_recover_from_panic
9: rayon_core::join::join_context::{{closure}}
10: rayon_core::registry::in_worker
11: rayon::iter::plumbing::bridge_producer_consumer::helper
12: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
13: rayon_core::registry::WorkerThread::wait_until_cold
14: rayon_core::join::join_recover_from_panic
15: rayon_core::join::join_context::{{closure}}
16: rayon_core::registry::in_worker
17: rayon::iter::plumbing::bridge_producer_consumer::helper
18: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
19: rayon_core::registry::WorkerThread::wait_until_cold
20: rayon_core::join::join_recover_from_panic
21: rayon_core::join::join_context::{{closure}}
22: rayon_core::registry::in_worker
23: rayon::iter::plumbing::bridge_producer_consumer::helper
24: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
25: rayon_core::registry::WorkerThread::wait_until_cold
26: rayon_core::join::join_recover_from_panic
27: rayon_core::join::join_context::{{closure}}
28: rayon_core::registry::in_worker
29: rayon::iter::plumbing::bridge_producer_consumer::helper
30: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
31: rayon_core::registry::WorkerThread::wait_until_cold
32: rayon_core::join::join_recover_from_panic
33: rayon_core::join::join_context::{{closure}}
34: <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute
35: rayon_core::registry::WorkerThread::wait_until_cold
36: rayon_core::registry::ThreadBuilder::run
note: Some details are omitted, run with `RUST_BACKTRACE=full` for a verbose backtrace.
johnlees commented
Thanks for the detailed report, I will look into this asap. I only tested with a two contig reference to map to so I probably made some error in the indexing code
johnlees commented
I had assumed only one contig (chromosome) would be skipped at a time, but here there are some short ones with no mapping k-mers. Just need to change an if to while which is a pleasing fix!
tmaklin commented
Well that was easy 😄!