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PacificBiosciences / trgt-denovo

De novo tandem repeat calling from PacBio HiFi data
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thread '<unnamed>' panicked at 'called `Option::unwrap()` on a `None` value', src/snp.rs:63:68 #1

Closed lauragails closed 3 months ago

lauragails commented 7 months ago

Hello - I'm excited to run your program! Initially I recieved an error: 

2024-02-12 16:36:26 [INFO] - trgt-denovo-0.1.0-1ba958a trio start
2024-02-12 16:36:29 [INFO] - Starting job pool with 1 threads...
2024-02-12 16:36:29 [WARN] - Skipping TRID=chr1_44835_44867 missing in C
thread '<unnamed>' panicked at 'called `Option::unwrap()` on a `None` value', src/snp.rs:63:68
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

Note that for each sample you have the following files, and I ran in the same directory as the files: sample.GRCh38.trgt.sorted.vcf.gz sample.GRCh38.trgt.sorted.vcf.gz.csi sample.GRCh38.trgt.spanning.sorted.bam sample.GRCh38.trgt.spanning.sorted.bam.bai

Output when I reran RUST_BACKTRACE=full /path/to/trgt-denovo-v0.1.0-linux_x86_64 trio --reference /path/to/reference/human_GRCh38_no_alt_analysis_set.fasta --bed /path/to/trgt/github/trgt/repeats/repeat_catalog.hg38.bed --father f.GRCh38.trgt --mother m.GRCh38.trgt --child c.GRCh38.trgt --out /sc/arion/projects/buxbaj01a/sloofl01/pac_bio/results/trgt-denovo/021224//out_repeat_catalog.hg38.familyID.csv

2024-02-12 16:47:50 [INFO] - trgt-denovo-0.1.0-1ba958a trio start 2024-02-12 16:47:52 [INFO] - Starting job pool with 1 threads... 2024-02-12 16:47:52 [WARN] - Skipping TRID=chr1_44835_44867 missing in C thread '' panicked at 'called Option::unwrap() on a None value', src/snp.rs:63:68 stack backtrace: 0: 0x64118a - std::backtrace_rs::backtrace::libunwind::trace::h9a6b80bbf328ba5d at /rustc/90c541806f23a127002de5b4038be731ba1458ca/library/std/src/../../backtrace/src/backtrace/libunwind.rs:93:5 1: 0x64118a - std::backtrace_rs::backtrace::trace_unsynchronized::hd162ec543a11886b at /rustc/90c541806f23a127002de5b4038be731ba1458ca/library/std/src/../../backtrace/src/backtrace/mod.rs:66:5 2: 0x64118a - std::sys_common::backtrace::_print_fmt::h78a5099be12f51a6 at /rustc/90c541806f23a127002de5b4038be731ba1458ca/library/std/src/sys_common/backtrace.rs:65:5 3: 0x64118a - ::fmt::ha1c5390454d74f71 at /rustc/90c541806f23a127002de5b4038be731ba1458ca/library/std/src/sys_common/backtrace.rs:44:22 4: 0x6fd4ff - core::fmt::write::h9ffde816c577717b at /rustc/90c541806f23a127002de5b4038be731ba1458ca/library/core/src/fmt/mod.rs:1254:17 5: 0x63e3b5 - std::io::Write::write_fmt::h88186074961638e4 at /rustc/90c541806f23a127002de5b4038be731ba1458ca/library/std/src/io/mod.rs:1698:15 6: 0x640f55 - std::sys_common::backtrace::_print::h184198273ed08d59 at /rustc/90c541806f23a127002de5b4038be731ba1458ca/library/std/src/sys_common/backtrace.rs:47:5 7: 0x640f55 - std::sys_common::backtrace::print::h1b4d8e7add699453 at /rustc/90c541806f23a127002de5b4038be731ba1458ca/library/std/src/sys_common/backtrace.rs:34:9 8: 0x64270e - std::panicking::default_hook::{{closure}}::h393bcea75423915a at /rustc/90c541806f23a127002de5b4038be731ba1458ca/library/std/src/panicking.rs:269:22 9: 0x6424b5 - std::panicking::default_hook::h48c64f31d8b3fd03 at /rustc/90c541806f23a127002de5b4038be731ba1458ca/library/std/src/panicking.rs:288:9 10: 0x642c6e - std::panicking::rust_panic_with_hook::hafdc493a79370062 at /rustc/90c541806f23a127002de5b4038be731ba1458ca/library/std/src/panicking.rs:691:13 11: 0x642b22 - std::panicking::begin_panic_handler::{{closure}}::h0a64bc82e36bedc7 at /rustc/90c541806f23a127002de5b4038be731ba1458ca/library/std/src/panicking.rs:580:13 12: 0x6415f6 - std::sys_common::backtrace::rust_end_short_backtrace::hc203444fb7416a16 at /rustc/90c541806f23a127002de5b4038be731ba1458ca/library/std/src/sys_common/backtrace.rs:150:18 13: 0x6428c2 - rust_begin_unwind at /rustc/90c541806f23a127002de5b4038be731ba1458ca/library/std/src/panicking.rs:578:5 14: 0x419e23 - core::panicking::panic_fmt::h0f6ef0178afce4f2 at /rustc/90c541806f23a127002de5b4038be731ba1458ca/library/core/src/panicking.rs:67:14 15: 0x419ebd - core::panicking::panic::h0ead933cb8f56d66 at /rustc/90c541806f23a127002de5b4038be731ba1458ca/library/core/src/panicking.rs:117:5 16: 0x438c6c - trgt_denovo::snp::TrinaryMatrix::new::h8ca0b5a58b0d9f91 17: 0x46d561 - trgt_denovo::allele::process_alleles::h094f131f4aff6078 18: 0x434ce6 - std::thread::local::LocalKey::with::h91283eb91d958ade 19: 0x46ff43 - <rayon::iter::map_with::MapWithFolder<C,U,F> as rayon::iter::plumbing::Folder>::consume::h87429c0780b97b7c 20: 0x47dd80 - <&rayon::iter::par_bridge::IterParallelProducer as rayon::iter::plumbing::UnindexedProducer>::fold_with::h0c63b0e2fac569c3 21: 0x482f76 - rayon::iter::plumbing::bridge_unindexed_producer_consumer::h6c9689ce76a38bf3 22: 0x475f58 - rayon_core::join::join_context::{{closure}}::h78115c239a86ce9a 23: 0x476f99 - rayon_core::registry::in_worker::h0a63140bf1da3a2c 24: 0x482f08 - rayon::iter::plumbing::bridge_unindexed_producer_consumer::h6c9689ce76a38bf3 25: 0x48393f - <rayon::iter::par_bridge::IterBridge as rayon::iter::ParallelIterator>::drive_unindexed::h6348866b0be6559a 26: 0x43ae90 - <core::panic::unwind_safe::AssertUnwindSafe as core::ops::function::FnOnce<()>>::call_once::ha8c572a74d22ea73 27: 0x48edb7 - <rayon_core::job::StackJob<L,F,R> as rayon_core::job::Job>::execute::h4ba9d53d320ed063 28: 0x4078a8 - rayon_core::registry::WorkerThread::wait_until_cold::hdf559a144669d50c 29: 0x4a22ca - rayon_core::registry::ThreadBuilder::run::hfad351f1e411dc1d 30: 0x4a52e9 - std::sys_common::backtrace::rust_begin_short_backtrace::hd33919d34582822b 31: 0x4a75e0 - core::ops::function::FnOnce::call_once{{vtable.shim}}::hbc390d93a9f9279c 32: 0x6454c5 - <alloc::boxed::Box<F,A> as core::ops::function::FnOnce>::call_once::ha1f2224656a778fb at /rustc/90c541806f23a127002de5b4038be731ba1458ca/library/alloc/src/boxed.rs:1973:9 33: 0x6454c5 - <alloc::boxed::Box<F,A> as core::ops::function::FnOnce>::call_once::haa29ed9703f354b7 at /rustc/90c541806f23a127002de5b4038be731ba1458ca/library/alloc/src/boxed.rs:1973:9 34: 0x6454c5 - std::sys::unix::thread::Thread::new::thread_start::h33b6dae3e3692197 at /rustc/90c541806f23a127002de5b4038be731ba1458ca/library/std/src/sys/unix/thread.rs:108:17 35: 0x65c253 - start_thread at /mnt/tc-build/src/glibc-2.17/nptl/pthread_create.c:308:7 36: 0x69a999 - clone at /mnt/tc-build/src/glibc-2.17/misc/../sysdeps/unix/sysv/linux/x86_64/clone.S:113 37: 0x0 -

Thank you!

tmokveld commented 7 months ago

Hi,

Thank you for your interest!

Your issue seems to be related to the processing of flanking variation, which is an unstable feature. Could you try re-running these same data with the latest TRGT-denovo release?