search

10XGenomics / vartrix

Single-Cell Genotyping Tool
MIT License
200 stars 26 forks source link

vartrix crashes with "assertion failed: col < self.cols" #47

Closed gokceneraslan closed 4 years ago

gokceneraslan commented 4 years ago

Hi,

I'm using souporcell (https://github.com/wheaton5/souporcell/) for genotype-based demultiplexing and in one of my samples, vartrix crashes with the following crash report:

name = 'vartrix'
operating_system = 'unix:Debian'
crate_version = '1.1.3'
explanation = '''
Cause: assertion failed: col < self.cols. Panic occurred in file '/mnt/home/ian.fiddes/.cargo/registry/src/github.com-1ecc6299db9ec823/sprs-0.6.2/src/sparse/triplet.rs' at line 142
'''
method = 'Panic'
backtrace = '''
stack backtrace:
   0:     0x562bc98eff8d - backtrace::backtrace::libunwind::trace::h0450ee9701db9b56
                        at /mnt/home/ian.fiddes/.cargo/registry/src/github.com-1ecc6299db9ec823/backtrace-0.3.9/src/backtrace/libunwind.rs:53
                         - backtrace::backtrace::trace::h9a495a5fb843afd0
                        at /mnt/home/ian.fiddes/.cargo/registry/src/github.com-1ecc6299db9ec823/backtrace-0.3.9/src/backtrace/mod.rs:42
   1:     0x562bc98ef0e2 - backtrace::capture::Backtrace::new_unresolved::he8700c7c2914edf9
                        at /mnt/home/ian.fiddes/.cargo/registry/src/github.com-1ecc6299db9ec823/backtrace-0.3.9/src/capture.rs:88
                         - backtrace::capture::Backtrace::new::h3441f72ebb513354
                        at /mnt/home/ian.fiddes/.cargo/registry/src/github.com-1ecc6299db9ec823/backtrace-0.3.9/src/capture.rs:63
                         - <backtrace::capture::Backtrace as core::default::Default>::default::hdff5cb6156d225b4
                        at /mnt/home/ian.fiddes/.cargo/registry/src/github.com-1ecc6299db9ec823/backtrace-0.3.9/src/capture.rs:235
   2:     0x562bc98de8e2 - human_panic::report::Report::new::h325ba580fbc9e03e
                        at /mnt/home/ian.fiddes/.cargo/registry/src/github.com-1ecc6299db9ec823/human-panic-1.0.1/src/report.rs:45
   3:     0x562bc98ddf97 - human_panic::handle_dump::hbabf58a26cf238b8
                        at /mnt/home/ian.fiddes/.cargo/registry/src/github.com-1ecc6299db9ec823/human-panic-1.0.1/src/lib.rs:197
   4:     0x562bc98afb98 - vartrix::main::{{closure}}::h419645f055558e66
                        at /mnt/yard2/ian/vartrix/<::human_panic::setup_panic macros>:18
   5:     0x562bc9a5ac69 - std::panicking::rust_panic_with_hook::h744417edfe714d72
                        at src/libstd/panicking.rs:482
   6:     0x562bc98b4af4 - std::panicking::begin_panic::h8d6596f4f0ccbd1f
                        at /rustc/2aa4c46cfdd726e97360c2734835aa3515e8c858/src/libstd/panicking.rs:412
   7:     0x562bc98d8cd7 - sprs::sparse::triplet::<impl sprs::sparse::TriMatBase<alloc::vec::Vec<I>, alloc::vec::Vec<N>>>::add_triplet::h6fc3f0de4dc030b2
                        at /mnt/yard2/ian/vartrix/<::std::macros::panic macros>:3
   8:     0x562bc98a5e1b - vartrix::_main::h7b280daad477f5bc
                        at src/main.rs:296
   9:     0x562bc98a15e0 - vartrix::main::h471b1b425af17703
                        at src/main.rs:152
  10:     0x562bc98b0fa2 - std::rt::lang_start::{{closure}}::h48619bd1f8ea0c15
                        at /rustc/2aa4c46cfdd726e97360c2734835aa3515e8c858/src/libstd/rt.rs:64
  11:     0x562bc9a5a592 - std::rt::lang_start_internal::{{closure}}::h8ad4264c6b68797c
                        at src/libstd/rt.rs:49
                         - std::panicking::try::do_call::h7a0381557c6c2cee
                        at src/libstd/panicking.rs:297
  12:     0x562bc9a62039 - __rust_maybe_catch_panic
                        at src/libpanic_unwind/lib.rs:92
  13:     0x562bc9a5b1a5 - std::panicking::try::h72cb0fef6e9c0ab1
                        at src/libstd/panicking.rs:276
                         - std::panic::catch_unwind::hbff071ae76e6f224
                        at src/libstd/panic.rs:388
                         - std::rt::lang_start_internal::he0d8d06abc6f912f
                        at src/libstd/rt.rs:48
  14:     0x562bc98afc17 - main
  15:     0x7f7d115e42e0 - __libc_start_main
  16:     0x562bc989ea58 - <unknown>'''

Any help is appreciated :)

gokceneraslan commented 4 years ago

OK, this is fixed after upgrading to the latest version (vartrix 1.1.16).

pmarks commented 4 years ago

Hi Gökçen,

Could you try out a new version of vartrix? Version 1.1.3 is quite old & we've fixed quite a lot of bugs. We have a pre-built binary here: https://github.com/10XGenomics/vartrix/releases/tag/v1.1.16

I'm going to file a ticket with souporcell to update to the latest version.

Thanks, Pat

On Wed, Aug 19, 2020 at 4:59 AM Gökçen Eraslan notifications@github.com wrote:

Hi,

I'm using souporcell (https://github.com/wheaton5/souporcell/) for genotype-based demultiplexing and in one of my samples, vartrix crashes with the following crash report:

name = 'vartrix' operating_system = 'unix:Debian' crate_version = '1.1.3' explanation = ''' Cause: assertion failed: col < self.cols. Panic occurred in file '/mnt/home/ian.fiddes/.cargo/registry/src/github.com-1ecc6299db9ec823/sprs-0.6.2/src/sparse/triplet.rs' at line 142 ''' method = 'Panic' backtrace = ''' stack backtrace: 0: 0x562bc98eff8d - backtrace::backtrace::libunwind::trace::h0450ee9701db9b56 at /mnt/home/ian.fiddes/.cargo/registry/src/github.com-1ecc6299db9ec823/backtrace-0.3.9/src/backtrace/libunwind.rs:53

  • backtrace::backtrace::trace::h9a495a5fb843afd0 at /mnt/home/ian.fiddes/.cargo/registry/src/github.com-1ecc6299db9ec823/backtrace-0.3.9/src/backtrace/mod.rs:42 1: 0x562bc98ef0e2 - backtrace::capture::Backtrace::new_unresolved::he8700c7c2914edf9 at /mnt/home/ian.fiddes/.cargo/registry/src/github.com-1ecc6299db9ec823/backtrace-0.3.9/src/capture.rs:88
  • backtrace::capture::Backtrace::new::h3441f72ebb513354 at /mnt/home/ian.fiddes/.cargo/registry/src/github.com-1ecc6299db9ec823/backtrace-0.3.9/src/capture.rs:63
  • ::default::hdff5cb6156d225b4 at /mnt/home/ian.fiddes/.cargo/registry/src/github.com-1ecc6299db9ec823/backtrace-0.3.9/src/capture.rs:235 2: 0x562bc98de8e2 - human_panic::report::Report::new::h325ba580fbc9e03e at /mnt/home/ian.fiddes/.cargo/registry/src/github.com-1ecc6299db9ec823/human-panic-1.0.1/src/report.rs:45 3: 0x562bc98ddf97 - human_panic::handle_dump::hbabf58a26cf238b8 at /mnt/home/ian.fiddes/.cargo/registry/src/github.com-1ecc6299db9ec823/human-panic-1.0.1/src/lib.rs:197 4: 0x562bc98afb98 - vartrix::main::{{closure}}::h419645f055558e66 at /mnt/yard2/ian/vartrix/<::human_panic::setup_panic macros>:18 5: 0x562bc9a5ac69 - std::panicking::rust_panic_with_hook::h744417edfe714d72 at src/libstd/panicking.rs:482 6: 0x562bc98b4af4 - std::panicking::begin_panic::h8d6596f4f0ccbd1f at /rustc/2aa4c46cfdd726e97360c2734835aa3515e8c858/src/libstd/panicking.rs:412 7: 0x562bc98d8cd7 - sprs::sparse::triplet::, alloc::vec::Vec>>::add_triplet::h6fc3f0de4dc030b2 at /mnt/yard2/ian/vartrix/<::std::macros::panic macros>:3 8: 0x562bc98a5e1b - vartrix::_main::h7b280daad477f5bc at src/main.rs:296 9: 0x562bc98a15e0 - vartrix::main::h471b1b425af17703 at src/main.rs:152 10: 0x562bc98b0fa2 - std::rt::lang_start::{{closure}}::h48619bd1f8ea0c15 at /rustc/2aa4c46cfdd726e97360c2734835aa3515e8c858/src/libstd/rt.rs:64 11: 0x562bc9a5a592 - std::rt::lang_start_internal::{{closure}}::h8ad4264c6b68797c at src/libstd/rt.rs:49
  • std::panicking::try::do_call::h7a0381557c6c2cee at src/libstd/panicking.rs:297 12: 0x562bc9a62039 - __rust_maybe_catch_panic at src/libpanic_unwind/lib.rs:92 13: 0x562bc9a5b1a5 - std::panicking::try::h72cb0fef6e9c0ab1 at src/libstd/panicking.rs:276
  • std::panic::catch_unwind::hbff071ae76e6f224 at src/libstd/panic.rs:388
  • std::rt::lang_start_internal::he0d8d06abc6f912f at src/libstd/rt.rs:48 14: 0x562bc98afc17 - main 15: 0x7f7d115e42e0 - __libc_start_main 16: 0x562bc989ea58 - '''

Any help is appreciated :)

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/10XGenomics/vartrix/issues/47, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAALGA7TC3LPKOFVGQHATCTSBO5AVANCNFSM4QE3NDHQ .

-- Patrick Marks Senior Director, Computational Biology patrick@10xgenomics.com name@10xgenomics.com [image: 10x Genomics] http://www.10xgenomics.com/ Office 925 123 4567 | Mobile 408 123 4567 6230 Stoneridge Mall Road Pleasanton, CA 94588-3260 | 10xgenomics.com http://www.10xgenomics.com/