thread 'main' panicked - v3 proseg

[GhobrialMoheb]

Hi, good morning,

While testing a dataset once with v2 proseg, and now with v3 proseg, I got this error:

00:00:00 ############################################################ | log-likelihood: -161026610 | assigned: 28360198 / 28368798 (99.97%) | non-background: (99.54%) thread 'main' panicked at /root/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/proseg-3.0.3/src/output.rs:484:69: called Result::unwrap() on an Err value: InvalidArgumentError("all columns in a record batch must have the same length") note: run with RUST_BACKTRACE=1 environment variable to display a backtrace

the output has only: -"proseg-counts.mtx" -"proseg-expected-counts.mtx"

and it doesn't have "proseg-output.zarr"

Any idea what could be the reason to this?

Thank you

[dcjones]

This should be fixed with proseg 3.0.5, which I published just now.

[GhobrialMoheb]

Thanks alot for your efforts

[ka-ora]

I am facing the same issue even on 3.0.5 at this time

[dcjones]

That's odd, could you post the exact error message you get?

[ka-ora]

Thanks, please see here:

RUST_BACKTRACE=full CUDA_VISIBLE_DEVICES=0 proseg --xenium --nthreads 36 transcripts_TMA.parquet Using 36 threads

thread 'main' panicked at src/sampler/transcripts.rs:582:14: called Option::unwrap() on a None value stack backtrace: 0: 0x5b058e174122 - <std::sys::backtrace::BacktraceLock::print::DisplayBacktrace as core::fmt::Display>::fmt::hf435e8e9347709a8 1: 0x5b058e197d53 - core::fmt::write::h0a51fad3804c5e7c 2: 0x5b058e171843 - std::io::Write::write_fmt::h9759e4151bf4a45e 3: 0x5b058e173f72 - std::sys::backtrace::BacktraceLock::print::h1ec5ce5bb8ee285e 4: 0x5b058e175126 - std::panicking::default_hook::{{closure}}::h5ffefe997a3c75e4 5: 0x5b058e174f29 - std::panicking::default_hook::h820c77ba0601d6bb 6: 0x5b058e175ab2 - std::panicking::rust_panic_with_hook::h8b29cbe181d50030 7: 0x5b058e175836 - std::panicking::begin_panic_handler::{{closure}}::h9f5b6f6dc6fde83e 8: 0x5b058e174629 - std::sys::backtrace::__rust_end_short_backtrace::hd7b0c344383b0b61 9: 0x5b058e1754fd - __rustc[5224e6b81cd82a8f]::rust_begin_unwind 10: 0x5b058d7b92f0 - core::panicking::panic_fmt::hc49fc28484033487 11: 0x5b058d7b937c - core::panicking::panic::h239804395728b21f 12: 0x5b058d7b9269 - core::option::unwrap_failed::hec54eb4737b382ca 13: 0x5b058d865d5a - proseg::sampler::transcripts::read_xenium_transcripts_parquet::h7af3653967a27b11 14: 0x5b058d85c419 - proseg::sampler::transcripts::read_transcripts_csv::hf9bdd2a3c1d19e38 15: 0x5b058d8b2451 - proseg::main::h064cef5fc623f17a 16: 0x5b058d8ac5a3 - std::sys::backtrace::__rust_begin_short_backtrace::ha137b2febc503ce9 17: 0x5b058d877049 - std::rt::lang_start::{{closure}}::h8639609ff56205c9 18: 0x5b058e169f80 - std::rt::lang_start_internal::h31bbb7f936fd6b5d 19: 0x5b058d8d82e5 - main 20: 0x74f907629d90 - __libc_start_call_main at ./csu/../sysdeps/nptl/libc_start_call_main.h:58:16 21: 0x74f907629e40 - __libc_start_main_impl at ./csu/../csu/libc-start.c:392:3 22: 0x5b058d7b9ad5 - _start 23: 0x0 -

[dcjones]

This looks like a different error, and judging from the line numbers an older version of proseg (you can check with proseg --version).

That probably doesn't matter though because the format is different than what proseg expects. I'm guessing this xenium data is either very new or fairly old. If it's on the older side, try using the transcripts.csv.gz file instead. If it's new, I'll try to figure out what the change was and update proseg.

[paularstrpo]

I am having the same issue with MERSCOPE data using the detected_transcripts.csv file as input.

[dcjones]

Could you post the version you're using (run proseg --version)?