Problems with to_basespace: thread 'main' panicked at 'called `Option::unwrap()` on a `None` value', src/to_basespace.rs:216:55

[Zhiliang-Zhang]

Hello,

I have received an error message as following when ran "to_basespace --gfa example.unitigs.gfa --sequences example.sequences" with example data.

Could you give me some advice? Thanks!

Zhiliang

[zhiliang@localhost example]$ RUST_BACKTRACE=full ../target/release/to_basespace --gfa example.unitigs.gfa --sequences example.sequences Done parsing GFA, got 1 unitigs. Done parsing .sequences file, recorded 0 sequences. thread 'main' panicked at 'called Option::unwrap() on a None value', src/to_basespace.rs:216:55 stack backtrace: 0: 0x55f28d16a8f0 - std::backtrace_rs::backtrace::libunwind::trace::h34055254b57d8e79 at /rustc/a178d0322ce20e33eac124758e837cbd80a6f633/library/std/src/../../backtrace/src/backtrace/libunwind.rs:90:5 1: 0x55f28d16a8f0 - std::backtrace_rs::backtrace::trace_unsynchronized::h8f1e3fbd9afff6ec at /rustc/a178d0322ce20e33eac124758e837cbd80a6f633/library/std/src/../../backtrace/src/backtrace/mod.rs:66:5 2: 0x55f28d16a8f0 - std::sys_common::backtrace::_print_fmt::h3a99a796b770c360 at /rustc/a178d0322ce20e33eac124758e837cbd80a6f633/library/std/src/sys_common/backtrace.rs:67:5 3: 0x55f28d16a8f0 - ::fmt::h32d1f94a80615d18 at /rustc/a178d0322ce20e33eac124758e837cbd80a6f633/library/std/src/sys_common/backtrace.rs:46:22 4: 0x55f28d18ab7c - core::fmt::write::h306731c068f7162c at /rustc/a178d0322ce20e33eac124758e837cbd80a6f633/library/core/src/fmt/mod.rs:1110:17 5: 0x55f28d168315 - std::io::Write::write_fmt::hd2fa90334eee2a21 at /rustc/a178d0322ce20e33eac124758e837cbd80a6f633/library/std/src/io/mod.rs:1588:15 6: 0x55f28d16c85b - std::sys_common::backtrace::_print::h5abaa2601a852287 at /rustc/a178d0322ce20e33eac124758e837cbd80a6f633/library/std/src/sys_common/backtrace.rs:49:5 7: 0x55f28d16c85b - std::sys_common::backtrace::print::h8d81445442bb638f at /rustc/a178d0322ce20e33eac124758e837cbd80a6f633/library/std/src/sys_common/backtrace.rs:36:9 8: 0x55f28d16c85b - std::panicking::default_hook::{{closure}}::hcfe804496a9fa747 at /rustc/a178d0322ce20e33eac124758e837cbd80a6f633/library/std/src/panicking.rs:208:50 9: 0x55f28d16c331 - std::panicking::default_hook::hbea8e3ccf2ba8901 at /rustc/a178d0322ce20e33eac124758e837cbd80a6f633/library/std/src/panicking.rs:225:9 10: 0x55f28d16cf24 - std::panicking::rust_panic_with_hook::h7ee9e1a2d0f8975a at /rustc/a178d0322ce20e33eac124758e837cbd80a6f633/library/std/src/panicking.rs:622:17 11: 0x55f28d16c9d7 - std::panicking::begin_panic_handler::{{closure}}::h8ab3b4491718b2c7 at /rustc/a178d0322ce20e33eac124758e837cbd80a6f633/library/std/src/panicking.rs:517:13 12: 0x55f28d16adec - std::sys_common::backtrace::rust_end_short_backtrace::hd489062ffa586a9f at /rustc/a178d0322ce20e33eac124758e837cbd80a6f633/library/std/src/sys_common/backtrace.rs:141:18 13: 0x55f28d16c969 - rust_begin_unwind at /rustc/a178d0322ce20e33eac124758e837cbd80a6f633/library/std/src/panicking.rs:515:5 14: 0x55f28d0f2e51 - core::panicking::panic_fmt::hca6330e3e14086b4 at /rustc/a178d0322ce20e33eac124758e837cbd80a6f633/library/core/src/panicking.rs:92:14 15: 0x55f28d0f2d9d - core::panicking::panic::h1a48d878ff3dcd40 at /rustc/a178d0322ce20e33eac124758e837cbd80a6f633/library/core/src/panicking.rs:50:5 16: 0x55f28d0fb5a6 - to_basespace::main::hf31f3484661a5776 17: 0x55f28d0f6193 - std::sys_common::backtrace::__rust_begin_short_backtrace::hf04ca134ae30e5e6 18: 0x55f28d0f61a9 - std::rt::lang_start::{{closure}}::h9452ba2bf9a0a5ac 19: 0x55f28d16d429 - core::ops::function::impls::<impl core::ops::function::FnOnce for &F>::call_once::h2aabc384aab89b7b at /rustc/a178d0322ce20e33eac124758e837cbd80a6f633/library/core/src/ops/function.rs:259:13 20: 0x55f28d16d429 - std::panicking::try::do_call::hc5fcacb7a85fc7b1 at /rustc/a178d0322ce20e33eac124758e837cbd80a6f633/library/std/src/panicking.rs:401:40 21: 0x55f28d16d429 - std::panicking::try::hb5d9603af3abbe3a at /rustc/a178d0322ce20e33eac124758e837cbd80a6f633/library/std/src/panicking.rs:365:19 22: 0x55f28d16d429 - std::panic::catch_unwind::h98fe6ac3925e64b4 at /rustc/a178d0322ce20e33eac124758e837cbd80a6f633/library/std/src/panic.rs:434:14 23: 0x55f28d16d429 - std::rt::lang_start_internal::h22ac7383c516f93e at /rustc/a178d0322ce20e33eac124758e837cbd80a6f633/library/std/src/rt.rs:34:21 24: 0x55f28d0fc412 - main 25: 0x7f6b9f66a555 - libc_start_main 26: 0x55f28d0f3621 - 27: 0x0 -

Hello @Zhiliang-Zhang,

The --sequences argument is actually a prefix, not the filename.

Can you try again with --sequences example and let me know?

Thanks! Barış

[Zhiliang-Zhang]

Hi Barış,

I run successfully. Thanks for your quick response. I will close this comment.

Bests, zhiliang