what index file does rust hificnv expect? is there a way to explicitly specify the index?

[Carl-labhub]

I move sample1.bam.gz and sample1.bam.tbi.gz to a new directory along with refGenome.fasta, unzip, and call hificnv with

hificnv --bam sample1.bam --ref refgenome.fasta --threads 10 --output-prefix s1out

I get the following error and uninformative backtrace. I assume hificnv simply cant find the index. how can I explicitly specify the reference?

[E::idx_find_and_load] Could not retrieve index file for 'm84165_231116_151833_s4.hifi_reads.bc2001.bam' thread 'main' panicked at 'called Result::unwrap()on anErrvalue: BamInvalidIndex { target: "m84165_231116_151833_s4.hifi_reads.bc2001.bam" }', src/cli.rs:226:80 stack backtrace: 0: 0x82bb7a - std::backtrace_rs::backtrace::libunwind::trace::ha271a8a7e1f3d4ef at /rustc/9eb3afe9ebe9c7d2b84b71002d44f4a0edac95e0/library/std/src/../../backtrace/src/backtrace/libunwind.rs:93:5 1: 0x82bb7a - std::backtrace_rs::backtrace::trace_unsynchronized::h85739da0352c791a at /rustc/9eb3afe9ebe9c7d2b84b71002d44f4a0edac95e0/library/std/src/../../backtrace/src/backtrace/mod.rs:66:5 2: 0x82bb7a - std::sys_common::backtrace::_print_fmt::hbc6ebcfb2910b329 at /rustc/9eb3afe9ebe9c7d2b84b71002d44f4a0edac95e0/library/std/src/sys_common/backtrace.rs:65:5 3: 0x82bb7a - <std::sys_common::backtrace::_print::DisplayBacktrace as core::fmt::Display>::fmt::he1c117e52d53614f at /rustc/9eb3afe9ebe9c7d2b84b71002d44f4a0edac95e0/library/std/src/sys_common/backtrace.rs:44:22 4: 0x9219fe - core::fmt::write::h25eb51b9526b8e0c at /rustc/9eb3afe9ebe9c7d2b84b71002d44f4a0edac95e0/library/core/src/fmt/mod.rs:1213:17 5: 0x829475 - std::io::Write::write_fmt::ha9edec5fb1621933 at /rustc/9eb3afe9ebe9c7d2b84b71002d44f4a0edac95e0/library/std/src/io/mod.rs:1682:15 6: 0x82b945 - std::sys_common::backtrace::_print::hf8657cd429fc3452 at /rustc/9eb3afe9ebe9c7d2b84b71002d44f4a0edac95e0/library/std/src/sys_common/backtrace.rs:47:5 7: 0x82b945 - std::sys_common::backtrace::print::h41b9b18ed86f86bd at /rustc/9eb3afe9ebe9c7d2b84b71002d44f4a0edac95e0/library/std/src/sys_common/backtrace.rs:34:9 8: 0x82d12f - std::panicking::default_hook::{{closure}}::h22a91871f4454152 at /rustc/9eb3afe9ebe9c7d2b84b71002d44f4a0edac95e0/library/std/src/panicking.rs:267:22 9: 0x82ce6b - std::panicking::default_hook::h21ddc36de0cd4ae7 at /rustc/9eb3afe9ebe9c7d2b84b71002d44f4a0edac95e0/library/std/src/panicking.rs:286:9 10: 0x82d839 - std::panicking::rust_panic_with_hook::h5059419d6d59b3d0 at /rustc/9eb3afe9ebe9c7d2b84b71002d44f4a0edac95e0/library/std/src/panicking.rs:688:13 11: 0x82d5d9 - std::panicking::begin_panic_handler::{{closure}}::h0f383c291cd78343 at /rustc/9eb3afe9ebe9c7d2b84b71002d44f4a0edac95e0/library/std/src/panicking.rs:579:13 12: 0x82c02c - std::sys_common::backtrace::__rust_end_short_backtrace::h70ab22f2ad318cdd at /rustc/9eb3afe9ebe9c7d2b84b71002d44f4a0edac95e0/library/std/src/sys_common/backtrace.rs:137:18 13: 0x82d2e2 - rust_begin_unwind at /rustc/9eb3afe9ebe9c7d2b84b71002d44f4a0edac95e0/library/std/src/panicking.rs:575:5 14: 0x40f2f3 - core::panicking::panic_fmt::hd1d46bcde3c61d72 at /rustc/9eb3afe9ebe9c7d2b84b71002d44f4a0edac95e0/library/core/src/panicking.rs:64:14 15: 0x40f7a3 - core::result::unwrap_failed::h456a23f68607268c at /rustc/9eb3afe9ebe9c7d2b84b71002d44f4a0edac95e0/library/core/src/result.rs:1790:5 16: 0x43baaa - hificnv::main::h4ce7aff8eb915e27 17: 0x4428d3 - std::sys_common::backtrace::__rust_begin_short_backtrace::hff535d6baf85e36b 18: 0x4507d9 - std::rt::lang_start::{{closure}}::h7700578965062055 19: 0x82435c - core::ops::function::impls::<impl core::ops::function::FnOnce<A> for &F>::call_once::h203afb3af230319a at /rustc/9eb3afe9ebe9c7d2b84b71002d44f4a0edac95e0/library/core/src/ops/function.rs:287:13 20: 0x82435c - std::panicking::try::do_call::hf68e87013b70f3c5 at /rustc/9eb3afe9ebe9c7d2b84b71002d44f4a0edac95e0/library/std/src/panicking.rs:483:40 21: 0x82435c - std::panicking::try::h040ea8f298390ba2 at /rustc/9eb3afe9ebe9c7d2b84b71002d44f4a0edac95e0/library/std/src/panicking.rs:447:19 22: 0x82435c - std::panic::catch_unwind::h1e17b198887a05fa at /rustc/9eb3afe9ebe9c7d2b84b71002d44f4a0edac95e0/library/std/src/panic.rs:140:14 23: 0x82435c - std::rt::lang_start_internal::{{closure}}::hfb902d8927e51b86 at /rustc/9eb3afe9ebe9c7d2b84b71002d44f4a0edac95e0/library/std/src/rt.rs:148:48 24: 0x82435c - std::panicking::try::do_call::h354e6eb41f2e7d42 at /rustc/9eb3afe9ebe9c7d2b84b71002d44f4a0edac95e0/library/std/src/panicking.rs:483:40 25: 0x82435c - std::panicking::try::h4a39749cd018228c at /rustc/9eb3afe9ebe9c7d2b84b71002d44f4a0edac95e0/library/std/src/panicking.rs:447:19 26: 0x82435c - std::panic::catch_unwind::h30bce83b8de61cca at /rustc/9eb3afe9ebe9c7d2b84b71002d44f4a0edac95e0/library/std/src/panic.rs:140:14 27: 0x82435c - std::rt::lang_start_internal::h8f7e70b1a2558118 at /rustc/9eb3afe9ebe9c7d2b84b71002d44f4a0edac95e0/library/std/src/rt.rs:148:20 28: 0x441f2f - main 29: 0x86a725 - __libc_start_main at /mnt/tc-build/src/glibc-2.17/csu/libc-start.c:258:16 30: 0x40fc1a - <unknown> at /mnt/tc-build/src/glibc-2.17/csu/../sysdeps/x86_64/start.S:123 31: 0x0 - <unknown>

[ctsa]

Thanks @Carl-labhub , HiFiCNV expects a bam file to have an index with a .bai extension -- in this case m84165_231116_151833_s4.hifi_reads.bc2001.bam.bai. This is the default naming convention from indexing the bam using samtools, e.g.:

samtools index m84165_231116_151833_s4.hifi_reads.bc2001.bam

Agreed this backtrace is unhelpful -- we'll see if we can patch this to give a simple error message instead.

[Carl-labhub]

Wow I don't know why I assumed it would be somehow distinct from the usual .bai. Thank you for your speedy response.