hifihla call-reads: thread 'main' panicked at src/cli/callreads_cli.rs:320:14:

[hhuili]

Operating system LSB Version: :core-4.1-amd64:core-4.1-noarch:cxx-4.1-amd64:cxx-4.1-noarch:desktop-4.1-amd64:desktop-4.1-noarch:languages-4.1-amd64:languages-4.1-noarch:printing-4.1-amd64:printing-4.1-noarch Distributor ID: CentOS Description: CentOS Linux release 7.9.2009 (Core) Release: 7.9.2009 Codename: Core

Package name hifihla v0.3.0

Conda environment Name Version BuildChannel _libgcc_mutex 0.1 conda_forge https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge _openmp_mutex 4.5 2_gnu https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge hifihla 0.3.0 hdfd78af_0 bioconda libgcc-ng 13.2.0 h807b86a_5 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libgomp 13.2.0 h807b86a_5 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libstdcxx-ng 13.2.0 h7e041cc_5 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge libzlib 1.2.13 hd590300_5 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge meryl 1.4.1 h4ac6f70_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda pbtk 3.1.1 h9ee0642_0 bioconda winnowmap 2.03 h43eeafb_2 bioconda

Describe the bug I used hifihla call-reads to call HLA loci from an aligned BAM of HiFi reads. My data were shorter (~5kb) Target Enrichment HiFi Reads. HiFi reads were aligned to GRCh38/T2T using minimap2 and Winnowmap, but encountered the same error (see Error message).

Error message nohup: ignoring input thread 'main' panicked at src/cli/callreads_cli.rs:320:14: bad fetch: Fetch stack backtrace: 0: rust_begin_unwind at /rustc/cc66ad468955717ab92600c770da8c1601a4ff33/library/std/src/panicking.rs:595:5 1: core::panicking::panic_fmt at /rustc/cc66ad468955717ab92600c770da8c1601a4ff33/library/core/src/panicking.rs:67:14 2: core::result::unwrap_failed at /rustc/cc66ad468955717ab92600c770da8c1601a4ff33/library/core/src/result.rs:1652:5 3: hifihla::cli::callreads_cli::hifihla_call_reads_main 4: hifihla::main note: Some details are omitted, run with RUST_BACKTRACE=full for a verbose backtrace. ./02.run_hifihla.sh: line 12: 156288 Aborted (core dumped) $hifihla_dir/hifihla call-reads -j 8 -a $bam_dir/$sample.sort.bam --outdir ./02.hifihla Done!

To Reproduce We can send our data for testing via priviate email if it is needed.

[jrharting]

Hi! This looks like a fetch error in htslib -- are you able to view the bam files in igv and view the data at HLA-a/b/c? I would def be interested in checking these data out if you can share. My email is jharting@pacb.com. Thank you!

[jrharting]

make sure to use the grch38_notalts ref. here is a link: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz

[jrharting]

incorrect reference