Panic occurred in file 'src/libcore/result.rs' at line 999

[YiweiNiu]

Hello,

I am using the scHLAcount binary from here.

Here is the command and error message.

$ ANNODIR=/home/niuyw/RefData
$ IMGT_HLA=$ANNODIR/IMGT_HLA/3.37.0

$ WORKDIR=/home/niuyw/Project/Data_processing
$ barcodes=$WORKDIR/cellranger/$dataset/${sample}_5/outs/filtered_feature_bc_matrix/barcodes.tsv.gz
$ bam=$WORKDIR/cellranger/$dataset/${sample}_5/outs/possorted_genome_bam.bam

$ sc_hla_count_linux -d $IMGT_HLA --bam $bam --cell-barcodes $barcodes -o $outdir
Sharding sequences...
Got 320987 sequence chunks
Assembling 106 shards...

Done separate de Bruijn graph construction
Starting merging disjoint graphs
Merger of graphs complete
Indexing de Bruijn graph
Total 52478 kmers to process in dbg
Making mphf of kmers
Assigning offsets to kmers
Well, this is embarrassing.

sc_hla_count had a problem and crashed. To help us diagnose the problem you can send us a crash report.

We have generated a report file at "/tmp/report-f9d423dd-656e-4afa-9d1d-1c2ac0a9dd96.toml". Submit an issue or email with the subject of "sc_hla_count Crash Report" and include the report as an attachment.

- Authors: Charlotte Darby <cdarby@jhu.edu>, Ian Fiddes <ian.t.fiddes@gmail.com>, Patrick Marks <patrick@10xgenomics.com>

We take privacy seriously, and do not perform any automated error collection. In order to improve the software, we rely on people to submit reports.

Thank you kindly!

Here is the content from /tmp/report-f9d423dd-656e-4afa-9d1d-1c2ac0a9dd96.toml:

name = 'sc_hla_count'
operating_system = 'unix:CentOS'
crate_version = '0.1.0'
explanation = '''
Panic occurred in file 'src/libcore/result.rs' at line 999
'''
method = 'Panic'
backtrace = '''
stack backtrace:
   0: backtrace::backtrace::libunwind::trace::hb73dfa724f78bc0d (0x2b64668daa07)
             at /mnt/home/patrick/.cargo/registry/src/github.com-1ecc6299db9ec823/backtrace-0.3.35/src/backtrace/libunwind.rs:88
      backtrace::backtrace::trace_unsynchronized::hd68d5720b8eeecb4
             at /mnt/home/patrick/.cargo/registry/src/github.com-1ecc6299db9ec823/backtrace-0.3.35/src/backtrace/mod.rs:66
      backtrace::backtrace::trace::h07a8a1b16091cf6f
             at /mnt/home/patrick/.cargo/registry/src/github.com-1ecc6299db9ec823/backtrace-0.3.35/src/backtrace/mod.rs:53
   1: backtrace::capture::Backtrace::create::ha2012ed583b4dee0 (0x2b64668d9f63)
             at /mnt/home/patrick/.cargo/registry/src/github.com-1ecc6299db9ec823/backtrace-0.3.35/src/capture.rs:163
      backtrace::capture::Backtrace::new::h2402c178e424aa5f
             at /mnt/home/patrick/.cargo/registry/src/github.com-1ecc6299db9ec823/backtrace-0.3.35/src/capture.rs:127
   2: human_panic::report::Report::new::h5e9fc17a20b5f651 (0x2b64668c8ef7)
             at /mnt/home/patrick/.cargo/registry/src/github.com-1ecc6299db9ec823/human-panic-1.0.1/src/report.rs:45
   3: human_panic::handle_dump::h6497bba18125ae8e (0x2b64668c85e7)
             at /mnt/home/patrick/.cargo/registry/src/github.com-1ecc6299db9ec823/human-panic-1.0.1/src/lib.rs:197
   4: sc_hla_count::main::{{closure}}::h4d1b937fa8891909 (0x2b646681a129)
             at /mnt/home/pat/code/scHLAcount/<::human_panic::setup_panic macros>:18
   5: std::panicking::rust_panic_with_hook::hffcefc09751839d1 (0x2b6466a00da9)
             at src/libstd/panicking.rs:481
   6: std::panicking::continue_panic_fmt::hc0f142c930c846fc (0x2b6466a00842)
             at src/libstd/panicking.rs:384
   7: rust_begin_unwind (0x2b6466a00726)
             at src/libstd/panicking.rs:311
   8: core::panicking::panic_fmt::h2daf88b2616ca2b2 (0x2b6466a1fa3d)
             at src/libcore/panicking.rs:85
   9: core::result::unwrap_failed::hd456c5071e5912eb (0x2b6466815b75)
             at /rustc/eae3437dfe991621e8afdc82734f4a172d7ddf9b/src/libcore/macros.rs:18
  10: core::result::Result<T,E>::unwrap::hf45d4303449490a0 (0x2b6466820671)
             at /rustc/eae3437dfe991621e8afdc82734f4a172d7ddf9b/src/libcore/result.rs:800
      sc_hla_count::_main::h60c6e0494337c80f
             at src/main.rs:215
  11: sc_hla_count::main::he49cdf9c5df2b57b (0x2b6466819f83)
             at src/main.rs:139
  12: std::rt::lang_start::{{closure}}::h93883743bb8c8181 (0x2b64667f5ce3)
             at /rustc/eae3437dfe991621e8afdc82734f4a172d7ddf9b/src/libstd/rt.rs:64
  13: std::rt::lang_start_internal::{{closure}}::h447d8812e3ee306d (0x2b6466a006c3)
             at src/libstd/rt.rs:49
      std::panicking::try::do_call::h4a61cb372364c745
             at src/libstd/panicking.rs:296
  14: __rust_maybe_catch_panic (0x2b6466a07c4a)
             at src/libpanic_unwind/lib.rs:82
  15: std::panicking::try::hdf71f938885bca42 (0x2b6466a0128d)
             at src/libstd/panicking.rs:275
      std::panic::catch_unwind::h7e85dbf162b1611a
             at src/libstd/panic.rs:394
      std::rt::lang_start_internal::h1e06cc26b9fc25ea
             at src/libstd/rt.rs:48
  16: main (0x2b6466821788)
  17: __libc_start_main (0x2b6467811d5d)
  18: <unknown> (0x2b64667cdc99)'''

Do you know how to solve this?

Bests, Yiwei Niu

[cdarby]

Is your cell barcodes file unzipped? It needs to be a plain text file with one barcode per line.

[YiweiNiu]

Thank you! It works now.