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10XGenomics / scHLAcount

Count HLA alleles in single-cell RNA-seq data
MIT License
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sc_hla_count_linux run error #14

Open tuqiang2014 opened 3 years ago

tuqiang2014 commented 3 years ago

when i run : 

$ ./sc_hla_count_linux  -b   outs/possorted_genome_bam.bam  -c   outs/filtered_feature_bc_matrix/barcodes.tsv.gz  -o  ./outs  -d   HLA/IPDIMGT/download

report it to me 

Sharding sequences...
Got 373889 sequence chunks
Assembling 114 shards...

Done separate de Bruijn graph construction
Starting merging disjoint graphs
Merger of graphs complete
Indexing de Bruijn graph
Total 58019 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-57629317-ba89-4832-a4a9-32bebd0b9b5d.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.

How can i check the error ?

thanks

cdarby commented 3 years ago

What about the report file path shown in the error message?

tuqiang2014 commented 3 years ago

What about the report file path shown in the error message?

when i Run test file is OK . But can not run with Cellranger outs file , error report :

$ cat /tmp/report-c3d89696-fdc9-44e3-a275-34875f7f4769.toml  
name = 'sc_hla_count'
operating_system = 'unix:CentOS'
crate_version = '0.1.0'
explanation = '''
Panic occurred in file 'src/libcore/option.rs' at line 347
'''
method = 'Panic'
backtrace = '''
stack backtrace:
   0: backtrace::backtrace::libunwind::trace::hb73dfa724f78bc0d (0x565288349a07)
             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 (0x565288348f63)
             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 (0x565288337ef7)
             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 (0x5652883375e7)
             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 (0x565288289129)
             at /mnt/home/pat/code/scHLAcount/<::human_panic::setup_panic macros>:18
   5: std::panicking::rust_panic_with_hook::hffcefc09751839d1 (0x56528846fda9)
             at src/libstd/panicking.rs:481
   6: std::panicking::continue_panic_fmt::hc0f142c930c846fc (0x56528846f842)
             at src/libstd/panicking.rs:384
   7: rust_begin_unwind (0x56528846f726)
             at src/libstd/panicking.rs:311
   8: core::panicking::panic_fmt::h2daf88b2616ca2b2 (0x56528848ea3d)
             at src/libcore/panicking.rs:85
   9: core::panicking::panic::h2d0bc53a963fb996 (0x56528848e97c)
             at src/libcore/panicking.rs:49
  10: core::option::Option<T>::unwrap::hbcc241c67317b537 (0x565288257428)
             at /rustc/eae3437dfe991621e8afdc82734f4a172d7ddf9b/src/libcore/macros.rs:12
      sc_hla_count::mapping::BamSeqReader::fetch::hf81cf3042ac7d942
             at src/mapping.rs:52
      sc_hla_count::mapping::mapping_wrapper::hd4dba6eb8a8c6fa1
             at src/mapping.rs:320
  11: sc_hla_count::_main::h60c6e0494337c80f (0x56528828edc3)
             at src/main.rs:198
  12: sc_hla_count::main::he49cdf9c5df2b57b (0x565288288f83)
             at src/main.rs:139
  13: std::rt::lang_start::{{closure}}::h93883743bb8c8181 (0x565288264ce3)
             at /rustc/eae3437dfe991621e8afdc82734f4a172d7ddf9b/src/libstd/rt.rs:64
  14: std::rt::lang_start_internal::{{closure}}::h447d8812e3ee306d (0x56528846f6c3)
             at src/libstd/rt.rs:49
      std::panicking::try::do_call::h4a61cb372364c745
             at src/libstd/panicking.rs:296
  15: __rust_maybe_catch_panic (0x565288476c4a)
             at src/libpanic_unwind/lib.rs:82
  16: std::panicking::try::hdf71f938885bca42 (0x56528847028d)
             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
  17: main (0x565288290788)
  18: __libc_start_main (0x7f77d02203d5)
  19: <unknown> (0x56528823cc99)'''
tuqiang2014 commented 3 years ago

What about the report file path shown in the error message?

when i Run test file is OK . But can not run with Cellranger( 4.0 ) outs file , error report :

$ cat /tmp/report-c3d89696-fdc9-44e3-a275-34875f7f4769.toml  
name = 'sc_hla_count'
operating_system = 'unix:CentOS'
crate_version = '0.1.0'
explanation = '''
Panic occurred in file 'src/libcore/option.rs' at line 347
'''
method = 'Panic'
backtrace = '''
stack backtrace:
   0: backtrace::backtrace::libunwind::trace::hb73dfa724f78bc0d (0x565288349a07)
             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 (0x565288348f63)
             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 (0x565288337ef7)
             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 (0x5652883375e7)
             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 (0x565288289129)
             at /mnt/home/pat/code/scHLAcount/<::human_panic::setup_panic macros>:18
   5: std::panicking::rust_panic_with_hook::hffcefc09751839d1 (0x56528846fda9)
             at src/libstd/panicking.rs:481
   6: std::panicking::continue_panic_fmt::hc0f142c930c846fc (0x56528846f842)
             at src/libstd/panicking.rs:384
   7: rust_begin_unwind (0x56528846f726)
             at src/libstd/panicking.rs:311
   8: core::panicking::panic_fmt::h2daf88b2616ca2b2 (0x56528848ea3d)
             at src/libcore/panicking.rs:85
   9: core::panicking::panic::h2d0bc53a963fb996 (0x56528848e97c)
             at src/libcore/panicking.rs:49
  10: core::option::Option<T>::unwrap::hbcc241c67317b537 (0x565288257428)
             at /rustc/eae3437dfe991621e8afdc82734f4a172d7ddf9b/src/libcore/macros.rs:12
      sc_hla_count::mapping::BamSeqReader::fetch::hf81cf3042ac7d942
             at src/mapping.rs:52
      sc_hla_count::mapping::mapping_wrapper::hd4dba6eb8a8c6fa1
             at src/mapping.rs:320
  11: sc_hla_count::_main::h60c6e0494337c80f (0x56528828edc3)
             at src/main.rs:198
  12: sc_hla_count::main::he49cdf9c5df2b57b (0x565288288f83)
             at src/main.rs:139
  13: std::rt::lang_start::{{closure}}::h93883743bb8c8181 (0x565288264ce3)
             at /rustc/eae3437dfe991621e8afdc82734f4a172d7ddf9b/src/libstd/rt.rs:64
  14: std::rt::lang_start_internal::{{closure}}::h447d8812e3ee306d (0x56528846f6c3)
             at src/libstd/rt.rs:49
      std::panicking::try::do_call::h4a61cb372364c745
             at src/libstd/panicking.rs:296
  15: __rust_maybe_catch_panic (0x565288476c4a)
             at src/libpanic_unwind/lib.rs:82
  16: std::panicking::try::hdf71f938885bca42 (0x56528847028d)
             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
  17: main (0x565288290788)
  18: __libc_start_main (0x7f77d02203d5)
  19: <unknown> (0x56528823cc99)'''
micans commented 3 years ago

It crashed for me with the exact same error. Two things to watch out for:

First, the difference with the supplied test bam file was that my bam files have 'chr1' rather than '1' etc. This can be fixed by samtools reheader:

samtools reheader -c 'perl -pe "s/^(@SQ.*)(\tSN:)chr/\$1\$2/"' in.bam > out.bam

(I got led to this by using --log-level debug; it stopped right after 15:37:10 [INFO] Mapping reads from BAM to database). After that it worked.

A second thing is that it still crashed for me, this time due to the barcode file being compressed (I presume). The error went away after uncompressing it; the program doesn't warn in the compressed case.

rrydbirk commented 2 years ago

It crashed for me with the exact same error. Two things to watch out for:

First, the difference with the supplied test bam file was that my bam files have 'chr1' rather than '1' etc. This can be fixed by samtools reheader:

samtools reheader -c 'perl -pe "s/^(@SQ.*)(\tSN:)chr/\$1\$2/"' in.bam > out.bam

(I got led to this by using --log-level debug; it stopped right after 15:37:10 [INFO] Mapping reads from BAM to database). After that it worked.

A second thing is that it still crashed for me, this time due to the barcode file being compressed (I presume). The error went away after uncompressing it; the program doesn't warn in the compressed case.

I had the exact same problem, but it was enough for me to just gunzip the barcodes file. Thanks @micans!