Control: tags -1 + confirmed Greetings,
For reference, the issue caused by blasr looks like this in
pbsuite's autopkgtest in unstable:
autopkgtest [15:27:50]: test run-unit-test: [-----------------------
PIEMapping
Please Cite: English, Adam C., William J. Salerno, Jeffery G.
Reid. "PBHoney: identyfying genomic variants via
long-read discordance and interrupted mapping."
BMC Bioinformatics 2014, 15:180 (June 10, 2014).
doi:10.1186/1471-2105-15-180
2025-02-16 14:27:50,543 [INFO] Running /usr/bin/Honey pie
filtered_subreads.fastq lambda_modified.fasta -o mappingFinal.sam
2025-02-16 14:27:50,543 [INFO] Running Blasr
2025-02-16 14:28:21,727 [INFO] [0, b'[INFO] 2025-02-16T14:27:50 [blasr]
started.\n[INFO] 2025-02-16T14:28:21 [blasr] ended.\n', None]
2025-02-16 14:28:21,727 [INFO] Mapping Tails
2025-02-16 14:28:21,727 [INFO] Extracting tails
2025-02-16 14:28:21,891 [INFO] Parsed 433 reads
2025-02-16 14:28:21,891 [INFO] Found 278 tails
2025-02-16 14:28:21,891 [INFO] 21 reads had double tails
2025-02-16 14:28:21,891 [INFO] Running Blasr
2025-02-16 14:28:22,201 [ERROR] blasr mapping failed!
2025-02-16 14:28:22,201 [ERROR] RETCODE 134
2025-02-16 14:28:22,201 [ERROR] STDOUT b"[INFO] 2025-02-16T14:28:21
[blasr] started.\n/usr/include/c++/14/bits/stl_vector.h:1130:
std::vector<_Tp, _Alloc>::reference std::vector<_Tp,
_Alloc>::operator[](size_type) [with _Tp = ChainedMatchPos;
_Alloc = std::allocator<ChainedMatchPos>;
reference = ChainedMatchPos&;
size_type = long unsigned int]: Assertion '__n < this->size()'
failed.\nAborted\n"
2025-02-16 14:28:22,202 [ERROR] STDERR None
2025-02-16 14:28:22,202 [ERROR] Exiting
[…]
There are further error messages, but they are caused by the
initial Honey command's failure to produce files that are
further on processed. I don't really have much idea how to
resolve any of the two issues.
For reference,
--
.''`. Étienne Mollier <emoll...@debian.org>
: :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
`. `' sent from my alarm clock
`-
signature.asc
Description: PGP signature
