Hi Maintainer

Sometime around 2024-12-26, pbsuite's autopkgtest regressed in
testing [1].  I've copied what I hope is the relevant part of the log
below.

This regression allowed blasr/5.3.5+dfsg-7 to migrate to testing.

Regards
Graham


[1] https://ci.debian.net/packages/p/pbsuite/testing/amd64/


74s 2024-12-26 05:20:04,185 [INFO] Running /usr/bin/Honey spots
--reference lambda_modified.fasta mappingFinal.bam
74s Traceback (most recent call last):
74s File "/usr/bin/Honey", line 51, in <module>
74s parseArgs()
74s File "/usr/bin/Honey", line 48, in parseArgs
74s STAGES[args.stage](args.options)
74s File "/usr/lib/python3/dist-packages/pbsuite/honey/HSpots.py",
line 1092, in run
74s bam = pysam.Samfile(args.bam)
74s ^^^^^^^^^^^^^^^^^^^^^^^
74s File "pysam/libcalignmentfile.pyx", line 751, in
pysam.libcalignmentfile.AlignmentFile.__cinit__
74s File "pysam/libcalignmentfile.pyx", line 956, in
pysam.libcalignmentfile.AlignmentFile._open
74s ValueError: file does not contain alignment data

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,

Hi,

not sure whether pbsuite should remain in Debian.  In any case its
test suite has uncovered an issue in blasr.  This is officially
replaced by

https://github.com/PacificBiosciences/pbmm2

   "Benchmarks show that pbmm2 outperforms BLASR in sequence identity,
    number of mapped bases, and especially runtime. pbmm2 is the official
    replacement for BLASR."

If anyone has time to do this it would be welcome.  If not I might
spent some time in May next year.

Kind regards
    Andreas.