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#1091721 pbsuite: autopkgtest regression in testing #1091721

Package:: src:pbsuite

Source:: src:pbsuite

Submitter:: Graham Inggs

Date:: 2026-10-23 15:53:02 UTC

Severity:: normal

Tags:

#1091721#5

Date:: 2024-12-30 12:40:13 UTC

From:

To:

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

#1091721#10

Date:: 2025-02-16 14:59:35 UTC

From:

To:

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,

#1091721#17

Date:: 2025-12-15 14:40:41 UTC

From:

To:

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.

#1091721#22

Date:: 2026-10-23 14:45:01 UTC

From:

To:

The problem is caused by an issue in pbseqlib thus reassigning

#1091721#29

Date:: 2026-10-23 15:24:57 UTC

From:

To:

Hello,

Bug #1091721 in pbseqlib reported by you has been fixed in the
Git repository and is awaiting an upload. You can see the commit
message below and you can check the diff of the fix at:

https://salsa.debian.org/med-team/pbseqlib/-/commit/b74b9cd84770616bde752be10fe6067c01093753

(this message was generated automatically)
-- 
Greetings

https://bugs.debian.org/1091721

#1091721#36

Date:: 2026-10-23 15:51:31 UTC

From:

To:

We believe that the bug you reported is fixed in the latest version of
pbseqlib, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1091721@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated pbseqlib package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)
Format: 1.8
Date: Fri, 23 Oct 2026 15:42:19 +0200
Source: pbseqlib
Architecture: source
Version: 5.3.5+dfsg-13
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Closes: 1091721
Changes:
 pbseqlib (5.3.5+dfsg-13) unstable; urgency=medium
 .
   * Guard out-of-range reads when an anchor match list has exactly one entry
     Closes: #1091721
   * Remove redundant fields from d/watch
   * Set upstream metadata fields: Bug-Submit.
Checksums-Sha1:
 21a0d4694061b1f98945575f2cfbd36e5ca24470 2494 pbseqlib_5.3.5+dfsg-13.dsc
 33f998a6ab57c2beacd15dc8d3dd52f275bb30ee 13668 pbseqlib_5.3.5+dfsg-13.debian.tar.xz
 c31f818f40a3e9f26688b4434e41156403b3c604 11450 pbseqlib_5.3.5+dfsg-13_amd64.buildinfo
Checksums-Sha256:
 c49f27ea29af10027ffba2b2a14e5d9e515afe066340d49e5336be2f517fa991 2494 pbseqlib_5.3.5+dfsg-13.dsc
 32f93a9975decc76cda5b49a8ecf529ae88ddf2ef3f2b16ede848ea2d67338ab 13668 pbseqlib_5.3.5+dfsg-13.debian.tar.xz
 e88d031837838fb043402c69b79f2dfca873b46afa46aff2fb39de5726a2e0db 11450 pbseqlib_5.3.5+dfsg-13_amd64.buildinfo
Files:
 b4504438714cbe79fbc088f07534d991 2494 science optional pbseqlib_5.3.5+dfsg-13.dsc
 e24fa867b6f9e36e85d646f576f0e4ab 13668 science optional pbseqlib_5.3.5+dfsg-13.debian.tar.xz
 a594f6326dced7eef1d611c4acd494ed 11450 science optional pbseqlib_5.3.5+dfsg-13_amd64.buildinfo
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#1091721 pbsuite: autopkgtest regression in testing #1091721

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