Your message dated Thu, 29 Dec 2016 07:19:02 +0000
with message-id <e1cmuzo-000bn8...@fasolo.debian.org>
and subject line Bug#844034: fixed in pbsuite 15.8.24+dfsg-2
has caused the Debian Bug report #844034,
regarding pbhoney: incompatible with blasr 5.x
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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immediately.)
--
844034: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=844034
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: pbhoney
Version: 15.8.24+dfsg-1
Severity: serious
Control: forwarded -1 https://sourceforge.net/p/pb-jelly/tickets/5/
As blasr has been updated to 5.x in Unstable/Testing, pbhoney no longer works
due to the interface change there. blasr options in 5.x have been changed from
single dashes to double dashes.
pbhoney test log [1]:
~~~
2016-11-11 21:16:47,957 [INFO] Running /usr/bin/Honey pie
filtered_subreads.fastq lambda_modified.fasta -o mappingFinal.sam
2016-11-11 21:16:47,957 [INFO] Running Blasr
2016-11-11 21:16:47,965 [ERROR] blasr mapping failed!
2016-11-11 21:16:47,965 [ERROR] RETCODE 1
2016-11-11 21:16:47,965 [ERROR] STDOUT Options for blasr
Basic usage: 'blasr reads.{bam|fasta|bax.h5|fofn} genome.fasta [-options]
option Description (default_value).
~~~
1.https://ci.debian.net/data/packages/unstable/amd64/p/pbsuite/20161111_211518.autopkgtest.log.gz
--- End Message ---
--- Begin Message ---
Source: pbsuite
Source-Version: 15.8.24+dfsg-2
We believe that the bug you reported is fixed in the latest version of
pbsuite, 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 844...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Afif Elghraoui <a...@debian.org> (supplier of updated pbsuite 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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Wed, 28 Dec 2016 22:42:12 -0800
Source: pbsuite
Binary: pbsuite python-pbsuite-utils pbjelly pbhoney python-pbbanana
Architecture: source
Version: 15.8.24+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
pbhoney - genomic structural variation discovery
pbjelly - genome assembly upgrading tool
pbsuite - software for Pacific Biosciences sequencing data
python-pbbanana - additional utilities for the pbsuite
python-pbsuite-utils - software for Pacific Biosciences sequencing data --
Python utilit
Closes: 844034
Changes:
pbsuite (15.8.24+dfsg-2) unstable; urgency=medium
.
* Update pbsuite for compatibility with blasr 5 (Closes: #844034)
* Bump Standards-Version to 3.9.8
* Add dependency on intervaltree-bio to restore PBHoney's ComplexResolver
* debian/rules: don't use buildsystem=pybuild
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