Re: [Seqan-dev] BZip2 not found
Hi,
I get the following error message when executing bam_stats from the
extras/demos...
When I looked in the sources I saw that you are using Stream<Bgzf>
bamStream; to open the stream... and with the BZlib2 not found can this
be the reason for the problem?
But if this is so, why is this not picked up during compilation????
Thanks for looking into this,
Bernd
bash-3.2$ ./bam_stats -B
/pasteur/solexa2/solexa_travail/PF2/bowtie_genomes/af1163.fa
/pasteur/hiseq/hiseq_travail/pf2/2011-Runs/111122_sn322_0173_BD0DY9ACXX/Gerald/L3_A
F8/tophat-af1163/accepted_hits.bam
/pasteur/solexa2/solexa_travail/PF2/programs/seqan/workspace/seqan/core/include/seqan/sequence/sequence_interface.h:804
Assertion failed : pos <= static_cast<TPos>(length
(me)) was: 1571263 > 1571256 (Trying to get an iterator behind a
container through iter().)
stack trace:
0 [0x4599ae] seqan::ClassTest::fail() + 0xe
1 [0x45dc3d]
seqan::Iterator<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5_>, seqan::Alloc<void> >, seqan::Tag<seqan::Rooted_>
const>::Type seqan
::iter<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>,
seqan::Alloc<void> >, unsigned long,
seqan::Rooted_>(seqan::String<seqan::SimpleType<unsigned char, s
eqan::Dna5_>, seqan::Alloc<void> >&, unsigned long,
seqan::Tag<seqan::Rooted_>) + 0x6d
2 [0x45c924]
seqan::Iterator<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5_>, seqan::Alloc<void> >,
seqan::DefaultGetIteratorSpec<seqan::String<s
eqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<void> >
>::Type>::Type seqan::iter<seqan::String<seqan::SimpleType<unsigned
char, seqan::Dna5_>, seqan::Alloc<
void> >, unsigned long>(seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5_>, seqan::Alloc<void> >&, unsigned long) + 0x24
3 [0x45c7fd]
seqan::Iterator<seqan::Gaps<seqan::String<seqan::SimpleType<unsigned
char, seqan::Dna5_>, seqan::Alloc<void> >, seqan::ArrayGaps>, seqan::Tag<seq
an::Standard_> const>::Type
seqan::_iteratorGapsArray<seqan::Gaps<seqan::String<seqan::SimpleType<unsigned
char, seqan::Dna5_>, seqan::Alloc<void> >, seqan::ArrayGaps>, u
nsigned long>(seqan::Gaps<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5_>, seqan::Alloc<void> >, seqan::ArrayGaps>&, unsigned long)
+ 0x1cd
4 [0x45c554]
seqan::Iterator<seqan::Gaps<seqan::String<seqan::SimpleType<unsigned
char, seqan::Dna5_>, seqan::Alloc<void> >, seqan::ArrayGaps>, seqan::Tag<seq
an::Rooted_> const>::Type
seqan::iter<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5_>, seqan::Alloc<void> >, unsigned long,
seqan::Rooted_>(seqan::Gaps<seqan
::String<seqan::SimpleType<unsigned char, seqan::Dna5_>,
seqan::Alloc<void> >, seqan::ArrayGaps>&, unsigned long,
seqan::Tag<seqan::Rooted_>) + 0x24
5 [0x45c51b]
seqan::Iterator<seqan::Gaps<seqan::String<seqan::SimpleType<unsigned
char, seqan::Dna5_>, seqan::Alloc<void> >, seqan::ArrayGaps>, seqan::Tag<seq
an::Rooted_> const>::Type
seqan::begin<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5_>, seqan::Alloc<void> >, seqan::ArrayGaps,
seqan::Rooted_>(seqan::Gaps<s
eqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>,
seqan::Alloc<void> >, seqan::ArrayGaps>&, seqan::Tag<seqan::Rooted_>) + 0x3b
6 [0x4576bc]
seqan::Iterator<seqan::Gaps<seqan::String<seqan::SimpleType<unsigned
char, seqan::Dna5_>, seqan::Alloc<void> >, seqan::ArrayGaps>, seqan::Default
GetIteratorSpec<seqan::Gaps<seqan::String<seqan::SimpleType<unsigned
char, seqan::Dna5_>, seqan::Alloc<void> >, seqan::ArrayGaps>
>::Type>::Type seqan::begin<seqan::Gaps<
seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>,
seqan::Alloc<void> >, seqan::ArrayGaps>
>(seqan::Gaps<seqan::String<seqan::SimpleType<unsigned char, seqan::
Dna5_>, seqan::Alloc<void> >, seqan::ArrayGaps>&) + 0x1c
7 [0x460703] unsigned int
seqan::cigarToGapAnchorContig<seqan::String<seqan::CigarElement<char,
unsigned int>, seqan::Alloc<void> >, seqan::Gaps<seqan::String
<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<void> >,
seqan::ArrayGaps> >(seqan::String<seqan::CigarElement<char, unsigned
int>, seqan::Alloc<void> > con
st&, seqan::Gaps<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5_>, seqan::Alloc<void> >, seqan::ArrayGaps>&) + 0x23
8 [0x4575d6] void
seqan::bamRecordToAlignment<seqan::String<seqan::SimpleType<unsigned
char, seqan::Dna5_>, seqan::Alloc<void> >, seqan::ArrayGaps, seqan::Str
ing<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<void> >
>(seqan::Align<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5_>, seqan::Alloc<void> >
, seqan::ArrayGaps>&, seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5_>, seqan::Alloc<void> >&, seqan::BamAlignmentRecord&) + 0xa6
9 [0x4543bb] int
doWork<seqan::Stream<seqan::Tag<seqan::Bgzf_> >,
seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>,
seqan::Alloc<void> >, seqan::O
wner<seqan::Tag<seqan::Default_> >, seqan::Tag<seqan::Bam_>
>(seqan::Stream<seqan::Tag<seqan::Bgzf_> >&,
seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, s
eqan::Dna5_>, seqan::Alloc<void> >,
seqan::Owner<seqan::Tag<seqan::Default_> > >&, Options const&,
seqan::Tag<seqan::Bam_> const&) + 0x41b
10 [0x45120f] main + 0x8df
11 [0x3782c1d994] __libc_start_main + 0xf4
12 [0x44fba9] __gxx_personality_v0 + 0xe9
Aborted
On 4/20/2012 9:41 AM, Holtgrewe, Manuel wrote:
BZIP2 is not needed for BAM. You only need it for the BZ2Stream to work, e.g. if your reads are bz2 compressed. BZ2 has good compression at a trade-off of quite high running times so people in Bioinformatics usually prefer zlib.
On Debian/Ubuntu, you need libbz2-dev for BZip2 support.
*m
________________________________________
From: Bernd Jagla [bernd.jagla@pasteur.fr]
Sent: Friday, April 20, 2012 9:37 AM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] BZip2 not found
Hi,
I get the following error message when executing cmake:
BZip2 libraries could not be found!
As I am not system administrator, which libraries do I have to ask for
to be installed on a Linux system?
Does this affect reading / writing BAM files? (I was under the
impression that only Zlib is needed)
When installing BZip2 locally how do I tell cmake about where to find
the library?
Thanks a lot for your continued support,
Bernd
_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seqan-dev
_______________________________________________
seqan-dev mailing list
seqan-dev@lists.fu-berlin.de
https://lists.fu-berlin.de/listinfo/seqan-dev
