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Old 07-27-2011, 09:34 PM   #41
chenyao
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I think I still didn't install the cufflink succefully. I don't know what's wrong
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Old 07-28-2011, 12:42 AM   #42
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I don't see any wrong in "make" and "make install",

but the "Processing Locus" is error
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Old 07-28-2011, 07:13 AM   #43
Tiger123
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I also noticed your processing locus. I got the output as:

> Processed 1 loci. [*************************] 100%

But, the warning sign is still there. I contacted a cufflink expert. He mentioned that the test_data.sam is a bit old. So, there might be clashes with the new updates.
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Old 07-28-2011, 07:41 AM   #44
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Quote:
Originally Posted by Tiger123 View Post
I also noticed your processing locus. I got the output as:

> Processed 1 loci. [*************************] 100%

But, the warning sign is still there. I contacted a cufflink expert. He mentioned that the test_data.sam is a bit old. So, there might be clashes with the new updates.
I don't think the version of test data is the problem, cause we use the same data. And I also tried the real .bam data, which all get wrong in the Processing loci. I can't figure out what's the problem.
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Old 07-28-2011, 10:49 AM   #45
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-Chenyao

Are you getting a segmentation fault? On your processed hits?
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Old 07-28-2011, 05:01 PM   #46
chenyao
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Quote:
Originally Posted by harlock0083 View Post
-Chenyao

Are you getting a segmentation fault? On your processed hits?
Exactly, If I only used .bam file, that's what I get:
-----------------------
You are using Cufflinks v1.0.3, which is the most recent release.
[08:53:42] Inspecting reads and determining fragment length distribution.
> Processed 82462 loci. [*************************] 100%
Warning: Using default Gaussian distribution due to insufficient paired-end reads in open ranges. It is recommended that correct paramaters (--frag-len-mean and --frag-len-std-dev) be provided.
> Map Properties:
> Total Map Mass: 902937.00
> Read Type: 38bp single-end
> Fragment Length Distribution: Truncated Gaussian (default)
> Default Mean: 200
> Default Std Dev: 80
[08:54:12] Assembling transcripts and estimating abundances.
> Processing Locus chr1:3040607-3040643 [ ] 0%Segmentation fault

-------------------

If I add the reference genome, that's what I get:
--------------------------------------
> Processed 25678 loci. [*************************] 100%
Warning: Using default Gaussian distribution due to insufficient paired-end reads in open ranges. It is recommended that correct paramaters (--frag-len-mean and --frag-len-std-dev) be provided.
> Map Properties:
> Total Map Mass: 902937.00
> Read Type: 0bp single-end
> Fragment Length Distribution: Truncated Gaussian (default)
> Default Mean: 200
> Default Std Dev: 80
[08:58:26] Estimating transcript abundances.
> Processing Locus 18:3266353-3327517 [************************ ] 99%Segmentation fault

Notably, the first one can get the right read,but still get fault in the last step
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Old 07-29-2011, 06:36 AM   #47
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Could you list your system specs, linux distribution, and steps you took to compile boost and samtools. Also use the "-v" option on your test run to see if you can see where the error occurs.
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Old 08-01-2011, 11:31 PM   #48
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Quote:
Originally Posted by harlock0083 View Post
Could you list your system specs, linux distribution, and steps you took to compile boost and samtools. Also use the "-v" option on your test run to see if you can see where the error occurs.
I have the problem when installing boost,which can not be detected, so I use "sudo get" as Tiger suggested, and it "configure" well, but I can not "make" successfully. I though maybe because of I wrongly pointed the path of boost. After I change the path, the cufflinks successfully make.

I use "-v" option, the error is:
Inspecting bundle 2:180323949-180330541 with 0 reads
Inspecting bundle 2:180332494-180377413 with 0 reads
Inspecting bundle 2:180392668-180444704 with 0 reads
Inspecting bundle 2:180444821-180453438 with 0 reads
Inspecting bundle 2:180459967-180476985 with 0 reads
Inspecting bundle 2:180500918-180511605 with 0 reads
Inspecting bundle 2:180553047-180559335 with 0 reads

Map Properties:
> Total Map Mass: 712614.00
> Read Type: 0bp single-end
> Fragment Length Distribution: Truncated Gaussian (default)
> Default Mean: 200
> Default Std Dev: 80
0 ReadHits still live
Found 177 reference contigs
Total map density: 712614.000000
[15:23:19] Estimating transcript abundances.
Segmentation fault
----------------------
Any thoughts?
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Old 08-02-2011, 10:57 PM   #49
chenyao
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who can help me?
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Old 08-03-2011, 08:16 AM   #50
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Hi Chenyao,

I ran cufflinks on a research dataset. The output is below:

You are using Cufflinks v1.0.3, which is the most recent release.
[11:59:07] Inspecting reads and determining fragment length distribution.
> Processed 71057 loci. [*************************] 100%
Warning: Using default Gaussian distribution due to insufficient paired-end reads in open ranges. It is recommended that correct paramaters (--frag-len-mean and --frag-len-std-dev) be provided.
> Map Properties:
> Total Map Mass: 2534201.50
> Read Type: 75bp single-end
> Fragment Length Distribution: Truncated Gaussian (default)
> Default Mean: 200
> Default Std Dev: 80
[11:59:47] Assembling transcripts and estimating abundances.
> Processed 71057 loci. [*************************] 100%

Even though, the warning is still present, I didn't get segmentation fault.
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Old 12-17-2011, 03:58 AM   #51
Dedeusan
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Default Could't make cufflinks

Hello all!
I am trying to install Cufflinks in a 64b ubuntu-linux machine and I am having lots of problems. I have install boost in usr/local as the guide in the cufflink web says but when I tried to make this is what I get:

sandra@sandra-VirtualBox:~/cufflinks-0.9.3$ sudo make
make all-recursive
make[1]: se ingresa al directorio «/home/sandra/cufflinks-0.9.3»
Making all in src
make[2]: se ingresa al directorio «/home/sandra/cufflinks-0.9.3/src»
g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -pthread -I/home/sandra/boost_1_48_0/include -I/usr/local/include -o cufflinks -L/home/sandra/boost_1_48_0/lib -L/usr/local/lib cufflinks.o libcufflinks.a libgc.a -lbam -lz
cufflinks.o: In function `sleep<boost::date_time::subsecond_duration<boost:osix_time::time_duration, 1000l> >':
/usr/include/boost/thread/pthread/thread_data.hpp:138: undefined reference to `boost::this_thread::sleep(boost:osix_time:time const&)'
cufflinks.o: In function `thread_data_base':
/usr/include/boost/thread/pthread/thread_data.hpp:67: undefined reference to `vtable for boost::detail::thread_data_base'
cufflinks.o: In function `thread<void (*)(const RefSequenceTable&, HitBundle*, BiasLearner*, long double, _IO_FILE*, _IO_FILE*, _IO_FILE*), boost::reference_wrapper<const RefSequenceTable>, HitBundle*, BiasLearner*, long double, _IO_FILE*, _IO_FILE*, _IO_FILE*>':
/usr/include/boost/thread/detail/thread.hpp:293: undefined reference to `boost::thread::start_thread()'
cufflinks.o: In function `assemble_hits(BundleFactory&, BiasLearner*)':
/home/sandra/cufflinks-0.9.3/src/cufflinks.cpp:953: undefined reference to `boost::thread::~thread()'
cufflinks.o: In function `sleep<boost::date_time::subsecond_duration<boost:osix_time::time_duration, 1000l> >':
/usr/include/boost/thread/pthread/thread_data.hpp:138: undefined reference to `boost::this_thread::sleep(boost:osix_time:time const&)'
cufflinks.o: In function `assemble_hits(BundleFactory&, BiasLearner*)':
/home/sandra/cufflinks-0.9.3/src/cufflinks.cpp:953: undefined reference to `boost::thread::~thread()'
cufflinks.o: In function `boost::thread_specific_ptr<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >::get() const':
/usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
/usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
/usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
/usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
cufflinks.o: In function `boost::thread_specific_ptr<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >::reset(std::basic_string<char, std::char_traits<char>, std::allocator<char> >*)':
/usr/include/boost/thread/tss.hpp:105: undefined reference to `boost::detail::set_tss_data(void const*, boost::shared_ptr<boost::detail::tss_cleanup_function>, void*, bool)'
cufflinks.o: In function `boost::thread_specific_ptr<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >::get() const':
/usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
cufflinks.o: In function `at_thread_exit<void (*)()>':
/usr/include/boost/thread/detail/thread.hpp:521: undefined reference to `boost::detail::add_thread_exit_function(boost::detail::thread_exit_function_base*)'
cufflinks.o: In function `boost::thread_specific_ptr<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >::get() const':
/usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
/usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
cufflinks.o: In function `~thread_data':
/usr/include/boost/thread/detail/thread.hpp:40: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
/usr/include/boost/thread/detail/thread.hpp:40: undefined reference to `boost::detail::thread_data_base::~thread_data_base()'
cufflinks.o.rodata._ZTIN5boost6detail11thread_dataINS_3_bi6bind_tIvPFvRK16RefSequenceTableP9HitBundleP11BiasLearnereP8_IO_FILESC_SC_ENS2_5list7INS_17reference_wrapperIS5_EENS2_5valueIS8_EENSI_ISA_EENSI_IeEENSI_ISC_EESM_SM_EEEEEE[typeinfo for boost::detail::thread_data<boost::_bi::bind_t<void, void (*)(RefSequenceTable const&, HitBundle*, BiasLearner*, long double, _IO_FILE*, _IO_FILE*, _IO_FILE*), boost::_bi::list7<boost::reference_wrapper<RefSequenceTable const>, boost::_bi::value<HitBundle*>, boost::_bi::value<BiasLearner*>, boost::_bi::value<long double>, boost::_bi::value<_IO_FILE*>, boost::_bi::value<_IO_FILE*>, boost::_bi::value<_IO_FILE*> > > >]+0x10): undefined reference to `typeinfo for boost::detail::thread_data_base'
libcufflinks.a(common.o): In function `~thread_specific_ptr':
/usr/include/boost/thread/tss.hpp:79: undefined reference to `boost::detail::set_tss_data(void const*, boost::shared_ptr<boost::detail::tss_cleanup_function>, void*, bool)'
libcufflinks.a(assemble.o): In function `boost::thread_specific_ptr<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >:perator->() const':
/usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
libcufflinks.a(assemble.o): In function `boost::thread_specific_ptr<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >::get() const':
/usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
/usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
/usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
/usr/include/boost/thread/tss.hpp:84: undefined reference to `boost::detail::get_tss_data(void const*)'
libcufflinks.a(assemble.o):/usr/include/boost/thread/tss.hpp:84: more undefined references to `boost::detail::get_tss_data(void const*)' follow
collect2: ld devolvió el estado de salida 1
make[2]: *** [cufflinks] Error 1
make[2]: se sale del directorio «/home/sandra/cufflinks-0.9.3/src»
make[1]: *** [all-recursive] Error 1
make[1]: se sale del directorio «/home/sandra/cufflinks-0.9.3»
make: *** [all] Error 2



What is happening?
Thanks for any help!
Sandra
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Old 03-30-2012, 08:02 AM   #52
himanshu04
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Hey Sandra ,
I am facing the same issue as you did. How did you install cufflinks after this error.? Although I am installing cufflinks 1.3.0.
Any help is much appreciated.
Thanks,
Himanshu Sharma.
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Old 03-30-2012, 08:39 AM   #53
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Hello all,
Is there anyone who knows the solution to this problem. Please help me .
Thanks.
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Old 03-30-2012, 11:23 AM   #54
Dedeusan
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Hello,
Finally I couldn't make it so I was working in galaxy instead. Hope anyone will reply this post, but if not, just take a look at the web: https://main.g2.bx.psu.edu/
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Old 03-31-2012, 12:17 AM   #55
dpryan
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There's a problem with the linker either not being able to find some/all of the boost library or the linking being done in an order wherein something is being linked before a dependency. Frankly, the easiest way to install cufflinks is to just download the binary.
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Old 04-17-2013, 05:33 PM   #56
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Hi all,

I have installed successfully from source code, here is the step:
1. install boost (boost_1_47_0)
2. install samtools
3. install eigen
4. install cufflinks (cufflinks-2.1.1)
./configure --with-boost=/path/to/lib/boost_1_47_0/ --prefix=/path/to/cufflinks-2.1.1/ --with-bam=/path/to/bam/ --with-eigen=/path/to/Eigen/ --with-boost-libdir=/path/to/lib/boost_1_47_0/include/ --with-boost-thread=/path/to/lib/boost_1_47_0/lib/libboost_thread.so

NOTE: /path/to/bam/ directory contain the following directories:
include/bam
include/Eigen #the subdirectory of eigen after uncompressed eigen package
lib/libbam.a

Explaination of the error message:
The thread package in the include//boost/thread directory cann't be compiled successfully by cufflinks, so we can use the compiled library when we install boost.

Last edited by pengchy; 04-17-2013 at 05:34 PM. Reason: add version information
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Old 05-12-2013, 03:13 AM   #57
Dave-bo_Baggins
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I have been working on trying to build cufflinks for the past few days and so far I keep getting stuck with the same error
checking for boostlib >= 1.47.0... configure: error: We could not detect the boost libraries (version 1.47 or higher). If you have a staged boost library (still not installed) please specify $BOOST_ROOT in your environment and do not give a PATH to --with-boost option. If you are sure you have boost installed, then check your version number looking in <boost/version.hpp>. See http://randspringer.de/boost for more documentation.
I have installed
  1. boost_1_53_0
  2. samtools(samtools-0.1.19)
  3. eigen (eigen-eigen-2249f9c22fe8)
  4. install cufflinks (cufflinks-2.1.1)

for boost I did the following:
./bootstrap.sh
./b2
The Boost C++ Libraries were successfully built!
The following directory should be added to compiler include paths:
/home/mrmary/ngs/applications/boost_1_53_0
The following directory should be added to linker library paths:
/home/mrmary/ngs/applications/boost_1_53_0/stage/lib
I continued forward with this command.
./bjam --prefix=/home/mrmary/ngs/applications/boost_1_53_0
--toolset=gcc link=static runtime-link=static stage install
then i went cd'ed into my cufflinks directory and entered the following
./configure --prefix=/home/mrmary/ngs/applications/cufflinks-2.1.1 --with-boost=/home/mrmary/ngs/applications/boost_1_53_0 --with-boost-thread=/usr/lib64/boost141/libboost_thread-mt.so --with-bam=/usr/local/include/bam --with-eigen=/usr/local/include/Eigen
when that didn't work I modified the command a little and tried again

./configure --prefix=/home/mrmary/ngs/applications/cufflinks-2.1.1 --with-boost=/home/mrmary/ngs/applications/boost_1_53_0/stage/lib --with-boost-thread=/usr/lib64/boost141/libboost_thread-mt.so --with-bam=/usr/local/include/bam --with-eigen=/usr/local/include/Eigen


any help would be god send at this point. Much thanks and regards

Dave
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Old 05-12-2013, 06:07 AM   #58
pengchy
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try specify:
--with-boost-libdir=/path/to/lib/boost_1_47_0/include/
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Old 05-12-2013, 12:28 PM   #59
Dave-bo_Baggins
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Thanks Pengchy for answering I really appreciate it

This is what I tried again:

./configure
--prefix=/home/mrmary/ngs/applications/cufflinks-2.1.1/
--with-boost-libdir=/home/mrmary/ngs/applications/boost_1_53_0/
--with-boost-thread=/usr/lib64/boost141/libboost_thread-mt.so
--with-bam=/usr/local/include/bam/
--with-eigen=/usr/local/include/Eigen/

Im a little confused when I ran the ./b2 command to build boost I got the following recommendations:

The following directory should be added to compiler include paths:
/home/mrmary/ngs/applications/boost_1_53_0
The following directory should be added to linker library paths:
/home/mrmary/ngs/applications/boost_1_53_0/stage/lib

Im not sure where I should add the include paths and what path --with-boost-libdir is asking for

Thanks anyone and everyone who reads this

Dave
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Old 05-12-2013, 04:30 PM   #60
GenoMax
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Dave: Where exactly did you install boost libraries? Are they in "/usr/local" or in your home directory?

You may have already seen the instructions here: http://cufflinks.cbcb.umd.edu/tutorial.html#inst Depending on where you installed the boost libraries add that path using " --with-boost=/path/to/boost"

Here are a couple of threads for reference: http://seqanswers.com/forums/showthread.php?t=19805 and http://seqanswers.com/forums/showthread.php?t=14224
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