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From: Mehmood K. <mal...@kt...> - 2015-11-13 07:57:47
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Hi John, Thanks for your email. I just came from vacation. Fastphylo 1.0.1 is the latest version. You can build it from the source code following the instructions: http://fastphylo.sourceforge.net/#building_from_source Best, Mehmood --------------------------------- Best Regards, Mehmood Alam Khan PhD Candidate, Department of Computational Biology, Royal Institute of Technology, Science for Life Laboratory, School of Computer Science and Communication, Visiting address: KISP (Karolinska Institutet Science Park) Tomtebodavägen 23A 17121 Solna Sweden Email: mal...@kt...<mailto:mal...@kt...> Phone: +46 08-52481190 Website: http://www.csc.kth.se/~malagori/ On Nov 9, 2015, at 4:04 PM, John Vollmers <jo...@ds...<mailto:jo...@ds...>> wrote: Hi, On the fastphylo website you include instructions for installing from a .deb package, and state that the latest version of fastphylo is 1.0.1. However no .deb packages can be found for the newest version (The standard download directs me to fastphylo-0.9.0-Linux.deb), only tar.gz files containing the source code for compiling yourself. Is this a mistake or is there a reason for this (like e.g version 0.9.0 being the last recommended "stable" version)? greetings, john ------------------------------------------------------------------------------ Presto, an open source distributed SQL query engine for big data, initially developed by Facebook, enables you to easily query your data on Hadoop in a more interactive manner. Teradata is also now providing full enterprise support for Presto. Download a free open source copy now. http://pubads.g.doubleclick.net/gampad/clk?id=250295911&iu=/4140 _______________________________________________ Fastphylo-users mailing list Fas...@li... https://lists.sourceforge.net/lists/listinfo/fastphylo-users |
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From: John V. <jo...@ds...> - 2015-11-09 15:12:16
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Hi, On the fastphylo website you include instructions for installing from a .deb package, and state that the latest version of fastphylo is 1.0.1. However no .deb packages can be found for the newest version (The standard download directs me to fastphylo-0.9.0-Linux.deb), only tar.gz files containing the source code for compiling yourself. Is this a mistake or is there a reason for this (like e.g version 0.9.0 being the last recommended "stable" version)? greetings, john |
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From: Mehmood K. <mal...@kt...> - 2013-06-17 15:50:13
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Hi, A new version of Fastphylo has been released now i.e. fastphylo 1.0.0. You can find the documentation at http://fastphylo.sourceforge.net/. Best Regards, Mehmood Alam Khan ----------------------------------------------- PhD Candidate, CSC/ CB, KTH. Science for Life Laboratory, PO Box 1031, 17121 Solna, Sweden http://www.csc.kth.se/~malagori/ tel 08-52481190 ----------------------------------------------- |
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From: Erik S. <eri...@gm...> - 2013-03-12 12:38:04
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I got a question about how many decimals we should write for the numbers in the fastphylo distance matrix XML file. Here are some details: The Relaxng schema http://fastphylo.sourceforge.net/#fastphylo_distance_matrix_xml_format uses the XML schema datatype "float" for the content of the "entry" xml elements. Reading http://www.w3.org/TR/xmlschema-2/#float we see that the textual representation of the float is described in the standard: IEEE 754-1985 It is interesting to know if such textual representation is given by printf("%f", num) I don't know by heart. We need to check this. If we have a need for evan more decimals than what a float can contain, we could start using the XML schema datatype "double". cheers, Erik |
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From: Mehmood K. <mal...@kt...> - 2012-08-02 15:10:08
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Fixed...fasta format bug On Aug 1, 2012, at 3:54 AM, Mehmood Khan wrote: Fixed for phylip format. now working on fasta format... /Mehmood On Jul 31, 2012, at 8:43 PM, Mehmood Khan wrote: FASTPROT fails while reading protein sequences in fasta format: /bin$ ./fastprot -I fasta /scratch/malagori/data/proteinSeqs.fasta <?xml version="1.0"?> <root> <runs> ----------------- Exception File: /scratch/malagori/fastphylo/trunk/src/c++/programs/fastprot/FastaInputStream.cpp Function: readSeq Line: 78 Message: Malformed Fasta format ----------------- SIMILARLY, it fails for phylip format too. <proteinSeqs.fasta><protein.phylip.txt>------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________ Fastphylo-users mailing list Fas...@li...<mailto:Fas...@li...> https://lists.sourceforge.net/lists/listinfo/fastphylo-users ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________ Fastphylo-users mailing list Fas...@li...<mailto:Fas...@li...> https://lists.sourceforge.net/lists/listinfo/fastphylo-users |
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From: Mehmood K. <mal...@kt...> - 2012-08-01 01:54:57
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Fixed for phylip format. now working on fasta format... /Mehmood On Jul 31, 2012, at 8:43 PM, Mehmood Khan wrote: FASTPROT fails while reading protein sequences in fasta format: /bin$ ./fastprot -I fasta /scratch/malagori/data/proteinSeqs.fasta <?xml version="1.0"?> <root> <runs> ----------------- Exception File: /scratch/malagori/fastphylo/trunk/src/c++/programs/fastprot/FastaInputStream.cpp Function: readSeq Line: 78 Message: Malformed Fasta format ----------------- SIMILARLY, it fails for phylip format too. <proteinSeqs.fasta><protein.phylip.txt>------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________ Fastphylo-users mailing list Fas...@li...<mailto:Fas...@li...> https://lists.sourceforge.net/lists/listinfo/fastphylo-users |
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From: Mehmood K. <mal...@kt...> - 2012-07-31 18:44:03
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10 234 Cow MAYPMQLGFQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKL Carp MAHPTQLGFKDAAMPVMEELLHFHDHALMIVLLISTLVLYIITAMVSTKL Chicken MANHSQLGFQDASSPIMEELVEFHDHALMVALAICSLVLYLLTLMLMEKL Human MAHAAQVGLQDATSPIMEELITFHDHALMIIFLICFLVLYALFLTLTTKL Loach MAHPTQLGFQDAASPVMEELLHFHDHALMIVFLISALVLYVIITTVSTKL Mouse MAYPFQLGLQDATSPIMEELMNFHDHTLMIVFLISSLVLYIISLMLTTKL Rat MAYPFQLGLQDATSPIMEELTNFHDHTLMIVFLISSLVLYIISLMLTTKL Seal MAYPLQMGLQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKL Whale MAYPFQLGFQDAASPIMEELLHFHDHTLMIVFLISSLVLYIITLMLTTKL Frog MAHPSQLGFQDAASPIMEELLHFHDHTLMAVFLISTLVLYIITIMMTTKL THTSTMDAQEVETIWTILPAIILILIALPSLRILYMMDEINNPSLTVKTM TNKYILDSQEIEIVWTILPAVILVLIALPSLRILYLMDEINDPHLTIKAM S-SNTVDAQEVELIWTILPAIVLVLLALPSLQILYMMDEIDEPDLTLKAI TNTNISDAQEMETVWTILPAIILVLIALPSLRILYMTDEVNDPSLTIKSI TNMYILDSQEIEIVWTVLPALILILIALPSLRILYLMDEINDPHLTIKAM THTSTMDAQEVETIWTILPAVILIMIALPSLRILYMMDEINNPVLTVKTM THTSTMDAQEVETIWTILPAVILILIALPSLRILYMMDEINNPVLTVKTM THTSTMDAQEVETVWTILPAIILILIALPSLRILYMMDEINNPSLTVKTM THTSTMDAQEVETVWTILPAIILILIALPSLRILYMMDEVNNPSLTVKTM TNTNLMDAQEIEMVWTIMPAISLIMIALPSLRILYLMDEVNDPHLTIKAI GHQWYWSYEYTDYEDLSFDSYMIPTSELKPGELRLLEVDNRVVLPMEMTI GHQWYWSYEYTDYENLGFDSYMVPTQDLAPGQFRLLETDHRMVVPMESPV GHQWYWTYEYTDFKDLSFDSYMTPTTDLPLGHFRLLEVDHRIVIPMESPI GHQWYWTYEYTDYGGLIFNSYMLPPLFLEPGDLRLLDVDNRVVLPIEAPI GHQWYWSYEYTDYENLSFDSYMIPTQDLTPGQFRLLETDHRMVVPMESPI GHQWYWSYEYTDYEDLCFDSYMIPTNDLKPGELRLLEVDNRVVLPMELPI GHQWYWSYEYTDYEDLCFDSYMIPTNDLKPGELRLLEVDNRVVLPMELPI GHQWYWSYEYTDYEDLNFDSYMIPTQELKPGELRLLEVDNRVVLPMEMTI GHQWYWSYEYTDYEDLSFDSYMIPTSDLKPGELRLLEVDNRVVLPMEMTI GHQWYWSYEYTNYEDLSFDSYMIPTNDLTPGQFRLLEVDNRMVVPMESPT RMLVSSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMSSRPGLYYGQCSEIC RVLVSAEDVLHSWAVPSLGVKMDAVPGRLNQAAFIASRPGVFYGQCSEIC RVIITADDVLHSWAVPALGVKTDAIPGRLNQTSFITTRPGVFYGQCSEIC RMMITSQDVLHSWAVPTLGLKTDAIPGRLNQTTFTATRPGVYYGQCSEIC RILVSAEDVLHSWALPAMGVKMDAVPGRLNQTAFIASRPGVFYGQCSEIC RMLISSEDVLHSWAVPSLGLKTDAIPGRLNQATVTSNRPGLFYGQCSEIC RMLISSEDVLHSWAIPSLGLKTDAIPGRLNQATVTSNRPGLFYGQCSEIC RMLISSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMTMRPGLYYGQCSEIC RMLVSSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMSTRPGLFYGQCSEIC RLLVTAEDVLHSWAVPSLGVKTDAIPGRLHQTSFIATRPGVFYGQCSEIC GSNHSFMPIVLELVPLKYFEKWSASML------- GANHSFMPIVVEAVPLEHFENWSSLMLEDASLGS GANHSYMPIVVESTPLKHFEAWSSL------LSS GANHSFMPIVLELIPLKIFEM-------GPVFTL GANHSFMPIVVEAVPLSHFENWSTLMLKDASLGS GSNHSFMPIVLEMVPLKYFENWSASMI------- GSNHSFMPIVLEMVPLKYFENWSASMI------- GSNHSFMPIVLELVPLSHFEKWSTSML------- GSNHSFMPIVLELVPLEVFEKWSVSML------- GANHSFMPIVVEAVPLTDFENWSSSML-EASL-- |
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From: Mehmood K. <mal...@kt...> - 2012-07-30 15:03:17
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Fixed... I was making mistake in writing xml to file.
<?xml version="1.0"?>
<root>
<runs>
<run id="run1" dim="3">
<identities>
<identity name="Alpha"/>
<identity name="Beta"/>
<identity name="Gamma"/>
</identities>
<tree>
<count>1</count>
<newick-xml><branch><leaf>Gamma</leaf><leaf>Beta</leaf><leaf>Alpha</leaf></branch></newick-xml>
<newick>(Gamma,Beta,Alpha);</newick>
</tree>
</run>
<run id="run2" dim="3">
<identities>
<identity name="Alpha"/>
<identity name="Beta"/>
<identity name="Gamma"/>
</identities>
<tree>
<count>1</count>
<newick-xml><branch><leaf>Gamma</leaf><leaf>Beta</leaf><leaf>Alpha</leaf></branch></newick-xml>
<newick>(Gamma,Beta,Alpha);</newick>
</tree>
</run>
</runs>
</root>
On Jul 30, 2012, at 3:46 PM, Mehmood Khan wrote:
Hi,
It seems like the XML functionality for FNJ is not working, getting this error with the input file attached here...
error:
malagori@nitrogen:/tmp/install/bin$ ./fnj -I xml ~/svn/fastphylo/fdist_xml_xml.out
<?xml version="1.0"?>
<root>
<runs>
/afs/pdc.kth.se/home/m/malagori/svn/fastphylo/fdist_xml_xml.out:16: element dm: Relax-NG validity error : Did not expect element dm there
-----------------
Exception
File: /afs/pdc.kth.se/home/m/malagori/svn/fastphylo/trunk/src/c++/programs/fnj/XmlInputStream.cpp
Function: readDM
Line: 71
Message: xml input does not validate
-----------------
Cheers,
Mehmood
<fdist_xml_xml.out>------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
Fastphylo-users mailing list
Fas...@li...<mailto:Fas...@li...>
https://lists.sourceforge.net/lists/listinfo/fastphylo-users
|
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From: Mehmood K. <mal...@kt...> - 2012-02-29 13:41:17
|
Fixed ! On Feb 29, 2012, at 9:39 AM, Mehmood Khan wrote: > I tried to install openmpi using macports on mac but openmpi port lacks mpif90. > > 130-229-49-49:~ malagori$ mpif90 --help > -------------------------------------------------------------------------- > Unfortunately, this installation of Open MPI was not compiled with > Fortran 90 support. As such, the mpif90 compiler is non-functional. > > -------------------------------------------------------------------------- > > We need mpif90 for FASTPHYLO to work. Is there any alternatives to install openmpi with mpif90 working properly? > > Below is a portion from cmake error message: > > -------------------------------------error------------------------------------- > -- Unable to determine MPI from MPI driver /usr/bin/mpif90 > -- Could NOT find MPI_Fortran (missing: MPI_Fortran_LIBRARIES MPI_Fortran_INCLUDE_PATH) > > Can any one help please? > > cheers, > /mehmood > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > Fastphylo-users mailing list > Fas...@li... > https://lists.sourceforge.net/lists/listinfo/fastphylo-users |
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From: Mehmood K. <mal...@kt...> - 2012-02-29 08:39:56
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I tried to install openmpi using macports on mac but openmpi port lacks mpif90. 130-229-49-49:~ malagori$ mpif90 --help -------------------------------------------------------------------------- Unfortunately, this installation of Open MPI was not compiled with Fortran 90 support. As such, the mpif90 compiler is non-functional. -------------------------------------------------------------------------- We need mpif90 for FASTPHYLO to work. Is there any alternatives to install openmpi with mpif90 working properly? Below is a portion from cmake error message: -------------------------------------error------------------------------------- -- Unable to determine MPI from MPI driver /usr/bin/mpif90 -- Could NOT find MPI_Fortran (missing: MPI_Fortran_LIBRARIES MPI_Fortran_INCLUDE_PATH) Can any one help please? cheers, /mehmood |
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From: Mehmood K. <mal...@kt...> - 2012-02-27 12:20:49
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Hi, I have integrated FASTPROT to the trunk but when I try to compile it, I receive "Undefined Symbols" errors. I already installed "Atlas" package on mac but still no cure. I even look on Stackoverflow.com but no remedy found yet :( Can any one help? /Mehmood -----------------------------------------------------------errors-------------------------------- 130-229-49-49:build-trunk-1 malagori$ make [ 42%] Built target fastphylo [ 60%] Built target fastdist Linking CXX executable fastprot ld: warning: path '/opt/local/lib/libxml2.dylib' following -L not a directory ld: warning: directory 'FALSE' following -L not found Undefined symbols: "_dgemm_", referenced from: Matrix::mult(Matrix const&, Matrix const&, bool, bool)in Matrix.cpp.o "_dgetrf_", referenced from: Matrix::expm(std::vector<double, std::allocator<double> > const&) constin Matrix.cpp.o "_dgetri_", referenced from: Matrix::expm(std::vector<double, std::allocator<double> > const&) constin Matrix.cpp.o Matrix::expm(std::vector<double, std::allocator<double> > const&) constin Matrix.cpp.o "_dgeev_", referenced from: Matrix::expm(std::vector<double, std::allocator<double> > const&) constin Matrix.cpp.o Matrix::expm(std::vector<double, std::allocator<double> > const&) constin Matrix.cpp.o ld: symbol(s) not found collect2: ld returned 1 exit status make[2]: *** [src/c++/fastprot] Error 1 make[1]: *** [src/c++/CMakeFiles/fastprot.dir/all] Error 2 make: *** [all] Error 2 |
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From: Erik S. <eri...@gm...> - 2011-09-02 21:48:17
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On Fri, Sep 2, 2011 at 6:55 PM, Mehmood Khan <mal...@kt...> wrote: > CMake Error at src/c++/cmake_install.cmake:31 (FILE): > file cannot create directory: /install-trunk-1/bin. Maybe need > administrative privileges. It looks like you invoked cmake with the option -DCMAKE_INSTALL_PREFIX=/install-trunk-1 Only root has write access in the directory / $ ls -ld / drwxr-xr-x 24 root root 4096 2011-08-19 19:22 / To avoid the error, choose a directory where you have write access. cheers, Erik |
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From: Erik S. <eri...@gm...> - 2011-09-02 21:38:48
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On Fri, Sep 2, 2011 at 5:43 PM, Mehmood Khan <mal...@kt...> wrote: > sh: line 1: 4743 Done cat seq.phylip_multialignment > 4744 | fastdist -I phylip_multialignment -O phylip_dm -b 3 -r 2 > 4745 Segmentation fault | fnj -I phylip_dm -O xml -r 2 -d 4 If there is a segmentation fault somewhere in the chain of pipes I would suggest saving the output between the pipes cat seq.phylip_multialignment | fastdist -I phylip_multialignment -O phylip_dm -b 3 -r 2 > /tmp/result and then cat /tmp/result | fnj -I phylip_dm -O xml -r 2 -d 4 then you will see in which command the segmentation fault occurs. To diagnose the segmentation fault I recommend using a debugger, for instance gdb. cheers Erik |
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From: Mehmood K. <mal...@kt...> - 2011-09-02 16:55:18
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Can any one help? /mehmood [ 95%] Building CXX object src/c++/CMakeFiles/fnj.dir/programs/fnj/XmlInputStream.cpp.o Linking CXX executable fnj [100%] Built target fnj [ 58%] Built target fastphylo [ 80%] Built target fastdist [100%] Built target fnj Install the project... -- Install configuration: "" CMake Error at src/c++/cmake_install.cmake:31 (FILE): file cannot create directory: /install-trunk-1/bin. Maybe need administrative privileges. Call Stack (most recent call first): cmake_install.cmake:32 (INCLUDE) |
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From: Mehmood K. <mal...@kt...> - 2011-09-02 15:43:13
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hi,
Can any buddy help?
regards,
mehmood
Scanning dependencies of target docbook-doc
[ 76%] Generating xincluded_files/fnj_xml_stdin_xml_output
[ 76%] Generating xincluded_files/cat_seq_phylip_multialignment
[ 76%] Generating xincluded_files/cat_seq_xml
[ 76%] Generating xincluded_files/connecting_fnj_to_fastdist_with_a_pipe1
************
USER WARNING
file: /Users/malagori/Documents/Academic/project/svn/fastphylo/branches/speedups/src/c++/programs/fastdist/PhylipDmOutputStream.cpp
func: printRow
line: 32
warning float not finite (use fix factor) nan
************
sh: line 1: 4743 Done cat seq.phylip_multialignment
4744 | fastdist -I phylip_multialignment -O phylip_dm -b 3 -r 2
4745 Segmentation fault | fnj -I phylip_dm -O xml -r 2 -d 4
make[2]: *** [src/docbook/xincluded_files/connecting_fnj_to_fastdist_with_a_pipe1] Error 139
make[1]: *** [src/docbook/CMakeFiles/docbook-doc.dir/all] Error 2
make: *** [all] Error 2
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From: Erik S. <eri...@gm...> - 2009-09-07 15:27:05
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Some 64-bit compilation issues were resolved. Until the next release please use the source in the subversion trunk. svn co https://fastphylo.svn.sourceforge.net/svnroot/fastphylo fastphylo cheers, Erik |
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