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Installation error

Issue #77 resolved
Former user created an issue

Hello MetaBAT team,

I noticed that I might have an error while installation. Here I have pasted my script and command ran on hpcc terminal. Could you tell me if I can use or do something over to complete installation?

download

[leejooy5@dev-intel16-k80 megahit_assembly]$ wget https://bitbucket.org/berkeleylab/metabat/get/master.tar.gz --2019-10-14 15:09:07-- https://bitbucket.org/berkeleylab/metabat/get/master.tar.gz Resolving bitbucket.org (bitbucket.org)... 18.205.93.2, 18.205.93.1, 18.205.93.0, ... Connecting to bitbucket.org (bitbucket.org)|18.205.93.2|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 188546 (184K) [application/x-tar-gz] Saving to: ‘master.tar.gz’

100%[==============================================================================================>] 188,546 --.-K/s in 0.06s

2019-10-14 15:09:08 (3.17 MB/s) - ‘master.tar.gz’ saved [188546/188546] $ tar xzvf master.tar.gz

$ cd berkeleylab-metabat-6e3baed5c0e2

installation

[leejooy5@dev-intel16-k80 berkeleylab-metabat-6e3baed5c0e2]$ mkdir build && cd build && cmake .. && make && make install -- The C compiler identification is GNU 6.4.0 -- The CXX compiler identification is GNU 6.4.0 -- Check for working C compiler: /opt/software/GCCcore/6.4.0/bin/cc -- Check for working C compiler: /opt/software/GCCcore/6.4.0/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /opt/software/GCCcore/6.4.0/bin/c++ -- Check for working CXX compiler: /opt/software/GCCcore/6.4.0/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done Installing Release MetaBAT into /usr/local -- Boost version: 1.67.0 -- Found the following Boost libraries: -- program_options -- filesystem -- system -- graph -- serialization -- iostreams -- regex -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") Using OpenMP Boost cmake dir: Boost include: /opt/software/Boost/1.67.0-foss-2018a/include Boost libraries:/opt/software/Boost/1.67.0-foss-2018a/lib/libboost_program_options.a/opt/software/Boost/1.67.0-foss-2018a/lib/libboost_filesystem.a/opt/software/Boost/1.67.0-foss-2018a/lib/libboost_system.a/opt/software/Boost/1.67.0-foss-2018a/lib/libboost_graph.a/opt/software/Boost/1.67.0-foss-2018a/lib/libboost_serialization.a/opt/software/Boost/1.67.0-foss-2018a/lib/libboost_iostreams.a/opt/software/Boost/1.67.0-foss-2018a/lib/libboost_regex.a Boost lib ver:1_67 Boost lib dir:/opt/software/Boost/1.67.0-foss-2018a/lib -- Configuring done -- Generating done -- Build files have been written to: /mnt/home/leejooy5/otic_WMS_HiSeq/bbduk01/bbduk01_reads/phix_filtered/filtered_reads/host_filtered/host_removed_fastq/megahit_assembly/berkeleylab-metabat-6e3baed5c0e2/build Scanning dependencies of target zlib [ 4%] Creating directories for 'zlib' [ 8%] Performing download step (git clone) for 'zlib' -- zlib download command succeeded. See also /mnt/home/leejooy5/otic_WMS_HiSeq/bbduk01/bbduk01_reads/phix_filtered/filtered_reads/host_filtered/host_removed_fastq/megahit_assembly/berkeleylab-metabat-6e3baed5c0e2/build/contrib/zlib-prefix/src/zlib-stamp/zlib-download-.log [ 12%] No patch step for 'zlib' [ 16%] No update step for 'zlib' [ 20%] Performing configure step for 'zlib' Checking for gcc... Building static library libz.a version 1.2.11 with gcc. Checking for size_t... Yes. Checking for off64_t... Yes. Checking for fseeko... Yes. Checking for strerror... Yes. Checking for unistd.h... Yes. Checking for stdarg.h... Yes. Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf(). Checking for vsnprintf() in stdio.h... Yes. Checking for return value of vsnprintf()... Yes. Checking for attribute(visibility) support... Yes. [ 24%] Performing build step for 'zlib' [ 28%] Performing install step for 'zlib' -- zlib install command succeeded. See also /mnt/home/leejooy5/otic_WMS_HiSeq/bbduk01/bbduk01_reads/phix_filtered/filtered_reads/host_filtered/host_removed_fastq/megahit_assembly/berkeleylab-metabat-6e3baed5c0e2/build/contrib/zlib-prefix/src/zlib-stamp/zlib-install-.log [ 32%] Completed 'zlib' [ 32%] Built target zlib Scanning dependencies of target htslib [ 36%] Creating directories for 'htslib' [ 40%] Performing download step (git clone) for 'htslib' -- htslib download command succeeded. See also /mnt/home/leejooy5/otic_WMS_HiSeq/bbduk01/bbduk01_reads/phix_filtered/filtered_reads/host_filtered/host_removed_fastq/megahit_assembly/berkeleylab-metabat-6e3baed5c0e2/build/contrib/htslib-prefix/src/htslib-stamp/htslib-download-*.log [ 44%] No patch step for 'htslib' [ 48%] No update step for 'htslib' [ 52%] Performing configure step for 'htslib' checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... no checking shared library type for unknown-Linux... plain .so checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no configure: WARNING: GCS support not enabled: requires libcurl support configure: WARNING: S3 support not enabled: requires libcurl support checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h [ 56%] Performing build step for 'htslib' [ 60%] Performing install step for 'htslib' [ 64%] Completed 'htslib' [ 64%] Built target htslib Scanning dependencies of target check_git_repository [ 68%] Checking the git repository for changes... Creating new /mnt/home/leejooy5/otic_WMS_HiSeq/bbduk01/bbduk01_reads/phix_filtered/filtered_reads/host_filtered/host_removed_fastq/megahit_assembly/berkeleylab-metabat-6e3baed5c0e2/metabat_version.h with false [ 68%] Built target check_git_repository Scanning dependencies of target metabat2 [ 72%] Building CXX object src/CMakeFiles/metabat2.dir/metabat2.cpp.o [ 76%] Linking CXX executable metabat2 [ 76%] Built target metabat2 Scanning dependencies of target jgi_summarize_bam_contig_depths [ 80%] Building CXX object src/CMakeFiles/jgi_summarize_bam_contig_depths.dir/jgi_summarize_bam_contig_depths.cpp.o [ 84%] Linking CXX executable jgi_summarize_bam_contig_depths [ 84%] Built target jgi_summarize_bam_contig_depths Scanning dependencies of target metabat1 [ 88%] Building CXX object src/CMakeFiles/metabat1.dir/metabat1.cpp.o [ 92%] Linking CXX executable metabat1 [ 92%] Built target metabat1 Scanning dependencies of target contigOverlaps [ 96%] Building CXX object src/CMakeFiles/contigOverlaps.dir/contigOverlaps.cpp.o [100%] Linking CXX executable contigOverlaps [100%] Built target contigOverlaps [ 32%] Built target zlib [ 64%] Built target htslib [ 68%] Checking the git repository for changes... [ 68%] Built target check_git_repository [ 76%] Built target metabat2 [ 84%] Built target jgi_summarize_bam_contig_depths [ 92%] Built target metabat1 [100%] Built target contigOverlaps Install the project... -- Install configuration: "Release" -- Installing: /usr/local/bin/runMetaBat.sh CMake Error at cmake_install.cmake:41 (file): file INSTALL cannot copy file "/mnt/home/leejooy5/otic_WMS_HiSeq/bbduk01/bbduk01_reads/phix_filtered/filtered_reads/host_filtered/host_removed_fastq/megahit_assembly/berkeleylab-metabat-6e3baed5c0e2/runMetaBat.sh" to "/usr/local/bin/runMetaBat.sh".

make: *** [install] Error 1 #

Comments (4)

  1. Rob Egan

    You do not seem to have permission to write to /usr/local/bin. This is expected for normal users (i.e. without root privileges). You will need to choose a different install directory and you can use the standard CMAKE_INSTALL_PREFIX option to cmake to accomplish that.

    I’ll update the README

  2. Joo-Young Lee

    I am so sorry that I forgot sign in. I re-write more details here.

    ========

    Hello, MetaBAT team,

    I am a newbie in this field and currently working on my very first shotgun metagenome sequence to binning with after assembly with megahit. I followed tutorials (https://bitbucket.org/berkeleylab/metabat/src/master/) for download and installation of MetaBAT. I noticed error message after I ran command for installation in my working directory of hpcc. Here I described the loaded module and commands.

    First, I checked module loaded on hpcc and I thought those fit requirements to install.

    [leejooy5@dev-intel16-k80 megahit_assembly]$ module list

    Currently Loaded Modules:

    1) GCCcore/6.4.0 6) imkl/2018.1.163 11) zlib/1.2.11 16) Tcl/8.6.8 21) Java/1.8.0_152

    2) binutils/2.28 7) OpenBLAS/0.2.20 12) Boost/1.67.0 17) SQLite/3.21.0 22) MATLAB/2018a

    3) GNU/6.4.0-2.28 8) FFTW/3.3.7 13) CMake/3.11.1 18) GMP/6.1.2 23) powertools/1.2

    4) OpenMPI/2.1.2 9) ScaLAPACK/2.0.2-OpenBLAS-0.2.20 14) ncurses/6.0 19) libffi/3.2.1

    5) tbb/2018_U3 10) bzip2/1.0.6 15) libreadline/7.0 20) Python/3.6.4

    ‌

    Then, I downloaded stable release version

    [leejooy5@dev-intel16-k80 megahit_assembly] $ wget https://bitbucket.org/berkeleylab/metabat/get/master.tar.gz

    $ tar xzvf master.tar.gz

    $ cd berkeleylab-metabat-6e3baed5c0e2

    And I used #run the installation script as follows:

    [leejooy5@dev-intel16-k80 berkeleylab-metabat-6e3baed5c0e2]$ mkdir build && cd build && cmake .. && make && make install-->I concerned if I should have included specific directory in this command.

    Running command showed the following status on screen (for your convenience, I highlighted Error, no, none, warning in bold):

    =======================
    -- The C compiler identification is GNU 6.4.0
    -- The CXX compiler identification is GNU 6.4.0
    -- Check for working C compiler: /opt/software/GCCcore/6.4.0/bin/cc
    -- Check for working C compiler: /opt/software/GCCcore/6.4.0/bin/cc -- works
    -- Detecting C compiler ABI info
    -- Detecting C compiler ABI info - done
    -- Detecting C compile features
    -- Detecting C compile features - done
    -- Check for working CXX compiler: /opt/software/GCCcore/6.4.0/bin/c++
    -- Check for working CXX compiler: /opt/software/GCCcore/6.4.0/bin/c++ -- works
    -- Detecting CXX compiler ABI info
    -- Detecting CXX compiler ABI info - done
    -- Detecting CXX compile features
    -- Detecting CXX compile features - done
    Installing Release MetaBAT into /usr/local
    -- Boost version: 1.67.0
    -- Found the following Boost libraries:
    -- program_options
    -- filesystem
    -- system
    -- graph
    -- serialization
    -- iostreams
    -- regex
    -- Found OpenMP_C: -fopenmp (found version "4.5")
    -- Found OpenMP_CXX: -fopenmp (found version "4.5")
    -- Found OpenMP: TRUE (found version "4.5")
    Using OpenMP
    Boost cmake dir:
    Boost include: /opt/software/Boost/1.67.0-foss-2018a/include
    Boost libraries:/opt/software/Boost/1.67.0-foss-2018a/lib/libboost_program_options.a/opt/software/Boost/1.67.0-foss-2018a/lib/libboost_filesystem.a/opt/software/Boost/1.67.0-foss-2018a/lib/libboost_system.a/opt/software/Boost/1.67.0-foss-2018a/lib/libboost_graph.a/opt/software/Boost/1.67.0-foss-2018a/lib/libboost_serialization.a/opt/software/Boost/1.67.0-foss-2018a/lib/libboost_iostreams.a/opt/software/Boost/1.67.0-foss-2018a/lib/libboost_regex.a
    Boost lib ver:1_67
    Boost lib dir:/opt/software/Boost/1.67.0-foss-2018a/lib
    -- Configuring done
    -- Generating done
    -- Build files have been written to: /mnt/home/leejooy5/otic_WMS_HiSeq/bbduk01/bbduk01_reads/phix_filtered/filtered_reads/host_filtered/host_removed_fastq/megahit_assembly/berkeleylab-metabat-6e3baed5c0e2/build
    Scanning dependencies of target zlib
    [ 4%] Creating directories for 'zlib'
    [ 8%] Performing download step (git clone) for 'zlib'
    -- zlib download command succeeded. See also /mnt/home/leejooy5/otic_WMS_HiSeq/bbduk01/bbduk01_reads/phix_filtered/filtered_reads/host_filtered/host_removed_fastq/megahit_assembly/berkeleylab-metabat-6e3baed5c0e2/build/contrib/zlib-prefix/src/zlib-stamp/zlib-download-.log
    [ 12%] No patch step for 'zlib'
    [ 16%] No update step for 'zlib'
    [ 20%] Performing configure step for 'zlib'
    Checking for gcc...
    Building static library libz.a version 1.2.11 with gcc.
    Checking for size_t... Yes.
    Checking for off64_t... Yes.
    Checking for fseeko... Yes.
    Checking for strerror... Yes.
    Checking for unistd.h... Yes.
    Checking for stdarg.h... Yes.
    Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf().
    Checking for vsnprintf() in stdio.h... Yes.
    Checking for return value of vsnprintf()... Yes.
    Checking for attribute(visibility) support... Yes.
    [ 24%] Performing build step for 'zlib'
    [ 28%] Performing install step for 'zlib'
    -- zlib install command succeeded. See also /mnt/home/leejooy5/otic_WMS_HiSeq/bbduk01/bbduk01_reads/phix_filtered/filtered_reads/host_filtered/host_removed_fastq/megahit_assembly/berkeleylab-metabat-6e3baed5c0e2/build/contrib/zlib-prefix/src/zlib-stamp/zlib-install-.log
    [ 32%] Completed 'zlib'
    [ 32%] Built target zlib
    Scanning dependencies of target htslib
    [ 36%] Creating directories for 'htslib'
    [ 40%] Performing download step (git clone) for 'htslib'
    -- htslib download command succeeded. See also /mnt/home/leejooy5/otic_WMS_HiSeq/bbduk01/bbduk01_reads/phix_filtered/filtered_reads/host_filtered/host_removed_fastq/megahit_assembly/berkeleylab-metabat-6e3baed5c0e2/build/contrib/htslib-prefix/src/htslib-stamp/htslib-download-*.log
    [ 44%] No patch step for 'htslib'
    [ 48%] No update step for 'htslib'
    [ 52%] Performing configure step for 'htslib'
    checking for gcc... gcc
    checking whether the C compiler works... yes
    checking for C compiler default output file name... a.out
    checking for suffix of executables...
    checking whether we are cross compiling... no
    checking for suffix of object files... o
    checking whether we are using the GNU C compiler... yes
    checking whether gcc accepts -g... yes
    checking for gcc option to accept ISO C89... none needed
    checking for ranlib... ranlib
    checking for grep that handles long lines and -e... /usr/bin/grep
    checking for C compiler warning flags... -Wall
    checking for special C compiler options needed for large files... no
    checking for _FILE_OFFSET_BITS value needed for large files... no
    checking for _LARGEFILE_SOURCE value needed for large files... no
    checking shared library type for unknown-Linux... plain .so
    checking how to run the C preprocessor... gcc -E
    checking for egrep... /usr/bin/grep -E
    checking for ANSI C header files... yes
    checking for sys/types.h... yes
    checking for sys/stat.h... yes
    checking for stdlib.h... yes
    checking for string.h... yes
    checking for memory.h... yes
    checking for strings.h... yes
    checking for inttypes.h... yes
    checking for stdint.h... yes
    checking for unistd.h... yes
    checking for stdlib.h... (cached) yes
    checking for unistd.h... (cached) yes
    checking for sys/param.h... yes
    checking for getpagesize... yes
    checking for working mmap... yes
    checking for gmtime_r... yes
    checking for fsync... yes
    checking for drand48... yes
    checking whether fdatasync is declared... yes
    checking for fdatasync... yes
    checking for library containing log... -lm
    checking for zlib.h... yes
    checking for inflate in -lz... yes
    checking for library containing recv... none required
    checking for libdeflate.h... no
    checking for libdeflate_deflate_compress in -ldeflate... no
    configure: WARNING: GCS support not enabled: requires libcurl support
    configure: WARNING: S3 support not enabled: requires libcurl support
    checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
    configure: creating ./config.status
    config.status: creating config.mk
    config.status: creating htslib.pc.tmp
    config.status: creating config.h
    [ 56%] Performing build step for 'htslib'
    [ 60%] Performing install step for 'htslib'
    [ 64%] Completed 'htslib'
    [ 64%] Built target htslib
    Scanning dependencies of target check_git_repository
    [ 68%] Checking the git repository for changes...
    Creating new /mnt/home/leejooy5/otic_WMS_HiSeq/bbduk01/bbduk01_reads/phix_filtered/filtered_reads/host_filtered/host_removed_fastq/megahit_assembly/berkeleylab-metabat-6e3baed5c0e2/metabat_version.h with false
    [ 68%] Built target check_git_repository
    Scanning dependencies of target metabat2
    [ 72%] Building CXX object src/CMakeFiles/metabat2.dir/metabat2.cpp.o
    [ 76%] Linking CXX executable metabat2
    [ 76%] Built target metabat2
    Scanning dependencies of target jgi_summarize_bam_contig_depths
    [ 80%] Building CXX object src/CMakeFiles/jgi_summarize_bam_contig_depths.dir/jgi_summarize_bam_contig_depths.cpp.o
    [ 84%] Linking CXX executable jgi_summarize_bam_contig_depths
    [ 84%] Built target jgi_summarize_bam_contig_depths
    Scanning dependencies of target metabat1
    [ 88%] Building CXX object src/CMakeFiles/metabat1.dir/metabat1.cpp.o
    [ 92%] Linking CXX executable metabat1
    [ 92%] Built target metabat1
    Scanning dependencies of target contigOverlaps
    [ 96%] Building CXX object src/CMakeFiles/contigOverlaps.dir/contigOverlaps.cpp.o
    [100%] Linking CXX executable contigOverlaps
    [100%] Built target contigOverlaps
    [ 32%] Built target zlib
    [ 64%] Built target htslib
    [ 68%] Checking the git repository for changes...
    [ 68%] Built target check_git_repository
    [ 76%] Built target metabat2
    [ 84%] Built target jgi_summarize_bam_contig_depths
    [ 92%] Built target metabat1
    [100%] Built target contigOverlaps
    Install the project...
    -- Install configuration: "Release"
    -- Installing: /usr/local/bin/runMetaBat.sh
    CMake Error at cmake_install.cmake:41 (file):
    file INSTALL cannot copy file
    "/mnt/home/leejooy5/otic_WMS_HiSeq/bbduk01/bbduk01_reads/phix_filtered/filtered_reads/host_filtered/host_removed_fastq/megahit_assembly/berkeleylab-metabat-6e3baed5c0e2/runMetaBat.sh"
    to "/usr/local/bin/runMetaBat.sh".

    make: *** [install] Error 1

    ================

    I hope this can help you to point out my mistake. Thank you for your efforts to save padawans.

    ‌

    Best regards,

    Joo-Young

  3. Joo-Young Lee

    Hi Rob,

    Thank you for your lightening prompt help!

    I tried again following the updated README. No error message occurred this time and now I have bin folder.

    [leejooy5@dev-intel16-k80 berkeleylab-metabat-6e3baed5c0e2]$ ls -lht

    total 118K
    drwxr-x--- 7 leejooy5 mmg 8.0K Oct 14 19:10 build
    drwxr-x--- 2 leejooy5 mmg 8.0K Oct 14 19:10 bin
    -rw-r----- 1 leejooy5 mmg 352 Oct 14 15:23 metabat_version.h
    -rwxr-x--- 1 leejooy5 mmg 1.4K Oct 2 03:45 aggregateBinDepths.pl
    -rwxr-x--- 1 leejooy5 mmg 2.9K Oct 2 03:45 aggregateContigOverlapsByBin.pl
    -rw-r----- 1 leejooy5 mmg 1.4K Oct 2 03:45 bitbucket-pipelines.yml
    drwxr-x--- 2 leejooy5 mmg 8.0K Oct 2 03:45 cmake
    -rw-r----- 1 leejooy5 mmg 1.6K Oct 2 03:45 CMakeLists.txt
    -rw-r----- 1 leejooy5 mmg 1.1K Oct 2 03:45 Dockerfile
    -rw-r----- 1 leejooy5 mmg 2.0K Oct 2 03:45 INSTALL.md
    -rw-r----- 1 leejooy5 mmg 1.3K Oct 2 03:45 Legal.txt
    -rw-r----- 1 leejooy5 mmg 2.4K Oct 2 03:45 license.txt
    -rwxr-x--- 1 leejooy5 mmg 1.4K Oct 2 03:45 merge_depths.pl
    drwxr-x--- 2 leejooy5 mmg 8.0K Oct 2 03:45 MetaBAT2PaperSupplementaryScripts
    -rw-r----- 1 leejooy5 mmg 374 Oct 2 03:45 metabat_version.h.in
    -rw-r----- 1 leejooy5 mmg 27K Oct 2 03:45 README.md
    -rwxr-x--- 1 leejooy5 mmg 2.7K Oct 2 03:45 runMetaBat.sh
    drwxr-x--- 2 leejooy5 mmg 8.0K Oct 2 03:45 src
    drwxr-x--- 2 leejooy5 mmg 8.0K Oct 2 03:45 test

    [leejooy5@dev-intel16-k80 bin]$ ./runMetaBat.sh

    ./runMetaBat.sh <select metabat options> assembly.fa sample1.bam [ sample2.bam ...]
    You can specify any metabat options EXCEPT:
    -i --inFile
    -o --outFile
    -a --abdFile

    Also for depth calculations stage only, you can set the following environmental variables:
    PCTID=97 -- reads below this threshold will be discarded

    BADMAP=0 -- output the discarded reads to a sub directory
    MINDEPTH=1.0 -- require contigs to have this minimum depth to be output

    For full metabat options: metabat2 -h
    It seems like metabat is ready to work for my sequence. Thank you so much!

    ‌

    ‌

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