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Get assembly statistics from FASTA and FASTQ files

License: Other

C++ 83.27% Shell 8.80% C 0.11% Python 4.89% CMake 0.54% Makefile 1.88% M4 0.49% Dockerfile 0.03%

genomics sequencing next-generation-sequencing research bioinformatics global-health infectious-diseases pathogen

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Installation issue Assembly-Stats on Mac

Hi, I am trying to install assembly stats via manual installation on my machine.
I have installed zlib via Homebrew ahead of the installation.
I have downloaded the .gz file, positioned it into my Applications folder and then proceeded to the installation as indicated on your page.

I recover multiple errors.
First, while running "make test" i have this problem:


Running tests...
Test project /Applications/assembly-stats-master/build
    Start 1: runUnitTests
Could not find executable runUnitTests
Looked in the following places:
runUnitTests
runUnitTests
Release/runUnitTests
Release/runUnitTests
Debug/runUnitTests
Debug/runUnitTests
MinSizeRel/runUnitTests
MinSizeRel/runUnitTests
RelWithDebInfo/runUnitTests
RelWithDebInfo/runUnitTests
Deployment/runUnitTests
Deployment/runUnitTests
Development/runUnitTests
Development/runUnitTests
Unable to find executable: runUnitTests
1/1 Test #1: runUnitTests .....................***Not Run   0.00 sec

0% tests passed, 1 tests failed out of 1

Total Test time (real) =   0.00 sec

The following tests FAILED:
	  1 - runUnitTests (Not Run)
Errors while running CTest
Output from these tests are in: /Applications/assembly-stats-master/build/Testing/Temporary/LastTest.log
Use "--rerun-failed --output-on-failure" to re-run the failed cases verbosely.
make: *** [test] Error 8

Secondly, when i run "make install":

[  5%] Building CXX object gtest-1.7.0/CMakeFiles/gtest.dir/src/gtest-all.cc.o
[ 10%] Linking CXX static library libgtest.a
[ 10%] Built target gtest
[ 15%] Building CXX object gtest-1.7.0/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o
[ 21%] Linking CXX static library libgtest_main.a
[ 21%] Built target gtest_main
[ 26%] Building CXX object CMakeFiles/filetype.dir/filetype.cpp.o
In file included from /Applications/assembly-stats-master/filetype.cpp:1:
In file included from /Applications/assembly-stats-master/filetype.h:8:
In file included from /Applications/assembly-stats-master/build/external/bxzstr/include/bxzstr.hpp:18:
/Applications/assembly-stats-master/build/external/bxzstr/include/stream_wrapper.hpp:17:33: warning: defaulted function definitions are a C++11 extension [-Wc++11-extensions]
    virtual ~stream_wrapper() = default;
                                ^
In file included from /Applications/assembly-stats-master/filetype.cpp:1:
In file included from /Applications/assembly-stats-master/filetype.h:8:
In file included from /Applications/assembly-stats-master/build/external/bxzstr/include/bxzstr.hpp:19:
/Applications/assembly-stats-master/build/external/bxzstr/include/strict_fstream.hpp:62:18: error: exception specification of overriding function is more lax than base version
    const char * what() const noexcept { return _msg.c_str(); }
                 ^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.3.sdk/usr/include/c++/v1/exception:107:25: note: overridden virtual function is here
    virtual const char* what() const _NOEXCEPT;
                        ^
In file included from /Applications/assembly-stats-master/filetype.cpp:1:
In file included from /Applications/assembly-stats-master/filetype.h:8:
In file included from /Applications/assembly-stats-master/build/external/bxzstr/include/bxzstr.hpp:19:
/Applications/assembly-stats-master/build/external/bxzstr/include/strict_fstream.hpp:62:30: error: expected ';' at end of declaration list
    const char * what() const noexcept { return _msg.c_str(); }
                             ^
                             ;
/Applications/assembly-stats-master/build/external/bxzstr/include/strict_fstream.hpp:61:41: error: member initializer '_msg' does not name a non-static data member or base class
    Exception(const std::string& msg) : _msg(msg) {}
                                        ^~~~~~~~~
/Applications/assembly-stats-master/build/external/bxzstr/include/strict_fstream.hpp:152:18: warning: defaulted function definitions are a C++11 extension [-Wc++11-extensions]
    ifstream() = default;
                 ^
/Applications/assembly-stats-master/build/external/bxzstr/include/strict_fstream.hpp:172:18: warning: defaulted function definitions are a C++11 extension [-Wc++11-extensions]
    ofstream() = default;
                 ^
/Applications/assembly-stats-master/build/external/bxzstr/include/strict_fstream.hpp:191:17: warning: defaulted function definitions are a C++11 extension [-Wc++11-extensions]
    fstream() = default;
                ^
In file included from /Applications/assembly-stats-master/filetype.cpp:1:
In file included from /Applications/assembly-stats-master/filetype.h:8:
In file included from /Applications/assembly-stats-master/build/external/bxzstr/include/bxzstr.hpp:20:
In file included from /Applications/assembly-stats-master/build/external/bxzstr/include/compression_types.hpp:14:
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:64:18: error: exception specification of overriding function is more lax than base version
    const char * what() const noexcept { return _msg.c_str(); }
                 ^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.3.sdk/usr/include/c++/v1/exception:107:25: note: overridden virtual function is here
    virtual const char* what() const _NOEXCEPT;
                        ^
In file included from /Applications/assembly-stats-master/filetype.cpp:1:
In file included from /Applications/assembly-stats-master/filetype.h:8:
In file included from /Applications/assembly-stats-master/build/external/bxzstr/include/bxzstr.hpp:20:
In file included from /Applications/assembly-stats-master/build/external/bxzstr/include/compression_types.hpp:14:
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:64:30: error: expected ';' at end of declaration list
    const char * what() const noexcept { return _msg.c_str(); }
                             ^
                             ;
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:25:34: error: member initializer '_msg' does not name a non-static data member or base class
    bzException(const int ret) : _msg("bzlib: ") {
                                 ^~~~~~~~~~~~~~~
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:28:17: error: use of undeclared identifier '_msg'
                _msg += "BZ_CONFIG_ERROR: ";
                ^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:31:3: error: use of undeclared identifier '_msg'
                _msg += "BZ_SEQUENCE_ERROR: ";
                ^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:34:3: error: use of undeclared identifier '_msg'
                _msg += "BZ_PARAM_ERROR: ";
                ^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:37:3: error: use of undeclared identifier '_msg'
                _msg += "BZ_MEM_ERROR: ";
                ^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:40:3: error: use of undeclared identifier '_msg'
                _msg += "BZ_DATA_ERROR: ";
                ^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:43:3: error: use of undeclared identifier '_msg'
                _msg += "BZ_DATA_ERROR_MAGIC: ";
                ^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:46:3: error: use of undeclared identifier '_msg'
                _msg += "BZ_IO_ERROR: ";
                ^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:49:3: error: use of undeclared identifier '_msg'
                _msg += "BZ_UNEXPECTED_EOF: ";
                ^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:52:3: error: use of undeclared identifier '_msg'
                _msg += "BZ_OUTBUFF_FULL: ";
                ^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:57:3: error: use of undeclared identifier '_msg'
                _msg += "[" + oss.str() + "]: ";
                ^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:60:9: error: use of undeclared identifier '_msg'
        _msg += ret;
        ^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:62:42: error: member initializer '_msg' does not name a non-static data member or base class
    bzException(const std::string msg) : _msg(msg) {}
                                         ^~~~~~~~~
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:87:5: error: exception specification of overriding function is more lax than base version
    ~bz_stream_wrapper() {
    ^
/Applications/assembly-stats-master/build/external/bxzstr/include/stream_wrapper.hpp:17:13: note: overridden virtual function is here
    virtual ~stream_wrapper() = default;
            ^
In file included from /Applications/assembly-stats-master/filetype.cpp:1:
In file included from /Applications/assembly-stats-master/filetype.h:8:
In file included from /Applications/assembly-stats-master/build/external/bxzstr/include/bxzstr.hpp:20:
In file included from /Applications/assembly-stats-master/build/external/bxzstr/include/compression_types.hpp:14:
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:95:31: warning: 'override' keyword is a C++11 extension [-Wc++11-extensions]
    int decompress(const int) override {
                              ^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:100:45: warning: 'override' keyword is a C++11 extension [-Wc++11-extensions]
    int compress(const int _flags = BZ_RUN) override {
                                            ^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:105:29: warning: 'override' keyword is a C++11 extension [-Wc++11-extensions]
    bool stream_end() const override { return this->ret == BZ_STREAM_END; }
                            ^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:106:23: warning: 'override' keyword is a C++11 extension [-Wc++11-extensions]
    bool done() const override { return this->stream_end(); }
                      ^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:108:36: warning: 'override' keyword is a C++11 extension [-Wc++11-extensions]
    const uint8_t* next_in() const override { return (uint8_t*)bz_stream::next_in; }
                                   ^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:109:27: warning: 'override' keyword is a C++11 extension [-Wc++11-extensions]
    long avail_in() const override { return bz_stream::avail_in; }
                          ^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:110:31: warning: 'override' keyword is a C++11 extension [-Wc++11-extensions]
    uint8_t* next_out() const override { return (uint8_t*)bz_stream::next_out; }
                              ^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:111:28: warning: 'override' keyword is a C++11 extension [-Wc++11-extensions]
    long avail_out() const override { return bz_stream::avail_out; }
                           ^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:113:47: warning: 'override' keyword is a C++11 extension [-Wc++11-extensions]
    void set_next_in(const unsigned char* in) override { bz_stream::next_in = (char*)in; }
                                              ^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:114:38: warning: 'override' keyword is a C++11 extension [-Wc++11-extensions]
    void set_avail_in(const long in) override { bz_stream::avail_in = in; }
                                     ^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:115:42: warning: 'override' keyword is a C++11 extension [-Wc++11-extensions]
    void set_next_out(const uint8_t* in) override { bz_stream::next_out = (char*)in; }
                                         ^
/Applications/assembly-stats-master/build/external/bxzstr/include/bz_stream_wrapper.hpp:116:39: warning: 'override' keyword is a C++11 extension [-Wc++11-extensions]
    void set_avail_out(const long in) override { bz_stream::avail_out = in; }
                                      ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
16 warnings and 20 errors generated.
make[2]: *** [CMakeFiles/filetype.dir/filetype.cpp.o] Error 1
make[1]: *** [CMakeFiles/filetype.dir/all] Error 2
make: *** [all] Error 2

I have consulted multiple web resources but I could not find a solution.
How can I fix this?

EasyBuild installation recipe and a patch file

With this message, I would like to share an easyconfig file that I have just composed to install this tool on our Tier-2 machines. You may find the files via this PR: easybuilders/easybuild-easyconfigs#20281.

I have succeeded to install the tool and create the assembly-stats/1.0.1-GCCcore-11.3.0 on our Intel Skylake, Cascadelake and Icelake nodes, running on Rocky 8.9 OS.
The build was impossible without a small patch file (see the PR link above)

Handle gzipped input

Hello,

It would be nice if assembly-stats could handle gzipped input files.

Best,

Phil

N50 and L50

just one question, for assembly-stats example (in your main page), in N50=1687656 and n=5, n correspond to L50 ???
Thanks

$ assembly-stats Pf3D7_v3.fasta
stats for Pf3D7_v3.fasta
sum = 23328019, n = 16, ave = 1458001.19, largest = 3291936
N50 = 1687656, n = 5
N60 = 1472805, n = 7
N70 = 1445207, n = 8
N80 = 1343557, n = 10
N90 = 1067971, n = 12
N100 = 5967, n = 16
N_count = 0
Gaps = 0

Different output in single line vs multi line fasta

The software is giving different outputs for single vs multiline fasta.
Seems to be counting "#lines = bytes" added into contig size

Needs urgent fixing to avoid confusion. Or should alarm people while running the software.

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