Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • cd-hit-otu installation issue in Mac

    Dear all

    I am trying to install cd-hit-otu to follow up in some results in metagenomics that received from 16S Miseq sequencing. The idea is to replicate a workflow so I can learn how to do and use it with future samples. I am using Macqiime and now I am in the stage of filtering reads and OTU cluster with cd-hit-otu but when I am installing in terminal I get errors when I do the "make" command. I believe this is a Mac issue but I only have macs to work with so no option for me. Plus I am a newbie with python or any language code for what is worth so I have been holding my own with google search and forums but now I got stuck. Is there anyone that can drop me a hand with this. I deeply appreciate it! Here is the terminal output I am receiving when I try to make the first file.

    /Applications/Bioinformatics/cd-hit-otu-illumina-0.0.1/cd-hit-v4.5.5-2011-03-31
    :cd-hit-v4.5.5-2011-03-31 $ make
    g++ -O2 -DNO_OPENMP cdhit-common.c++ -c
    cdhit-common.c++:68:29: warning: format specifies type 'unsigned int' but the
    argument has type 'TempFile *' [-Wformat]
    sprintf( buf + len, "%x", this );
    ~~ ^~~~
    cdhit-common.c++:2260:38: warning: format specifies type 'int' but the argument
    has type 'unsigned long' [-Wformat]
    printf( "%-16s: %iM\n", "Sequence", mem/mega );
    ~~ ^~~~~~~~
    %lu
    cdhit-common.c++:2264:50: warning: format specifies type 'int' but the argument
    has type 'unsigned long' [-Wformat]
    printf( "%-16s: %i X %iM = %iM\n", "Buffer", T, mem/mega, T*mem/mega );
    ~~ ^~~~~~~~
    %lu
    cdhit-common.c++:2264:60: warning: format specifies type 'int' but the argument
    has type 'unsigned long' [-Wformat]
    printf( "%-16s: %i X %iM = %iM\n", "Buffer", T, mem/mega, T*mem/mega );
    ~~ ^~~~~~~~~~
    %lu
    cdhit-common.c++:2268:53: warning: format specifies type 'int' but the argument
    has type 'unsigned long' [-Wformat]
    printf( "%-16s: %i X %iM = %iM\n", "Table", table, mem/mega, tab...
    ~~ ^~~~~~~~
    %lu
    cdhit-common.c++:2268:63: warning: format specifies type 'int' but the argument
    has type 'unsigned long' [-Wformat]
    ..."%-16s: %i X %iM = %iM\n", "Table", table, mem/mega, table*mem/mega );
    ~~ ^~~~~~~~~~~~~~
    %lu
    cdhit-common.c++:2273:43: warning: format specifies type 'int' but the argument
    has type 'unsigned long' [-Wformat]
    printf( "%-16s: %iM\n", "Miscellaneous", mem/mega );
    ~~ ^~~~~~~~
    %lu
    cdhit-common.c++:2276:37: warning: format specifies type 'int' but the argument
    has type 'unsigned long' [-Wformat]
    printf( "%-16s: %iM\n\n", "Total", mem_need/mega );
    ~~ ^~~~~~~~~~~~~
    %lu
    cdhit-common.c++:2281:5: warning: format specifies type 'int' but the argument
    has type 'unsigned long' [-Wformat]
    50*table + mem_need/mega );
    ^~~~~~~~~~~~~~~~~~~~~~~~
    cdhit-common.c++:2478:62: warning: format specifies type 'int' but the argument
    has type 'size_type' (aka 'unsigned long') [-Wformat]
    ...new table with %8i representatives\n", word_table.sequences.size() );
    ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~
    %8lu
    cdhit-common.c++:2489:61: warning: format specifies type 'int' but the argument
    has type 'size_t' (aka 'unsigned long') [-Wformat]
    printf( "\nApprixmated maximum memory consumption: %iM\n", mem );
    ~~ ^~~
    %lu
    cdhit-common.c++:2996:61: warning: format specifies type 'int' but the argument
    has type 'size_t' (aka 'unsigned long') [-Wformat]
    printf( "\nApprixmated maximum memory consumption: %iM\n", mem );
    ~~ ^~~
    %lu
    In file included from cdhit-common.c++:28:
    ./cdhit-common.h:95:4: error: use of undeclared identifier 'push_back'
    push_back( item );
    ^
    this->
    cdhit-common.c++:704:14: note: in instantiation of member function
    'Vector<NVector<long long> >::Append' requested here
    score_mat.Append( row2 );
    ^
    /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/vector:685:36: note:
    must qualify identifier to find this declaration in dependent base class
    _LIBCPP_INLINE_VISIBILITY void push_back(const_reference __x);
    ^
    In file included from cdhit-common.c++:28:
    ./cdhit-common.h:95:4: error: use of undeclared identifier 'push_back'
    push_back( item );
    ^
    this->
    cdhit-common.c++:705:13: note: in instantiation of member function
    'Vector<NVector<int> >::Append' requested here
    back_mat.Append( row );
    ^
    /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/vector:685:36: note:
    must qualify identifier to find this declaration in dependent base class
    _LIBCPP_INLINE_VISIBILITY void push_back(const_reference __x);
    ^
    In file included from cdhit-common.c++:28:
    ./cdhit-common.h:95:4: error: use of undeclared identifier 'push_back'
    push_back( item );
    ^
    this->
    cdhit-common.c++:1249:12: note: in instantiation of member function
    'Vector<Sequence *>::Append' requested here
    sequences.Append( seq );
    ^
    /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/vector:685:36: note:
    must qualify identifier to find this declaration in dependent base class
    _LIBCPP_INLINE_VISIBILITY void push_back(const_reference __x);
    ^
    In file included from cdhit-common.c++:28:
    ./cdhit-common.h:95:4: error: use of undeclared identifier 'push_back'
    push_back( item );
    ^
    this->
    cdhit-common.c++:1897:16: note: in instantiation of member function
    'Vector<int>::Append' requested here
    clusters[id].Append( k );
    ^
    /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/vector:685:36: note:
    must qualify identifier to find this declaration in dependent base class
    _LIBCPP_INLINE_VISIBILITY void push_back(const_reference __x);
    ^
    12 warnings and 4 errors generated.
    make: *** [cdhit-common.o] Error 1
    :cd-hit-v4.5.5-2011-03-31 $

Latest Articles

Collapse

  • seqadmin
    Essential Discoveries and Tools in Epitranscriptomics
    by seqadmin




    The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
    Yesterday, 07:01 AM
  • seqadmin
    Current Approaches to Protein Sequencing
    by seqadmin


    Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
    04-04-2024, 04:25 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
58 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
54 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
45 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-04-2024, 09:00 AM
0 responses
55 views
0 likes
Last Post seqadmin  
Working...
X