Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • error while installing cufflinks 9.x

    hi, all,
    cufflinks version 0.8.3 works fine on my current system. try to update it,
    i have download the latest version of cufflinks v0.9.3, however, i failed to run the program on my cluster / failed to compile it.

    The x86_64 binary file can be execute directly, however, when i used it on a remote node (the running environment is linux cluster). ERRORS are:

    ./cufflinks: /lib64/libz.so.1: no version information available (required by ./cufflinks)
    cufflinks v0.9.3

    Due to this error, i try to compile cufflinks locally:
    The setting for the configuration is like:

    ./configure --prefix=/home/myuser/cufflinks/ --with-boost=/home/myuser/mylib/boost --with-bam=/home/myuser/mylib

    the boost version is 1.45
    and the structure of the /home/myuser/mylib directory is:
    mylib/lib/libbam.a
    mylib/include/bam/*.h

    The configuration process if fined, however, in compiling phase:
    ...
    bundles.h:546: warning: comparison between signed and unsigned integer expressions
    g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3 -DNDEBUG -pthread -I/home/SCE/jiangwenkai/mylib/boost/include -I/
    home/SCE/jiangwenkai/mylib/include -o cufflinks -L/home/SCE/jiangwenkai/mylib/boost/lib -L/home/SCE/jiangwenkai/mylib/lib cufflinks.o
    libcufflinks.a libgc.a -lboost_thread -lbam -lz
    /home/SCE/jiangwenkai/mylib/lib/libbam.a(bam_import.o): In function `__bam_get_lines':
    /home/SCE/jiangwenkai/samtools-0.1.11/bam_import.c:76: undefined reference to `gzopen64'
    /home/SCE/jiangwenkai/mylib/lib/libbam.a(bam_import.o): In function `sam_open':
    /home/SCE/jiangwenkai/samtools-0.1.11/bam_import.c:442: undefined reference to `gzopen64'
    /home/SCE/jiangwenkai/mylib/lib/libbam.a(bam_import.o): In function `sam_header_read2':
    /home/SCE/jiangwenkai/samtools-0.1.11/bam_import.c:126: undefined reference to `gzopen64'
    collect2: ld returned 1 exit status
    make[2]: *** [cufflinks] Error 1
    make[2]: Leaving directory `/home/SCE/jiangwenkai/RNA_seq/cufflinks-0.9.3/src'
    make[1]: *** [all-recursive] Error 1
    make[1]: Leaving directory `/home/SCE/jiangwenkai/RNA_seq/cufflinks-0.9.3'
    make: *** [all] Error 2

    I have google for this error, someone says that "undefined reference to `gzopen64'" error is caused by zlib settings, our system wide zlib library position is like this:

    ll /usr/local/lib |grep 'libz.'
    -rw-r--r-- 1 root root 135786 2010-11-08 15:34 libz.a
    lrwxrwxrwx 1 root root 13 2010-11-08 15:34 libz.so -> libz.so.1.2.5
    lrwxrwxrwx 1 root root 13 2010-11-08 15:34 libz.so.1 -> libz.so.1.2.5
    -rwxr-xr-x 1 root root 108533 2010-11-08 15:34 libz.so.1.2.5

    ll /usr/lib |grep 'libz.'
    lrwxrwxrwx 1 root root 6 2009-10-13 12:16 libgz.a -> libz.a
    lrwxrwxrwx 1 root root 14 2009-10-13 12:16 libgz.so.1 -> /lib/libz.so.1
    -rw-r--r-- 1 root root 87624 2006-06-16 20:02 libz.a
    lrwxrwxrwx 1 root root 13 2010-12-02 22:32 libz.so -> libz.so.1.2.5
    lrwxrwxrwx 1 root root 13 2010-12-02 22:32 libz.so.1 -> libz.so.1.2.5
    lrwxrwxrwx 1 root root 10 2009-10-13 12:16 libz.so.1-20101202 -> libgz.so.1
    -rwxr-xr-x 1 root root 108533 2010-11-08 15:34 libz.so.1.2.5
    lrwxrwxrwx 1 root root 14 2009-10-13 12:16 libz.so-20101202 -> /lib/libz.so.1

    objdump -T /usr/local/lib/libz.so.1.2.5 | grep gzopen64
    000061e0 g DF .text 00000014 ZLIB_1.2.3.3 gzopen64
    objdump -T /usr/lib/libz.so.1.2.5 | grep gzopen64
    000061e0 g DF .text 00000014 ZLIB_1.2.3.3 gzopen64

    I have try with --with-zlib=/usr/local/ --with-zlib=/usr/local/lib --with-zlib=/usr --with-zlib=/usr/lib --without-zlib, none of these opinions works, all go to the same error.

    does anyone know what is the problem?
    best
    regards!

Latest Articles

Collapse

  • 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
  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM

ad_right_rmr

Collapse

News

Collapse

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