Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Filter
  • Time
  • Show
Clear All
new posts
Previous template Next
  • SWP
    Member
    • Nov 2010
    • 20
    #1

    Dnaa

    Hello-

    Trying to install DNAA here. Following instructions in install I get the following error below. It appears that it's not finding BError.c, however, BError.c is found at the exact path it where it says it can't be found. I'm installing as root, so shouldn't be a permissions problem. Any advice would be awesome, thanks!

    make all-recursive
    make[1]: Entering directory `/home/user/software/dnaa-0.1.2'
    Making all in dkbaseencoding
    make[2]: Entering directory `/home/user/software/dnaa-0.1.2/dkbaseencoding'
    gcc -DHAVE_CONFIG_H -I. -I.. -Wall -g -O2 -pthread -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -m64 -MT dkbaseencoding.o -MD -MP -MF .deps/dkbaseencoding.Tpo -c -o dkbaseencoding.o dkbaseencoding.c
    mv -f .deps/dkbaseencoding.Tpo .deps/dkbaseencoding.Po
    make[2]: *** No rule to make target `../bfast/bfast/BError.c', needed by `BError.o'. Stop.
    make[2]: Leaving directory `/home/user/software/dnaa-0.1.2/dkbaseencoding'
    make[1]: *** [all-recursive] Error 1
    make[1]: Leaving directory `/home/user/software/dnaa-0.1.2'
    make: *** [all] Error 2
    Tags: None
  • nilshomer
    Nils Homer
    • Nov 2008
    • 1283
    #2
    Originally posted by SWP View Post
    Hello-

    Trying to install DNAA here. Following instructions in install I get the following error below. It appears that it's not finding BError.c, however, BError.c is found at the exact path it where it says it can't be found. I'm installing as root, so shouldn't be a permissions problem. Any advice would be awesome, thanks!

    make all-recursive
    make[1]: Entering directory `/home/user/software/dnaa-0.1.2'
    Making all in dkbaseencoding
    make[2]: Entering directory `/home/user/software/dnaa-0.1.2/dkbaseencoding'
    gcc -DHAVE_CONFIG_H -I. -I.. -Wall -g -O2 -pthread -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -m64 -MT dkbaseencoding.o -MD -MP -MF .deps/dkbaseencoding.Tpo -c -o dkbaseencoding.o dkbaseencoding.c
    mv -f .deps/dkbaseencoding.Tpo .deps/dkbaseencoding.Po
    make[2]: *** No rule to make target `../bfast/bfast/BError.c', needed by `BError.o'. Stop.
    make[2]: Leaving directory `/home/user/software/dnaa-0.1.2/dkbaseencoding'
    make[1]: *** [all-recursive] Error 1
    make[1]: Leaving directory `/home/user/software/dnaa-0.1.2'
    make: *** [all] Error 2
    Show an "ls -alh" of your root DNAA directory. Did you make sure to follow the install instructions in INSTALL exactly?

    Comment

    • SWP
      Member
      • Nov 2010
      • 20
      #3
      Originally posted by nilshomer View Post
      Show an "ls -alh" of your root DNAA directory. Did you make sure to follow the install instructions in INSTALL exactly?
      Almost exactly, I already had samtools and bfast installed and in my path, and I added the sym link for bfast.

      Here's the ls...

      drwxr-xr-x 10 501 cdrom 4.0K 2011-04-05 09:09 .
      drwxr-xr-x 15 user users 4.0K 2011-04-05 09:08 ..
      -rw-r--r-- 1 root root 34K 2011-04-05 09:08 aclocal.m4
      -rw-r--r-- 1 501 cdrom 102 2009-09-30 00:04 AUTHORS
      -rw-r--r-- 1 501 cdrom 45K 2009-09-30 00:04 autogen.sh
      drwxr-xr-x 2 root root 4.0K 2011-04-05 09:08 autom4te.cache
      -rw-r--r-- 1 501 cdrom 244 2010-04-28 22:30 ChangeLog
      drwxr-xr-x 2 501 cdrom 4.0K 2011-04-05 09:08 config
      -rw-r--r-- 1 root root 4.2K 2011-04-05 09:09 config.h
      -rw-r--r-- 1 root root 3.9K 2011-04-05 09:08 config.h.in
      -rw-r--r-- 1 501 cdrom 3.8K 2010-08-28 17:42 config.h.in~
      -rw-r--r-- 1 root root 28K 2011-04-05 09:09 config.log
      -rwxr-xr-x 1 root root 34K 2011-04-05 09:09 config.status
      -rwxr-xr-x 1 501 cdrom 198K 2011-04-05 09:08 configure
      -rw-r--r-- 1 501 cdrom 4.0K 2010-08-28 17:42 configure.ac
      -rw-r--r-- 1 501 cdrom 83 2009-09-30 00:04 COPYING
      drwxr-xr-x 3 501 cdrom 4.0K 2011-04-05 09:09 dkbaseencoding
      drwxr-xr-x 2 501 cdrom 4.0K 2011-04-05 09:08 dlib
      drwxr-xr-x 3 501 cdrom 4.0K 2011-04-05 09:09 dqc
      drwxr-xr-x 3 501 cdrom 4.0K 2011-04-05 09:09 dtranslocations
      drwxr-xr-x 3 501 cdrom 4.0K 2011-04-05 09:09 dutil
      drwxr-xr-x 3 501 cdrom 4.0K 2011-04-05 09:09 dwgsim
      -rw-r--r-- 1 501 cdrom 768 2010-04-07 09:21 INSTALL
      -rw-r--r-- 1 501 cdrom 18K 2009-09-30 00:04 LICENSE
      -rw-r--r-- 1 root root 24K 2011-04-05 09:09 Makefile
      -rw-r--r-- 1 501 cdrom 220 2010-04-28 17:03 Makefile.am
      -rw-r--r-- 1 root root 24K 2011-04-05 09:08 Makefile.in
      -rw-r--r-- 1 501 cdrom 28 2009-09-30 00:04 NEWS
      -rw-r--r-- 1 501 cdrom 2.4K 2010-04-07 09:21 README
      -rw-r--r-- 1 root root 23 2011-04-05 09:09 stamp-h1

      Comment

      • nilshomer
        Nils Homer
        • Nov 2008
        • 1283
        #4
        Where are the samtools and bfast symbolic links here? They should be in this directory.

        Comment

        • SWP
          Member
          • Nov 2010
          • 20
          #5
          thanks for your help <fixed>

          Got the sym links in the right place

          Comment

          • masterpiece
            Member
            • Mar 2009
            • 40
            #6
            Hi all,

            I found a blog showing how to set up the dnaa step by step. Hope this can solve the dnaa installation prob. BTW i've install under Fedora13 and its works

            Compiling BFAST and DNAA in CentOS 5.4
            http://kevin-gattaca.blogspot.com/2010/03/compiling-bfast-and-dnaa-in-centos-54.html
            Update finally got it to work. #prereqs GNU Autoconf version 2.59 GNU Automake version 1.9.6 GNU Libtool version 1.5.22 also requires...


            kamal

            Comment

            Previous template Next

            Latest Articles

            Collapse
            • SEQadmin2
              Nine Things a Sample Prep Scientist Thinks About Before Sequencing
              by SEQadmin2


              I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.

              Here are nine questions we think about, in roughly the order they matter, before...
              06-18-2026, 07:11 AM
            • SEQadmin2
              From Collection to Sequencing: Why Sample Preparation and Preservation Define Sequencing Data
              by SEQadmin2


              Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.

              The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
              ...
              06-02-2026, 10:05 AM
            View All

            ad_right_rmr

            Collapse

            News

            Collapse
            Topics Statistics Last Post
            New AI Model Captures Long-Range Genomic Signals to Improve RNA Splice Site Prediction by SEQadmin2
            Started by SEQadmin2, Yesterday, 05:37 AM
            0 responses
            6 views
            0 reactions
            		 Last Post SEQadmin2
            by SEQadmin2
            Yesterday, 05:37 AM  
            Large-Scale Protein Screen Uncovers Hidden Regulators of Alternative Polyadenylation by SEQadmin2
            Started by SEQadmin2, 06-26-2026, 11:10 AM
            0 responses
            16 views
            0 reactions
            		 Last Post SEQadmin2
            by SEQadmin2
            06-26-2026, 11:10 AM  
            Whole-Genome Sequencing Traces Faroe Islands Ancestry to a North Atlantic Founder Population by SEQadmin2
            Started by SEQadmin2, 06-17-2026, 06:09 AM
            0 responses
            51 views
            0 reactions
            		 Last Post SEQadmin2
            by SEQadmin2
            06-17-2026, 06:09 AM  
            Sequencing the Two-Toed Sloth Genome Reveals Jumping Genes Tied to Its Extreme Metabolism by SEQadmin2
            Started by SEQadmin2, 06-09-2026, 11:58 AM
            0 responses
            110 views
            0 reactions
            		 Last Post SEQadmin2
            by SEQadmin2
            06-09-2026, 11:58 AM  
            View All
            Working...