Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • 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

                      http://kevin-gattaca.blogspot.com/2010/03/compiling-bfast-and-dnaa-in-centos-54.html
                      http://kevin-gattaca.blogspot.com/2010/03/compiling-bfast-and-dnaa-in-centos-54.html


                      kamal

                        Comment

                        Previous template Next

                        Latest Articles

                        Collapse
                        • SEQadmin2
                          16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
                          by SEQadmin2





                          NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...
                          10-30-2026, 06:46 AM
                        • SEQadmin2
                          Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
                          by SEQadmin2



                          Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

                          Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating                          ...
                          10-14-2026, 09:55 AM
                        View All

                        ad_right_rmr

                        Collapse

                        News

                        Collapse
                        Topics Statistics Last Post
                        Gene Copies Once Dismissed as Junk DNA Shape Animal Adaptation and Human Disease by SEQadmin2
                        Started by SEQadmin2, Yesterday, 07:59 AM
                        0 responses
                        16 views
                        0 reactions
                        		 Last Post SEQadmin2
                        by SEQadmin2
                        Yesterday, 07:59 AM  
                        WashU Medicine Study Verifies Methods for Tracking Genetic Mosaicism by SEQadmin2
                        Started by SEQadmin2, 11-05-2026, 09:25 AM
                        0 responses
                        32 views
                        0 reactions
                        		 Last Post SEQadmin2
                        by SEQadmin2
                        11-05-2026, 09:25 AM  
                        HuBMAP Portal Offers Free Access to Single-Cell Data from Healthy Human Tissues by SEQadmin2
                        Started by SEQadmin2, 11-03-2026, 11:54 AM
                        0 responses
                        47 views
                        0 reactions
                        		 Last Post SEQadmin2
                        by SEQadmin2
                        11-03-2026, 11:54 AM  
                        Genome Sequencing Reveals Large, Repeat-Rich DNA in Trapdoor Spider Named for Stephen Colbert by SEQadmin2
                        Started by SEQadmin2, 10-28-2026, 09:57 AM
                        0 responses
                        172 views
                        0 reactions
                        		 Last Post SEQadmin2
                        by SEQadmin2
                        10-28-2026, 09:57 AM  
                        View All
                        Working...