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  • Error when running ABySS

    I am working on a centOS release 6.6 Linux cluster.

    I have Abyss and open mpi installed in my path:
    Code:
    $ which mpirun
    /c3se/apps/Glenn/openmpi/1.5.4/bin/mpirun
    $ which abyss-pe
    /c3se/NOBACKUP/groups/c3-sysbio/Softwares/glenn/Bioinformatics/abyss/abyss-1.5.2/bin/abyss-pe
    However, when I run abyss I get an error:
    Code:
    $ abyss-pe name=test k=25 in='test1.fastq test2.fastq'
    ABYSS -k25 -q3   --coverage-hist=coverage.hist -s test-bubbles.fa  -o test-1.fa test1.fastq test2.fastq 
    /bin/bash: ABYSS: command not found
    make: *** [test-1.fa] Error 127
    abyss it self seems to be recognized on the machine, since abyss-pe -h prints the options

  • #2
    Originally posted by EricSchon View Post
    /bin/bash: ABYSS: command not found
    Is there an executable with an all capital name ABYSS somewhere? The error message above says that that file is not found. Is that an alias you had to create when you installed the program?

    Comment


    • #3
      Originally posted by GenoMax View Post
      Is there an executable with an all capital name ABYSS somewhere?
      There is no executable called ABYSS in the abyss-1.5.2/bin dir:

      Code:
      $ ll /path/to/abyss/abyss-1.5.2/bin
      -rwxr-xr-x 1 c3-sysbio   975 Apr 27  2012 abyss-adjtodot.pl
      -rwxr-xr-x 1 c3-sysbio  6491 Jun  3  2014 abyss-bloom-dist.mk
      -rwxr-xr-x 1 c3-sysbio  1135 Jun  3  2014 abyss-bowtie
      -rwxr-xr-x 1 c3-sysbio  1192 Jun  3  2014 abyss-bowtie2
      -rwxr-xr-x 1 c3-sysbio  1208 Jun  3  2014 abyss-bwa
      -rwxr-xr-x 1 c3-sysbio  1454 Jun  3  2014 abyss-bwamem
      -rwxr-xr-x 1 c3-sysbio  1362 Jun  3  2014 abyss-bwasw
      -rwxr-xr-x 1 c3-sysbio  1997 Apr 27  2012 abyss-cstont
      -rwxr-xr-x 1 c3-sysbio  2536 Feb  4  2013 abyss-fac.pl
      -rwxr-xr-x 1 c3-sysbio  1280 Jun  3  2014 abyss-fatoagp
      -rwxr-xr-x 1 c3-sysbio  1482 Jun 24  2014 abyss-joindist
      -rwxr-xr-x 1 c3-sysbio    39 Jun  3  2014 abyss-kaligner
      -rwxr-xr-x 1 c3-sysbio 14905 Jun  3  2014 abyss-pe
      -rwxr-xr-x 1 c3-sysbio  4501 Jun  3  2014 abyss-samtoafg
      -rwxr-xr-x 1 c3-sysbio   209 Jun  3  2014 abyss-tabtomd
      -rw-rw-r-- 1 c3-sysbio 15255 Apr 21 09:47 Makefile
      -rw-r--r-- 1 c3-sysbio   294 Jul  8  2014 Makefile.am
      -rw-r--r-- 1 c3-sysbio 14310 Jul 10  2014 Makefile.in
      the same
      Code:
      /bin/bash: ABYSS: command not found
      was refered to in this http://seqanswers.com/forums/showthread.php?t=45216 thread, but it seems like the solution was not found.

      Comment


      • #4
        There should be a file named ABYSS (and ABYSS-P) in your install. Perhaps your compilation was incomplete?

        Comment


        • #5
          re-installing solved the problem... Thanks for answers

          Comment

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