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There should be a file named ABYSS (and ABYSS-P) in your install. Perhaps your compilation was incomplete?
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Originally posted by GenoMax View PostIs there an executable with an all capital name ABYSS somewhere?
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
Code:/bin/bash: ABYSS: command not found
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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
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
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