I am working on a centOS release 6.6 Linux cluster.
I have Abyss and open mpi installed in my path:
However, when I run abyss I get an error:
abyss it self seems to be recognized on the machine, since abyss-pe -h prints the options
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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