I am assembling paired-end RNA-Seq data. Running abyss-pe as follows: ~/downloads/abyss-1.3.4/bin/abyss-pe E=0 n=4 q=10 v=-v k=64 j=12 name=my_lib_name -C my_out_dirr in="<fq1> <fq2>" OVERLAP_OPTIONS='--no-scaffold' SIMPLEGRAPH_OPTIONS='--no-scaffold' MERGEPATHS_OPTIONS='--greedy' mp=''
Running this gives me following error:
which: no mpirun in (<system PATH>)
/bin/bash: mpirun: command not found
make: *** [<my lib>-1.fa] Error 127
I compiled abyss executable --without-mpi but still abyss-pe starts with mpirun. Any idea how to run it without having to use openmpi?
Thanks.
Can you provide how you installed/compiled abyss?
OpenMP and MPI are two different things. Take a look at this thread.
Thanks, st.ph.n. That clarifies a bit. Do you know if there was a way to run abyss-pe without mpirun?