Hi,

In my abyss-pe command line, I use "np=10" since I am running abyss-mpi. At the mapping stag in which abyss-pe calls abyss-map, it work only on on thread!

Here is the leading part of the abyss-pe command:

    $ /usr/local/abyss/1.9.0/bin/abyss-pe np=10 k=64 name=AbC -d \

Here is the abyss-map command that abyss-pe executes:

```
$ abyss-map -j1 -l64 P_R2_001_val_2.fq.gz P_R1_001_val_1.fq.gz Ab10_10-3.fa \
  | abyss-fixmate -l64 -h pe150_1-3.hist \
  | sort -snk3 -k4 \
  | DistanceEst -j1 -k64 -l64 -s200 -n10 -o pe150_1-3.dist pe150_1-3.hist
```

Is there any way to make abyss-pe run abyss-map multi-threaded, i.e j10 for instance? I thought that abyss-pe will always make `j=np`, but this is not true. I am using abyss v1.9.

Thanks
Hi malabady,

Use `j=10` in addition to `np=10` in your abyss-pe command line.

`j` specifies the number of threads to use, for programs in the ABySS pipeline that are multithreaded (e.g. `abyss-map`). `np` specifies the number of MPI processes (a.k.a. "MPI ranks") to `ABYSS-P`, which is the first stage of the ABySS pipeline. `ABYSS-P` is the only program in the assembly pipeline that uses MPI and it is not multithreaded. The remainder of the pipeline runs on only a single machine.

Edit: fix typo and clarify that `ABYSS-P` is not multithreaded.

Edit 2: Correction: Use `j=10` *in addition to* `np=10`. Mention that the later stages of the pipeline only run on a single cluster node.