Hi Ka,
I was not able to assemble the sample data by running `./assemble.sh` in the directory `transabyss-1.5.4/sample_dataset/`, it returns the same error.
Their suggested fix was to check ipv6, and I reinstalled openmpi on linuxbrew to check what the configuration options are.
```
./configure --prefix=/home/cjprybol/.linuxbrew/Cellar/open-mpi/1.10.2 --disable-silent-rules --enable-ipv6 --with-libevent=/home/cjprybol/.linuxbrew/opt/libevent --with-sge
```
As you can see, the ipv6 flag is there, so I guess that's not the issue. Not sure what may or may not be the problem with the other flags.
Because of that linuxbrew openmpi problem, I removed my abyss install from linuxbrew and tried to reinstall it using the openmpi library that was installed by the staff who manage the cluster.
Now I've bypassed the openmpi problem, but now I'm having problems with ABYSS-P. I'm not sure if now I should move over to an Abyss-specific help area, but if so, let me know.
Here are the several ways that I've tried to install abyss, and the errors associated with each. Now, either ABYSS-P cannot be found, or when ABYSS-P can be found, it is unable to find `libibverbs.so.1`. For the github installs, I also ran the procedure but did a `git checkout 1.5.2` to get the version specified in the readme for transabyss, and got the same output, so I've not included those attempts.
I'm happy to try and debug whichever error seems easiest to deal with. Googling the libibverbs.so.1 didn't return anything helpful, which was the error I tried to debug first.
The first line is the method for installation, and the rest of the code blocks are the truncated error messages / transabyss output with the relevant info.
```
brew install --ignore-dependencies abyss
CMD: bash -euo pipefail -c 'abyss-pe --directory=/share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/test.k25 k=25 name=test.k25 E=0 e=1 c=1 j=2 test.k25-1.fa test.k25-1.adj q=3 se="/share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_1.fq.gz /share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_2.fq.gz"'
make: Entering directory `/share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/test.k25'
/share/sw/free/openmpi/1.10.2/gcc/4.8/bin/mpirun -np 1 ABYSS-P -k25 -q3 -e1 -E0 -c1 --coverage-hist=coverage.hist -s test.k25-bubbles.fa -o test.k25-1.fa /share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_1.fq.gz /share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_2.fq.gz
ABYSS-P: error while loading shared libraries: libibverbs.so.1: cannot open shared object file: No such file or directory
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[44272,1],0]
Exit code: 127
--------------------------------------------------------------------------
```
```
brew install --build-from-source --ignore-dependencies abyss
CMD: bash -euo pipefail -c 'abyss-pe --directory=/share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/test.k25 k=25 name=test.k25 E=0 e=1 c=1 j=2 test.k25-1.fa test.k25-1.adj q=3 se="/share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_1.fq.gz /share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_2.fq.gz"'
make: Entering directory `/share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/test.k25'
/share/sw/free/openmpi/1.10.2/gcc/4.8/bin/mpirun -np 1 ABYSS-P -k25 -q3 -e1 -E0 -c1 --coverage-hist=coverage.hist -s test.k25-bubbles.fa -o test.k25-1.fa /share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_1.fq.gz /share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_2.fq.gz
--------------------------------------------------------------------------
mpirun was unable to find the specified executable file, and therefore
did not launch the job. This error was first reported for process
rank 0; it may have occurred for other processes as well.
NOTE: A common cause for this error is misspelling a mpirun command
line parameter option (remember that mpirun interprets the first
unrecognized command line token as the executable).
Node: sh-17-9
Executable: ABYSS-P
--------------------------------------------------------------------------
```
```
cd abyss
./autogen.sh
./configure \
--prefix=/share/PI/euan/cameron
make && make install
CMD: bash -euo pipefail -c 'abyss-pe --directory=/share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/test.k25 k=25 name=test.k25 E=0 e=1 c=1 j=2 test.k25-1.fa test.k25-1.adj q=3 se="/share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_1.fq.gz /share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_2.fq.gz"'
make: Entering directory `/share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/test.k25'
/share/sw/free/openmpi/1.10.2/gcc/4.8/bin/mpirun -np 1 ABYSS-P -k25 -q3 -e1 -E0 -c1 --coverage-hist=coverage.hist -s test.k25-bubbles.fa -o test.k25-1.fa /share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_1.fq.gz /share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_2.fq.gz
--------------------------------------------------------------------------
mpirun was unable to find the specified executable file, and therefore
did not launch the job. This error was first reported for process
rank 0; it may have occurred for other processes as well.
NOTE: A common cause for this error is misspelling a mpirun command
line parameter option (remember that mpirun interprets the first
unrecognized command line token as the executable).
Node: sh-17-9
Executable: ABYSS-P
--------------------------------------------------------------------------
```
```
cd abyss
./autogen.sh
./configure \
--prefix=/share/PI/euan/cameron \
--with-boost=/home/cjprybol/.linuxbrew/Cellar/boost/1.60.0_2/include \
--with-mpi=/share/sw/free/openmpi/1.10.2/gcc/4.8
make && make install
CMD: bash -euo pipefail -c 'abyss-pe --directory=/share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/test.k25 k=25 name=test.k25 E=0 e=1 c=1 j=2 test.k25-1.fa test.k25-1.adj q=3 se="/share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_1.fq.gz /share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_2.fq.gz"'
make: Entering directory `/share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/test.k25'
/share/sw/free/openmpi/1.10.2/gcc/4.8/bin/mpirun -np 1 ABYSS-P -k25 -q3 -e1 -E0 -c1 --coverage-hist=coverage.hist -s test.k25-bubbles.fa -o test.k25-1.fa /share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_1.fq.gz /share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_2.fq.gz
ABYSS-P: error while loading shared libraries: libibverbs.so.1: cannot open shared object file: No such file or directory
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[3147,1],0]
Exit code: 127
--------------------------------------------------------------------------
```