Running rMATS on HPC

[FarzanehRah]

Hi,

I ran rMATS on an HPC cluster, and there are two versions available as modules: rmats/4.1.2 and rmats/4.1.1. I also installed v4.3.0 from GitHub on the cluster (our clusters do not support conda). However, I’m encountering the same issue with all three versions:

traceback (most recent call last):
  File "~/rmats-turbo-master/rMATS_P/FDR.py", line 53, in <module>
    ifile = open(sys.argv[1]); title = ifile.readline()
FileNotFoundError: [Errno 2] No such file or directory: '../../output_11_24_comparison2/tmp/JC_SE/rMATS_result_P-V.txt'
paste: ../../output_11_24_comparison2/tmp/JC_SE/rMATS_result_FDR.txt: No such file or directory
........

I tried using the same versions of dependencies mentioned in the documentation, but for some, I wasn't able to use the specified versions (e.g., python/3.8.10 instead of python/3.6.12, proj4-fortran/1.0 ( proj4-fortran is a f77 and f90 wrappers for proj4) instead of gfortran (Fortran 77)). I am getting this error when running the following command (v4.3.0):

gdb ~/rmats-turbo-master/rMATS_C/rMATSexe 
r -i ../../output_11_24_comparison2/JC.raw.input.SE.txt -t 1 -o ../../output_11_24_comparison2/tmp/JC_SE/rMATS_result_P-V.txt -c 0.0001

~/rmats-turbo-master/rMATS_C/rMATSexe: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
[Inferior 1 (process 1718094) exited with code 0177]

Is there any solution to this on HPC?

Thank you!

[EricKutschera]

From ~/rmats-turbo-master/rMATS_C/rMATSexe: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory It looks like you were able to compile rMATSexe and it is looking for a specific version of libgfortran.so. The build uses -lgfortran and I think it would have needed to find libgfortran.so somewhere on your system for the build to succeed: https://github.com/Xinglab/rmats-turbo/blob/v4.3.0/rMATS_C/Makefile#L12 Maybe you have libgfortran.so.3 and just need to set LD_LIBRARY_PATH to let it find it

You could try installing gfortran and then building from the source code again: https://gcc.gnu.org/wiki/GFortran

[FarzanehRah]

Thank you so much for your quick reply, I really appreciate it. I will try installing gfortran and building rmats from source code again.