Getting error in running rMATS

Question

[Reza]

Hi everyone,

I'm trying to run rMATS to get alternative splicing but encountered some errors.

Errors found:

==========
Done processing each gene from dictionary to compile AS events
Found 14962 exon skipping events
Found 1100 exon MX events
Found 28836 alt SS events
There are 16303 alt 3 SS events and 12533 alt 5 SS events.
Found 25486 RI events
==========

Running the statistical part.
/home/ABZ/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_C/rMATSexe: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory
Traceback (most recent call last):
  File "/home/ABZ/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_P/FDR.py", line 45, in <module>
    ifile=open(sys.argv[1]);title=ifile.readline();
IOError: [Errno 2] No such file or directory: '/tmp/tmpQ7Q7J5/JC_SE/rMATS_result_P-V.txt'
paste: /tmp/tmpQ7Q7J5/JC_SE/rMATS_result_FDR.txt: No such file or directory
/home/ABZ/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_C/rMATSexe: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory
Traceback (most recent call last):
  File "/home/ABZ/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_P/FDR.py", line 45, in <module>
    ifile=open(sys.argv[1]);title=ifile.readline();
IOError: [Errno 2] No such file or directory: '/tmp/tmpQ7Q7J5/JCEC_SE/rMATS_result_P-V.txt'
paste: /tmp/tmpQ7Q7J5/JCEC_SE/rMATS_result_FDR.txt: No such file or directory
/home/ABZ/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_C/rMATSexe: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory
Traceback (most recent call last):
  File "/home/ABZ/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_P/FDR.py", line 45, in <module>
    ifile=open(sys.argv[1]);title=ifile.readline();
IOError: [Errno 2] No such file or directory: '/tmp/tmpQ7Q7J5/JC_MXE/rMATS_result_P-V.txt'
paste: /tmp/tmpQ7Q7J5/JC_MXE/rMATS_result_FDR.txt: No such file or directory
/home/ABZ/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_C/rMATSexe: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory
Traceback (most recent call last):
  File "/home/ABZ/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_P/FDR.py", line 45, in <module>
    ifile=open(sys.argv[1]);title=ifile.readline();
IOError: [Errno 2] No such file or directory: '/tmp/tmpQ7Q7J5/JCEC_MXE/rMATS_result_P-V.txt'
paste: /tmp/tmpQ7Q7J5/JCEC_MXE/rMATS_result_FDR.txt: No such file or directory
/home/ABZ/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_C/rMATSexe: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory
Traceback (most recent call last):
  File "/home/ABZ/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_P/FDR.py", line 45, in <module>
    ifile=open(sys.argv[1]);title=ifile.readline();
IOError: [Errno 2] No such file or directory: '/tmp/tmpQ7Q7J5/JC_A3SS/rMATS_result_P-V.txt'
paste: /tmp/tmpQ7Q7J5/JC_A3SS/rMATS_result_FDR.txt: No such file or directory
/home/ABZ/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_C/rMATSexe: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory
Traceback (most recent call last):
  File "/home/ABZ/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_P/FDR.py", line 45, in <module>
    ifile=open(sys.argv[1]);title=ifile.readline();
IOError: [Errno 2] No such file or directory: '/tmp/tmpQ7Q7J5/JCEC_A3SS/rMATS_result_P-V.txt'
paste: /tmp/tmpQ7Q7J5/JCEC_A3SS/rMATS_result_FDR.txt: No such file or directory
/home/ABZ/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_C/rMATSexe: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory
Traceback (most recent call last):
  File "/home/ABZ/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_P/FDR.py", line 45, in <module>
    ifile=open(sys.argv[1]);title=ifile.readline();
IOError: [Errno 2] No such file or directory: '/tmp/tmpQ7Q7J5/JC_A5SS/rMATS_result_P-V.txt'
paste: /tmp/tmpQ7Q7J5/JC_A5SS/rMATS_result_FDR.txt: No such file or directory
/home/ABZ/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_C/rMATSexe: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory
Traceback (most recent call last):
  File "/home/ABZ/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_P/FDR.py", line 45, in <module>
    ifile=open(sys.argv[1]);title=ifile.readline();
IOError: [Errno 2] No such file or directory: '/tmp/tmpQ7Q7J5/JCEC_A5SS/rMATS_result_P-V.txt'
paste: /tmp/tmpQ7Q7J5/JCEC_A5SS/rMATS_result_FDR.txt: No such file or directory
/home/ABZ/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_C/rMATSexe: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory
Traceback (most recent call last):
  File "/home/ABZ/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_P/FDR.py", line 45, in <module>
    ifile=open(sys.argv[1]);title=ifile.readline();
IOError: [Errno 2] No such file or directory: '/tmp/tmpQ7Q7J5/JC_RI/rMATS_result_P-V.txt'
paste: /tmp/tmpQ7Q7J5/JC_RI/rMATS_result_FDR.txt: No such file or directory
/home/ABZ/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_C/rMATSexe: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory
Traceback (most recent call last):
  File "/home/ABZ/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_P/FDR.py", line 45, in <module>
    ifile=open(sys.argv[1]);title=ifile.readline();
IOError: [Errno 2] No such file or directory: '/tmp/tmpQ7Q7J5/JCEC_RI/rMATS_result_P-V.txt'
paste: /tmp/tmpQ7Q7J5/JCEC_RI/rMATS_result_FDR.txt: No such file or directory
The statistical part is done.

Can anybody suggest me how to fix this error?

Thanks

Answer 1

[Kevin Blighe]

According to the Google Groups thread, the issue relates to the fact that rMATS was developed on Ubuntu 14.04 whilst, I am guessing, you are using Ubuntu 16.04 (like me).

I was able to reproduce your error with rMATS:

rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_C/rMATSexe
rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_C/rMATSexe: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory

The solution is:

1, install libgsl libraries

sudo apt-get install libgsl-dev

2, create a link between the 16.04 library file with that expected by rMATS

sudo ln /usr/lib/x86_64-linux-gnu/libgsl.so.19 /usr/lib/x86_64-linux-gnu/libgsl.so.0

3, run rMATS

rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_C/rMATSexe
number of thread=1; input file=input.txt; output folder=.; cutoff=0.0001;
Total Wallclock time taken 0 seconds 0 milliseconds
Wallclock time per thread taken 0 seconds 0 milliseconds

Kevin

[Ömer An]

@Kevin rocks, as usual !