Getting error in running rMATS
1
1
Entering edit mode
5.9 years ago
Reza ▴ 10

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

RNA-Seq software error rMATS alternative splicing • 5.0k views
ADD COMMENT
6
Entering edit mode
5.9 years ago

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

ADD COMMENT
1
Entering edit mode

@Kevin rocks, as usual !

ADD REPLY

Login before adding your answer.

Traffic: 1530 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6