Ubuntu 16 missing shared libraries

[Gy. Ákos Ákos]

Dear All,

I was planning to use rMATS, under Ubuntu 16.04.

I have installed the prebuilt  versions, selected the proper built (UCS4 in case of Ubuntu 16.04).

Everything seemed to be fine when i ran the program, however when the software started to run the "Statistical part" , the following errors appeared and also the statistics were missing.

Done processing each gene from dictionary to compile AS events
Found 5194 exon skipping events
Found 200 exon MX events
Found 0 alt SS events
There are 0 alt 3 SS events and 0 alt 5 SS events.
Found 0 RI events
==========

Running the statistical part.
/home/akos-linux/Programs/rMATS.4.0.1/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/akos-linux/Programs/rMATS.4.0.1/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/tmpze6QZe/JC_SE/rMATS_result_P-V.txt'
paste: /tmp/tmpze6QZe/JC_SE/rMATS_result_FDR.txt: No such file or directory
/home/akos-linux/Programs/rMATS.4.0.1/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/akos-linux/Programs/rMATS.4.0.1/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/tmpze6QZe/JCEC_SE/rMATS_result_P-V.txt'
paste: /tmp/tmpze6QZe/JCEC_SE/rMATS_result_FDR.txt: No such file or directory
/home/akos-linux/Programs/rMATS.4.0.1/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/akos-linux/Programs/rMATS.4.0.1/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/tmpze6QZe/JC_MXE/rMATS_result_P-V.txt'
paste: /tmp/tmpze6QZe/JC_MXE/rMATS_result_FDR.txt: No such file or directory
/home/akos-linux/Programs/rMATS.4.0.1/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/akos-linux/Programs/rMATS.4.0.1/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/tmpze6QZe/JCEC_MXE/rMATS_result_P-V.txt'
paste: /tmp/tmpze6QZe/JCEC_MXE/rMATS_result_FDR.txt: No such file or directory
/home/akos-linux/Programs/rMATS.4.0.1/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/akos-linux/Programs/rMATS.4.0.1/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/tmpze6QZe/JC_A3SS/rMATS_result_P-V.txt'
paste: /tmp/tmpze6QZe/JC_A3SS/rMATS_result_FDR.txt: No such file or directory
/home/akos-linux/Programs/rMATS.4.0.1/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/akos-linux/Programs/rMATS.4.0.1/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/tmpze6QZe/JCEC_A3SS/rMATS_result_P-V.txt'
paste: /tmp/tmpze6QZe/JCEC_A3SS/rMATS_result_FDR.txt: No such file or directory
/home/akos-linux/Programs/rMATS.4.0.1/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/akos-linux/Programs/rMATS.4.0.1/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/tmpze6QZe/JC_A5SS/rMATS_result_P-V.txt'
paste: /tmp/tmpze6QZe/JC_A5SS/rMATS_result_FDR.txt: No such file or directory
/home/akos-linux/Programs/rMATS.4.0.1/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/akos-linux/Programs/rMATS.4.0.1/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/tmpze6QZe/JCEC_A5SS/rMATS_result_P-V.txt'
paste: /tmp/tmpze6QZe/JCEC_A5SS/rMATS_result_FDR.txt: No such file or directory
/home/akos-linux/Programs/rMATS.4.0.1/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/akos-linux/Programs/rMATS.4.0.1/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/tmpze6QZe/JC_RI/rMATS_result_P-V.txt'
paste: /tmp/tmpze6QZe/JC_RI/rMATS_result_FDR.txt: No such file or directory
/home/akos-linux/Programs/rMATS.4.0.1/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/akos-linux/Programs/rMATS.4.0.1/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/tmpze6QZe/JCEC_RI/rMATS_result_P-V.txt'
paste: /tmp/tmpze6QZe/JCEC_RI/rMATS_result_FDR.txt: No such file or directory
The statistical part is done.
Done.

I guess rMATS is looking for some libraries that existed under ubuntu 14 , but became obsolete under version 16.04.
Is there any way to solve this problem under Ubuntu 16.04 to have statistics again?

Thank you for the help.

Regards.

[Shen Shihao]

Ubuntu 16.04 seems to have libgsl.so.19 in the libgsl2 package, instead of libgsl.so.0.

Have you tried to install it manually?

Shihao

[Gy. Ákos Ákos]

Hi,

Thank you for the response.

No , i Did not try to install it manually.
Unfortunately I am not that great in Linux. How do I install manually?

[Shen Shihao]

Try

sudo apt-get install libgsl-dev

On Saturday, December 23, 2017 at 5:18:51 AM UTC-6, Gy. Ákos Ákos wrote:

[Craig Monger]

I am also having this issue and this suggestion did not work for me. Did anybody find any way to fix this yet?

Regards,

Craig

[Naira Naouar]

Hi,

In fact, I don't know if it is a real fix but somehow I managed to have results correct results for the test data so I think it works...
I did install libgsl-dev and like you had the libgsl.so.19 and not the libgsl.so.0 needed for the software
...
So I created a libgsl.so.0 by copying the .19 into .0...
I am pretty sure at some point I might have some trouble but until now, everything was fine :D

So the sudo cp libgsl.so.19  libgsl.so.0 (in the appropriate /usr/local/lib or /usr/lib depending on your install) with admin privilegies (sudo makes it for you) worked for me....

However, I am aware that it might have some impact but until there is some fix in rMATS to take into account the ubuntu 16 new dependencies...


Naïra

[9043...@qq.com]

Hi,

The 4.0 version of rMATS was tested on Ubuntu 14 and it requires lisgls.so.0 for its operation, but it does not support libgsl.so.0 on Ubuntu 16.04. Instead, it uses libgsl2.


Therefore, you need to install libgsl2 first.

You can use the following command:$ sudo apt-get install libgls-dev;

and then find the libgls installation path, command: $ dpkg -L libbgls2

As the picture showing, finding the file 'libgsl.so.19' and its absolute path:

The next step is to copy this file to the /usr/lib directory; $ sudo cp /usr/lib/x86_64-linux-gun/libgsl.so.19 /usr/lib/libgsl.so.0

Update dynamic library files.
$ sudo ldconfig

Finally run your script. rmats.py ........


I think it works。

[Roman Spurdo]

You can download & install this lib manually.
https://packages.ubuntu.com/trusty/amd64/libgsl0ldbl/download
Use sudo dpkg -i %lib% for installing.

[Ittai Muller]

what did your statistical output show? mine doesn't show anything.

all files are still empty except for the fromGTF files.

[Juncheng Lin]

I also got empty files except for the fromGTFs. 

[Richard A]

Hi,

Just to confirm. I managed to get rMATS to run on Ubuntu 18.04 after receiving the same error at the statistical calculation. All I did was download the package below, double-click on it and it installed fine. The correct library files were correctly, and automatically, installed in the usr/bin directory.

Kind regards,

Richard

[mmmg...@gmail.com]

Hi, mine is empty too. Have you solved this problem? 

在 2018年9月14日星期五 UTC+8下午4:35:14，Juncheng Lin写道：

[Shihao Shen]

Hi,

If you can run the program, but the results are empty. It may be caused by a bam file parsing bug.

We have noticed that the bamtools library rMATS used may have parsing issues for some bam file formats. 

We are distributing a beta version of rMATS trying to resolving this and output more information about each bam file for debug. 

The beta version resolved a parsing issues caused by misreading the NH tag.

https://sourceforge.net/projects/rnaseq-mats/files/MATS/beta/rMATS.4.0.3beta.tgz/download

(USC4 only, please let me know if you need USC2)

Could you please try the beta version and let us know the output?

Thanks,

Shihao