rMATS.3.0.9 error

[Kavya Kannan]

I get the following error while running rMATS:

Traceback (most recent call last):

  File "RNASeq-MATS.py", line 204, in <module>

    myLen=int(output);

ValueError: invalid literal for int() with base 10: 'samtools: writing to standard output failed: Broken pipe\nsamtools: 100\nerror closing standard output: -1'

Any help with this would be appreciated.

Thanks,

Kavya

[rMATS team]

Hello,

Can you run testRun.sh to confirm the rMATS installation?

Thank you,

-rMATS team

[Kavya Kannan]

I ran testRun.sh, still I am getting the same error. I am getting this error in the rMATS python file. Any reason why this could be happening? The problem seems to arise when BAM files are used.

Thanks,

Kavya

[rmat...@gmail.com]

Getting error from testRun.sh implies the installation was not complete. Please check the installation of pre-requisites (numpy, scipy, and samtools) first.

-Juw Won

[Kavya Kannan]

Thanks for your response. It is running fine now. I loaded a different version of samtools which caused the problem.

[Sneha Shankar]

Hi Kavya, 

Which version of smalls did you use to correct the problem? I am encountering the same error.

[Stephen Floor]

Probably 0.1.19 - for many *seq tools, using the new samtools 1.x versions break everything since they are not backwards-compatible.

[biowa...@gmail.com]

Still getting the same error and tested 5 versions of samtools. Samtools is installed and set in PATH because I use it regularly. "ValueError: invalid literal for int() with base 10: 'samtools: writing to standard output failed: Broken pipe\nsamtools: error closing standard output: -150\n'"

Any help is appreciated

[alor...@uncc.edu]

I'm having the same problem.

Probably if the python dependencies are not installed, we would get an import error. But I will did a little deeper to see if I can find out what is wrong.

Related question: Do you have a favorite way to install -- and use -- python libraries on a system where you're don't have root privileges? (I'm trying to run this on a cluster where I can't install stuff in the standard locations.)

[alor...@uncc.edu]

I had the same problem. Using samtools 0.1.19 instead of 1.1 fixed it :-)