rMATs error: unknown file type

Question: rMATs error: unknown file type

6 months ago by

tomoya • 0

tomoya • 0 wrote:

I'm trying to analyzing splicing pattern between two groups. However, I have some errors when I try to test the below lines;

python rmats.py -b1 condition1_1.bam , condition1_2.bam -b2 condition2_1.bam , condition2_2.bam -gtf ASM223467v1.94.gtf -o rMATS -t paired -len 101 -c 0.0001 -analysis U -libType fr-firststrand -novelSS 1

And the error I got is below:

Traceback (most recent call last): File "rmats.py", line 17, in <module> from rmatspipeline import run_pipe ImportError: dlopen(/Users/rmatspipeline.so, 2): no suitable image found.  Did find: /Users/rmatspipeline.so: unknown file type, first eight bytes: 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00
/Users/rmatspipeline.so: unknown file type, first eight bytes: 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00

I would be most grateful if you could give me some advice. Thanks!

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modified 6 months ago by WouterDeCoster ♦ 40k • written 6 months ago by tomoya • 0

What is your operating system, MacOsX? How did you install rMATS?

ADD REPLY • link written 6 months ago by h.mon ♦ 27k

Thank you for your reply! Yes, MacOsX and I just put the rMATS files in the working directory. I think I didn't understand the basic things.

ADD REPLY • link written 6 months ago by tomoya • 0

Have you followed the installation guidelines?

ADD REPLY • link written 6 months ago by WouterDeCoster ♦ 40k

Thank you for your suggestion. I followed the installation guidelines and found installing gcc@5 seems to be failed. I got the below error:

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
gcc@5: This formula either does not compile or function as expected on macOS
versions newer than High Sierra due to an upstream incompatibility.
Error: An unsatisfied requirement failed this build.

I'll try to install xcode.

ADD REPLY • link modified 6 months ago by WouterDeCoster ♦ 40k • written 6 months ago by tomoya • 0

gcc@5: This formula either does not compile or function as expected on macOS versions newer than High Sierra due to an upstream incompatibility.

You may try with a newer gcc, try installing gcc-6:

brew install gcc@6

Then proceed with rMATS install.

ADD REPLY • link written 6 months ago by h.mon ♦ 27k

I tried gcc-6, however, I still have the same error (My operating system is macOS ver. 10.14.2). I also installed lumpy, Blas, lapack and gsl again but the result was same. Do I have to do something except moving rMATS.4.0.2 file to working directory for using rMATS correctly?

Also, does python version is important? When I checked my python version, it shows

Python 2.7.3 :: Continuum Analytics, Inc.

ADD REPLY • link modified 6 months ago • written 6 months ago by tomoya • 0

Thank you very much for your kind support! I figured out that rMATS 4.0.2 doesn't support MacOS now. So I decided to use the previous version (rMATS 3.2.5) and it works.

ADD REPLY • link written 6 months ago by tomoya • 0

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