Question: rMATs error: unknown file type
0
gravatar for tomoya
29 days ago by
tomoya0
tomoya0 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!

software error • 193 views
ADD COMMENTlink modified 28 days ago by WouterDeCoster37k • written 29 days ago by tomoya0

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

ADD REPLYlink written 29 days ago by h.mon24k

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 REPLYlink written 29 days ago by tomoya0

Have you followed the installation guidelines?

ADD REPLYlink written 29 days ago by WouterDeCoster37k

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 REPLYlink modified 29 days ago by WouterDeCoster37k • written 29 days ago by tomoya0

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 REPLYlink written 28 days ago by h.mon24k

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 REPLYlink modified 28 days ago • written 28 days ago by tomoya0

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 REPLYlink written 26 days ago by tomoya0
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