Error while running rmats.py #409
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Did you build from the source code yourself with Can you post the output from the command you used to build or install rmats? There may have been errors
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I used After this, i used ./rmats command to process my data, which gave me a module not found error. I do not have a file like |
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This is my output along with the command used to build rmats `[msc23104469@compute01 rmats-turbo]$ ./build_rmats --conda Channels:
Package Planenvironment location: /data4/msc23104469/rmats/rmats-turbo/conda_envs/rmats Proceed ([y]/n)? y Preparing transaction: done To activate this environment, use$ conda activate /data4/msc23104469/rmats/rmats-turbo/conda_envs/rmatsTo deactivate an active environment, use$ conda deactivateChannels:
Package Planenvironment location: /data4/msc23104469/rmats/rmats-turbo/conda_envs/rmats added / updated specs: The following packages will be downloaded: The following NEW packages will be INSTALLED: _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge Proceed ([y]/n)? y Downloading and Extracting Packages: Preparing transaction: done -- The C compiler identification is GNU 13.2.0 Update the VERSION argument value or use a ... suffix to tell -- Configuring done (3.2s) rm -f to ignore nonexistent files since *.dylib will only exist for maccd bamtools/lib; rm -f *.so .so. *.dylib |
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That build log seems to show that the There should have been lines like: The error is related to The build creates those lbfgs_scipy files based on this Makefile which mostly uses default behavior: https://github.com/Xinglab/rmats-turbo/blob/v4.3.0/rMATS_C/lbfgs_scipy/Makefile |
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### Thank you for your response. I removed any
rm -f to ignore nonexistent files since *.dylib will only exist for maccd bamtools/lib; rm -f *.so .so. *.dylib ### After edditing the L6 of Makefile to be: `(rmats) [msc23104469@compute01 rmats-turbo]$ ./build_rmats --conda Channels:
Package Planenvironment location: /data4/msc23104469/rmats/rmats-turbo/conda_envs/rmats Proceed ([y]/n)? y Preparing transaction: done To activate this environment, use$ conda activate /data4/msc23104469/rmats/rmats-turbo/conda_envs/rmatsTo deactivate an active environment, use$ conda deactivateChannels:
Package Planenvironment location: /data4/msc23104469/rmats/rmats-turbo/conda_envs/rmats added / updated specs: The following NEW packages will be INSTALLED: _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge Proceed ([y]/n)? y Downloading and Extracting Packages: Preparing transaction: done CMake Deprecation Warning at CMakeLists.txt:12 (cmake_minimum_required): Update the VERSION argument value or use a ... suffix to tell -- Configuring done (0.4s) rm -f to ignore nonexistent files since *.dylib will only exist for maccd bamtools/lib; rm -f *.so .so. *.dylib |
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The main errors seem to be: time.h should be in the standard library and math.h should be found based on In that build log it's using Did you change environment variables after the previous run that caused the compilers not to be found? Also one of the build logs used You could also try getting the built version from conda: If you install from conda then with that environment activated you can run with |
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I opened a new terminal and installed using `rmats) [msc23104469@lugh rmats-turbo]$ ./build_rmats --conda Channels:
Package Planenvironment location: /data4/msc23104469/rmats/rmats-turbo/conda_envs/rmats Proceed ([y]/n)? y Preparing transaction: done To activate this environment, use$ conda activate /data4/msc23104469/rmats/rmats-turbo/conda_envs/rmatsTo deactivate an active environment, use$ conda deactivateChannels:
Package Planenvironment location: /data4/msc23104469/rmats/rmats-turbo/conda_envs/rmats added / updated specs: The following packages will be downloaded: The following NEW packages will be INSTALLED: _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge Proceed ([y]/n)? y Downloading and Extracting Packages: Preparing transaction: done CMake Deprecation Warning at CMakeLists.txt:12 (cmake_minimum_required): Update the VERSION argument value or use a ... suffix to tell -- Configuring done (0.5s) rm -f to ignore nonexistent files since *.dylib will only exist for maccd bamtools/lib; rm -f *.so .so. *.dylib |
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When getting the built version of conda, the following are my commands and outputs After this, I ran rmats on my data and got the following |
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For Here's a similar post with a GLIBC_2.14 error: #150 If you install directly from conda then you can run rmats with just |
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I added I have also added the commands suggested in error: #150 |
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The line for the requirements file would be |
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Thank you for the clarification. I made the changes you suggested and got the following |
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Looks like it didn't find time.h and math.h. Those files should be in the sysroot package at You could try adding Also, that run used |
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I did the changes suggested and got the following |
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The following is my output now |
The conda environment includes blas and lapack. I think the conda compiler would find those libraries automatically, but the gcc from /opt doesn't. You could try editing this line: https://github.com/Xinglab/rmats-turbo/blob/v4.3.0/rMATS_pipeline/setup.py#L9 |
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I apologise, but this did not fix the problem. I am still getting the following error |
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I didn't realize that the errors like Instead, you could try adding an additional argument to: https://github.com/Xinglab/rmats-turbo/blob/v4.3.0/rMATS_C/Makefile#L40 |
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How do i fix the following error? |
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Here's what I suggested for the limits.h and stdio.h errors before: #409 (comment) But actually I think the leading |
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How to fix the following error? |
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Alternatively it seems like replacing |
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I am still getting the following error, after making the suggest changes |
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Your system doesn't seem to have the standard libraries in the expected places or at least From a previous post the With the conda environment activated that has the bioconda version installed you should be able to run just |
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Thank you for your suggestions. I used the docker image available for this, and it worked. |
rmats-turbo/rmats.py
Line 19 in 8601e7b
Traceback (most recent call last):
File "~/rmats/rmats-turbo/rmats.py", line 19, in
from rmatspipeline import run_pipe
ModuleNotFoundError: No module named 'rmatspipeline'
I keep getting this error while running rmats-turbo built using conda. How can I resolve this error?
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