cannot find rmatspipeline

[theokirkland]

I am trying to run rMATS on a Debian system with Parallels

I have downloaded the system and most of the dependencies BUT

(rmats_env) (base) parallels@debian-gnu-linux-12:~/rMATS/rmats-turbo/rmats_env$ pip list
Package Version

---

Cython 3.0.8
pip 24.0
rmats.rmatspipeline 0.0.0
setuptools 69.0.2
wheel 0.42.0

When I try to run rmats the error is that rmats pipeline is not found. Any suggestions?

Thanks Theo

[EricKutschera]

If you ran the build and it was successful then there should be a file like rmatspipeline.so

From the command prompt you posted it looks like you have a conda environment. In that case you could install the rmats package from bioconda:

conda install -c conda-forge -c bioconda rmats=4.2.0

[theokirkland]

Thank you so much for getting back to me. I can open the bam files now I get the error (when trying to run rmats.py) that it cannot do this line 19 from rmatspipeline import run_pipe when I look in the rMATS_pipeline folder I see ***@***.***:~/rMATS/rmats-turbo/rMATS_pipeline$ ls build rmats.rmatspipeline.egg-info unknown-0.0-py31_0.tar.bz2 when I look in ***@***.***:~/rMATS/rmats-turbo/rMATS_pipeline/rmatspipeline$ ls myenv rmatspipeline.cpp rmatspipeline.pyx nogilbam.pxd rmatspipeline_declarations.pxd tcx.h — in summary I can’t find the rmatspipeline package the program is requesting. Do you know what I’m doing wrong? Thanks Theo On Feb 16, 2024, at 7:57 AM, Eric Kutschera ***@***.***> wrote: If you ran the build and it was successful then there should be a file like rmatspipeline.so From the command prompt you posted it looks like you have a conda environment. In that case you could install the rmats package from bioconda: conda install -c conda-forge -c bioconda rmats=4.2.0 — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https://github.com/Xinglab/rmats-turbo/issues/365*issuecomment-1948723053__;Iw!!LLK065n_VXAQ!lHmxRf7GdPHEjbHdlZlg2x9jhf0mo9nn4bDAbdM_zB74j2c5jhNflJ2PM9OJWAssmg6GmMixAxUPjMYHIbJIys50jAI$>, or unsubscribe<https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AGHKSXSZQISY2YXWBE2ZOKDYT56YPAVCNFSM6AAAAABDIJWIGWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNBYG4ZDGMBVGM__;!!LLK065n_VXAQ!lHmxRf7GdPHEjbHdlZlg2x9jhf0mo9nn4bDAbdM_zB74j2c5jhNflJ2PM9OJWAssmg6GmMixAxUPjMYHIbJIh1gdBRE$>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[theokirkland]

Thanks for your help. I tried downloading the program again - here what I got (rmats_env_2) ***@***.***:~$ conda install -c conda-forge -c bioconda rmats=4.2.0 Channels: - conda-forge - bioconda Platform: linux-aarch64 Collecting package metadata (repodata.json): done Solving environment: failed PackagesNotFoundError: The following packages are not available from current channels: - rmats=4.2.0* Current channels: - https://conda.anaconda.org/conda-forge - https://conda.anaconda.org/bioconda To search for alternate channels that may provide the conda package you're looking for, navigate to https://anaconda.org and use the search bar at the top of the page. What am I doing wrong? Thanks Theo On Feb 16, 2024, at 7:57 AM, Eric Kutschera ***@***.***> wrote: If you ran the build and it was successful then there should be a file like rmatspipeline.so From the command prompt you posted it looks like you have a conda environment. In that case you could install the rmats package from bioconda: conda install -c conda-forge -c bioconda rmats=4.2.0 — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https://github.com/Xinglab/rmats-turbo/issues/365*issuecomment-1948723053__;Iw!!LLK065n_VXAQ!lHmxRf7GdPHEjbHdlZlg2x9jhf0mo9nn4bDAbdM_zB74j2c5jhNflJ2PM9OJWAssmg6GmMixAxUPjMYHIbJIys50jAI$>, or unsubscribe<https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AGHKSXSZQISY2YXWBE2ZOKDYT56YPAVCNFSM6AAAAABDIJWIGWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNBYG4ZDGMBVGM__;!!LLK065n_VXAQ!lHmxRf7GdPHEjbHdlZlg2x9jhf0mo9nn4bDAbdM_zB74j2c5jhNflJ2PM9OJWAssmg6GmMixAxUPjMYHIbJIh1gdBRE$>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[EricKutschera]

It looks like the issue is that bioconda doesn't support aarch64 (ARM) yet:
bioconda/bioconda-recipes#23454

You could either wait for bioconda to support aarch64, or you could install the dependencies and run the rMATS build script: https://github.com/Xinglab/rmats-turbo/tree/v4.2.0?tab=readme-ov-file#dependencies

[theokirkland]

I really appreciate your help. You have been incredibly patient. I removed the program and downloaded it again. When I ran build_rmats everything looked good (Skipped the download 1-99%) until [100%] Linking CXX executable /home/parallels/rMATS/rmats-turbo-4.2.0/bamtools/bin/bamtools make[3]: Leaving directory '/home/parallels/rMATS/rmats-turbo-4.2.0/bamtools/build' [100%] Built target bamtools_cmd make[2]: Leaving directory '/home/parallels/rMATS/rmats-turbo-4.2.0/bamtools/build' make[1]: Leaving directory '/home/parallels/rMATS/rmats-turbo-4.2.0/bamtools/build' # rm -f to ignore nonexistent files since *.dylib will only exist for mac cd bamtools/lib; rm -f *.so *.so.* *.dylib cd rMATS_C; make; make[1]: Entering directory '/home/parallels/rMATS/rmats-turbo-4.2.0/rMATS_C' cd lbfgs_scipy && make make[2]: Entering directory '/home/parallels/rMATS/rmats-turbo-4.2.0/rMATS_C/lbfgs_scipy' f77 -c -O2 -c -o lbfgsb.o lbfgsb.f f77 -c -O2 -c -o linpack.o linpack.f 77 -c -O2 -c -o timer.o timer.f make[2]: Leaving directory '/home/parallels/rMATS/rmats-turbo-4.2.0/rMATS_C/lbfgs_scipy' make[1]: Entering directory '/home/parallels/rMATS/rmats-turbo-4.2.0/rMATS_C' cd lbfgs_scipy && make make[2]: Entering directory '/home/parallels/rMATS/rmats-turbo-4.2.0/rMATS_C/lbfgs_scipy' f77 -c -O2 -c -o lbfgsb.o lbfgsb.f f77 -c -O2 -c -o linpack.o linpack.f f77 -c -O2 -c -o timer.o timer.f make[2]: Leaving directory '/home/parallels/rMATS/rmats-turbo-4.2.0/rMATS_C/lbfgs_scipy' cc -I/usr/include -Wall -O2 -msse2 -funroll-loops -fopenmp -o rMATSexe src/main.c src/myfunc.c src/util.c lbfgs_scipy/lbfgsb.o lbfgs_scipy/linpack.o lbfgs_scipy/timer.o -L/usr/lib/aarch64-linux-gnu -lgsl -lgslcblas -lm -lm -lgfortran -lgsl -lgslcblas -lgomp -lblas -llapack cc: error: unrecognized command-line option ‘-msse2’ make[1]: *** [Makefile:40: rMATSexe] Error 1 make[1]: Leaving directory '/home/parallels/rMATS/rmats-turbo-4.2.0/rMATS_C' make: *** [Makefile:6: build] Error 2 Now if I try to run ramts.py it says "from rmatspipeline import run_pipe ModuleNotFoundError: No module named ‘rmatspipeline’" I promise that I will quit at this point if that’s your suggestion - maybe I can find a real Linux machine to run this on. Thanks again, Theo On Feb 19, 2024, at 5:35 AM, Eric Kutschera ***@***.***> wrote: It looks like the issue is that bioconda doesn't support aarch64 (ARM) yet: bioconda/bioconda-recipes#23454<https://urldefense.com/v3/__https://github.com/bioconda/bioconda-recipes/issues/23454__;!!LLK065n_VXAQ!gkuxZ5i_0BCm30opYAJTWv1GNqlZm4LR0J_zetTW6ihhOkeb0iODaqlhVTeoTNZ7OnYN2NKZ63HJkoFpIU1eYE8k3Yg$> You could either wait for bioconda to support aarch64, or you could install the dependencies and run the rMATS build script: https://github.com/Xinglab/rmats-turbo/tree/v4.2.0?tab=readme-ov-file#dependencies<https://urldefense.com/v3/__https://github.com/Xinglab/rmats-turbo/tree/v4.2.0?tab=readme-ov-file*dependencies__;Iw!!LLK065n_VXAQ!gkuxZ5i_0BCm30opYAJTWv1GNqlZm4LR0J_zetTW6ihhOkeb0iODaqlhVTeoTNZ7OnYN2NKZ63HJkoFpIU1e56FjU-Q$> — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https://github.com/Xinglab/rmats-turbo/issues/365*issuecomment-1952469047__;Iw!!LLK065n_VXAQ!gkuxZ5i_0BCm30opYAJTWv1GNqlZm4LR0J_zetTW6ihhOkeb0iODaqlhVTeoTNZ7OnYN2NKZ63HJkoFpIU1eSOnLFYA$>, or unsubscribe<https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AGHKSXRBUX23LVJJPJXVODTYUNIL7AVCNFSM6AAAAABDIJWIGWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNJSGQ3DSMBUG4__;!!LLK065n_VXAQ!gkuxZ5i_0BCm30opYAJTWv1GNqlZm4LR0J_zetTW6ihhOkeb0iODaqlhVTeoTNZ7OnYN2NKZ63HJkoFpIU1edloYsoc$>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[EricKutschera]

-msse2 is a compiler flag that is added here:
https://github.com/Xinglab/rmats-turbo/blob/v4.2.0/rMATS_C/Makefile#L13

That flag is telling the compiler it can try to speed up the code with some special instructions. It's fine to just remove -msse2 from your downloaded copy of that file

[theokirkland]

Fantastic !!! - I got it installed. When I run it I get this (base) ***@***.***:~/rMATS/rmats-turbo-4.2.0$ python rmats.py --b1 ~/H_13.txt --b2 ~/S_2_13.txt --gtf ~/C_pos_2022.gtf -t single --readLength 50 --variable-read-length --nthread 8 --od results_20_20 --tmp TEMP2_20 gtf: 0.1092996597290039 There are 8438 distinct gene ID in the gtf file There are 8655 distinct transcript ID in the gtf file There are 8231 one-transcript genes in the gtf file There are 26958 exons in the gtf file There are 1716 one-exon transcripts in the gtf file There are 1714 one-transcript genes with only one exon in the transcript Average number of transcripts per gene is 1.025717 Average number of exons per transcript is 3.114731 Average number of exons per transcript excluding one-exon tx is 3.637700 Average number of gene per geneGroup is 2.991859 statistic: 0.0004696846008300781 Fail to open /home/parallels/C_pos_ncbi_S2.bam Fail to open /home/parallels/C_pos_ncbi_H2.bam My text files are like this /home/parallels/C_pos_ncbi_S1.bam, /home/parallels/C_pos_ncbi_S2.bam so it’s accepting the first BAM file but not the second. (They all look good when I run samtools quick check.) However, the number of transcripts found is tiny /home/parallels/C_pos_ncbi_H1.bam found 6 times in .rmats files /home/parallels/C_pos_ncbi_H2.bam not found in .rmats files /home/parallels/C_pos_ncbi_S1.bam found 6 times in .rmats files /home/parallels/C_pos_ncbi_S2.bam not found in .rmats files so maybe there is a fundamental problem with my data. Thanks again, Theo On Feb 20, 2024, at 6:24 AM, Eric Kutschera ***@***.***> wrote:

…

-msse2 is a compiler flag that is added here: https://github.com/Xinglab/rmats-turbo/blob/v4.2.0/rMATS_C/Makefile#L13<https://urldefense.com/v3/__https://github.com/Xinglab/rmats-turbo/blob/v4.2.0/rMATS_C/Makefile*L13__;Iw!!LLK065n_VXAQ!mo2KGFvkjJyBCGdTqoJmNED-lmsykvezepmvSwtRfB5lsHYgHfUAIoJZxFPw2538LmWPBRvFlSQ1aDWxGLk4gOtVt1U$> That flag is telling the compiler it can try to speed up the code with some special instructions. It's fine to just remove -msse2 from your downloaded copy of that file — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https://github.com/Xinglab/rmats-turbo/issues/365*issuecomment-1954325532__;Iw!!LLK065n_VXAQ!mo2KGFvkjJyBCGdTqoJmNED-lmsykvezepmvSwtRfB5lsHYgHfUAIoJZxFPw2538LmWPBRvFlSQ1aDWxGLk4hOtEjdE$>, or unsubscribe<https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AGHKSXQPH22H7TQVEO7PK6DYUSW25AVCNFSM6AAAAABDIJWIGWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNJUGMZDKNJTGI__;!!LLK065n_VXAQ!mo2KGFvkjJyBCGdTqoJmNED-lmsykvezepmvSwtRfB5lsHYgHfUAIoJZxFPw2538LmWPBRvFlSQ1aDWxGLk4EBytDLU$>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[EricKutschera]

It looks like the issue may be a space between files in your --b1 and --b2 files. rMATS expects the format to be just a comma ',' between file paths, not comma space ', '

The messages about "found 6 times in .rmats files" or "not found in .rmats files" should go away if you use a new --tmp dir (or remove the contents from previous runs) and rerun with fixed --b1 and --b2 files

[theokirkland]

Thanks again - This worker. Theo On Feb 20, 2024, at 10:21 AM, Eric Kutschera ***@***.***> wrote: It looks like the issue may be a space between files in your --b1 and --b2 files. rMATS expects the format to be just a comma ',' between file paths, not comma space ', ' The messages about "found 6 times in .rmats files" or "not found in .rmats files" should go away if you use a new --tmp dir (or remove the contents from previous runs) and rerun with fixed --b1 and --b2 files — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https://github.com/Xinglab/rmats-turbo/issues/365*issuecomment-1954809736__;Iw!!LLK065n_VXAQ!lizy572ASv5eU_KBkKzb6w99XTVoxsyP3oiM5kegfG7_62u2isMy_gkSyZwP3TWIxUnIdWKNDJO-PL8XWhuXy4FR6Ck$>, or unsubscribe<https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AGHKSXWLX4OPZIS4EMHDLJLYUTSRJAVCNFSM6AAAAABDIJWIGWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNJUHAYDSNZTGY__;!!LLK065n_VXAQ!lizy572ASv5eU_KBkKzb6w99XTVoxsyP3oiM5kegfG7_62u2isMy_gkSyZwP3TWIxUnIdWKNDJO-PL8XWhuX-S-dRZc$>. You are receiving this because you authored the thread.Message ID: ***@***.***>