rMATS fails in test run

[FrancescoFerrari88]

I have recently downloaded SEASTAR following instructions. When running the test script, the last part of the pipeline, rMATS, fails. I would like to know how to solve the problem, because I would really like to use the tool you wrote. Attached, you can find the output of the test run and, at then end, the list of packages installed in my conda environment.
output_test_1.txt
Thanks a lot for your support

[travis-m-blimkie]

Hello,
I was also encountering the same issue with SEASTAR, getting the same error at the rMATS step. I seemed to get it working by installing rMATS directly with conda (https://anaconda.org/bioconda/rmats).
Just a note, I did all of my SEASTAR installations in a separate conda environment, since it needed to down/up-grade multiple other packages.
Cheers!

[dbcraig]

I also setup a conda environment, but continued to have rMATS problems like @FrancescoFerrari88
The problem, in my case, was that Python code in rMATS_Unpaired.sh was failing to load numpy due to an MKL (Math Kernel Library) error (found this by removing the redirect of Python to null). Solution was to remove MKL from my conda environment:

conda install nomkl numpy scipy scikit-learn numexpr
conda remove mkl mkl-service

./test_SEASTAR.sh now runs to completion with no significant errors.

Hope this helps others!

[ami-day]

Many thanks for sharing this information - it fixed the errors I was getting too.

[athulmenon]

Hi @travis & @dbcraig,
Can you please share your Conda environment yml file? I am still facing the same error after installing rMats. Thank you.
Best,
Athul

[dbcraig]

This is a very old environment. I haven't used it in several years. Hope it helps.
Doug

environment_seastar.yml.txt

[travis-m-blimkie]

I don't have that environment set up any more, sorry! Hope you get the issue sorted out.

[athulmenon]

Thank you @dbcraig! Still its having some issues.

[athulmenon]

Thank you @travis. Will update if it works.

[mameshibaHub]

Hi.
I have been stacked in part "To perform rMATS package", too!!

Here would be the first Error message
cat: /home/homedir/Downloads/SEASTAR-master/testresult/tmp/RMATS/rMATS_Result.txt: No such file or directory.

I have tried the ways that travis and dbcraig showed in their upper message. But the outcome is the same. I would be happy if you give me some advice.
Also, I am looking forward to some programs to identify and quantify TSS only with RNA-seq data, like SEASTAR.

*My environment
Windows 11
Ubuntu 20.04 (WSL2)

SEASTAR-master
Cufflinks (2.1.0)
samtools (0.1.9)
bedtools (2.27.1)
R (3.0.2)
Anaconda for PYTHON 2.7 (confirmed that Numpy and Scipy worked)
rpy2-2.5.0 (only installed and unpacked to my Download dir under home dir)
bowtie index (made by myself with chr7.fa.gz from UCSC, (https://hgdownload.soe.ucsc.edu/goldenPath/hg19/chromosomes/))

I won't have any command and package for SEASTAR except these.

[athulmenon]

Same issue!

I am now trying out TSSPredator.

[JiachenWang-wjc]

Same issue