paired-stats output all 0

[bassanio]

Hi,

While I was executing Rmats with the paired-stats option the summary.txt output is having all 0 . Where as when I remove the paired-stats the output has some results

with paired-stats

Code

module purge
module load all
module load rmats/4.1.2

rmats.py \
--s1 Con1.txt \
--s2 Con2.txt \
--gtf /scratch/Reference_Genomes/In_house/Vertebrate_mammalian//HUMAN/Homo_sapiens.GRCh38.84.gtf \
--bi /scratch/user/SRA/INDEX_STAR_2.7.10b/ \
-t paired \
--readLength 150 \
--variable-read-length \
--novelSS \
--nthread 24 --paired-stats \
--od FASTQ_Paired/ \
--tmp FASTQ_Paired

output

EventType   TotalEventsJC   TotalEventsJCEC SignificantEventsJC SigEventsJCSample1HigherInclusion   SigEventsJCSample2HigherInclusion   SignificantEventsJCEC   SigEventsJCECSample1HigherInclusion SigEventsJCECSample2HigherInclusion
SE  0   0   0   0   0   0   0   0
A5SS    0   0   0   0   0   0   0   0
A3SS    0   0   0   0   0   0   0   0
MXE 0   0   0   0   0   0   0   0
RI  0   0   0   0   0   0   0   0

without paired-stats

Code

module purge
module load all
module load rmats/4.1.2

rmats.py \
--s1 Con1.txt \
--s2 Con2.txt \
--gtf /scratch/Reference_Genomes/In_house/Vertebrate_mammalian//HUMAN/Homo_sapiens.GRCh38.84.gtf \
--bi /scratch/user/SRA/INDEX_STAR_2.7.10b/ \
-t paired \
--readLength 150 \
--variable-read-length \
--novelSS \
--nthread 24  \
--od FASTQ/ \
--tmp FASTQ

output

EventType   TotalEventsJC   TotalEventsJCEC SignificantEventsJC SigEventsJCSample1HigherInclusion   SigEventsJCSample2HigherInclusion   SignificantEventsJCEC   SigEventsJCECSample1HigherInclusion SigEventsJCECSample2HigherInclusion
SE  188480  190258  760 395 365 1395    958 437
A5SS    54286   54417   282 230 52  388 338 50
A3SS    83239   83383   325 252 73  415 333 82
MXE 70086   70528   365 198 167 792 466 326
RI  25285   25308   1442    1343    99  1851    1736    115

Sample information

Con1 Sample list:

Trimmed/Sample001_Con1/Sample001_Con1_1PE.fastq.gz:Trimmed/Sample001_Con1/Sample001_Con1_2PE.fastq.gz,Trimmed/Sample023_Con1/Sample023_Con1_1PE.fastq.gz:Trimmed/Sample023_Con1/Sample023_Con1_2PE.fastq.gz,Trimmed/Sample054_Con1/Sample054_Con1_1PE.fastq.gz:Trimmed/Sample054_Con1/Sample054_Con1_2PE.fastq.gz,Trimmed/Sample056_Con1/Sample056_Con1_1PE.fastq.gz:Trimmed/Sample056_Con1/Sample056_Con1_2PE.fastq.gz,Trimmed/Sample073_Con1/Sample073_Con1_1PE.fastq.gz:Trimmed/Sample073_Con1/Sample073_Con1_2PE.fastq.gz,Trimmed/Sample078_Con1/Sample078_Con1_1PE.fastq.gz:Trimmed/Sample078_Con1/Sample078_Con1_2PE.fastq.gz,Trimmed/Sample102_Con1/Sample102_Con1_1PE.fastq.gz:Trimmed/Sample102_Con1/Sample102_Con1_2PE.fastq.gz,Trimmed/Sample111_Con1/Sample111_Con1_1PE.fastq.gz:Trimmed/Sample111_Con1/Sample111_Con1_2PE.fastq.gz,Trimmed/Sample116_Con1/Sample116_Con1_1PE.fastq.gz:Trimmed/Sample116_Con1/Sample116_Con1_2PE.fastq.gz,Trimmed/Sample120_Con1/Sample120_Con1_1PE.fastq.gz:Trimmed/Sample120_Con1/Sample120_Con1_2PE.fastq.gz,Trimmed/Sample123_Con1/Sample123_Con1_1PE.fastq.gz:Trimmed/Sample123_Con1/Sample123_Con1_2PE.fastq.gz

Con2 Sample list:

Trimmed/Sample001_Con2/Sample001_Con2_1PE.fastq.gz:Trimmed/Sample001_Con2/Sample001_Con2_2PE.fastq.gz,Trimmed/Sample023_Con2/Sample023_Con2_1PE.fastq.gz:Trimmed/Sample023_Con2/Sample023_Con2_2PE.fastq.gz,Trimmed/Sample054_Con2/Sample054_Con2_1PE.fastq.gz:Trimmed/Sample054_Con2/Sample054_Con2_2PE.fastq.gz,Trimmed/Sample056_Con2/Sample056_Con2_1PE.fastq.gz:Trimmed/Sample056_Con2/Sample056_Con2_2PE.fastq.gz,Trimmed/Sample073_Con2/Sample073_Con2_1PE.fastq.gz:Trimmed/Sample073_Con2/Sample073_Con2_2PE.fastq.gz,Trimmed/Sample078_Con2/Sample078_Con2_1PE.fastq.gz:Trimmed/Sample078_Con2/Sample078_Con2_2PE.fastq.gz,Trimmed/Sample102_Con2/Sample102_Con2_1PE.fastq.gz:Trimmed/Sample102_Con2/Sample102_Con2_2PE.fastq.gz,Trimmed/Sample111_Con2/Sample111_Con2_1PE.fastq.gz:Trimmed/Sample111_Con2/Sample111_Con2_2PE.fastq.gz,Trimmed/Sample116_Con2/Sample116_Con2_1PE.fastq.gz:Trimmed/Sample116_Con2/Sample116_Con2_2PE.fastq.gz,Trimmed/Sample120_Con2/Sample120_Con2_1PE.fastq.gz:Trimmed/Sample120_Con2/Sample120_Con2_2PE.fastq.gz,Trimmed/Sample123_Con2/Sample123_Con2_1PE.fastq.gz:Trimmed/Sample123_Con2/Sample123_Con2_2PE.fastq.gz

Please let me know on how to fix the same

[EricKutschera]

There may have been an error running the paired model. It should have printed out an error message starting with a line like error in paired model ...: https://github.com/Xinglab/rmats-turbo/blob/v4.3.0/rmats.py#L474

There should also be a log from the command in your --od directory FASTQ_Paired/tmp/JC_SE/rMATS_result_paired.txt

[bassanio]

Hi ,

Thank you for your response. Please find the error in the file

more tmp/*/*result_paired.txt
::::::::::::::
tmp/JC_A3SS/rMATS_result_paired.txt
::::::::::::::
Error in library("PAIRADISE") : there is no package called ‘PAIRADISE’
Execution halted

We installed the mats using the condo/mamba env

[EricKutschera]

The bioconda recipe just runs the main Makefile: https://github.com/bioconda/bioconda-recipes/blob/master/recipes/rmats

It doesn't install PAIRADISE which is an optional dependency only needed for --paired-stats. You can use this code to install PAIRADISE and its dependencies

conda activate {your conda env with rmats 4.3.0}
conda install -c conda-forge -c bioconda r-base=4.3 r-doparallel=1.0 r-foreach=1.5 r-iterators=1.0 r-nloptr=2.0
git clone https://github.com/Xinglab/PAIRADISE.git
Rscript install_r_deps.R paired

based on: https://github.com/Xinglab/rmats-turbo/blob/v4.3.0/paired_model_conda_requirements.txt https://github.com/Xinglab/rmats-turbo/blob/v4.3.0/build_rmats#L91