rMATs error: unrecoginzed parameter name "genomeType" in input "genomeParameters.txt"

[Yan Zhou]

Hi, Eric and Group,

I'm new to rMATs for splicing analysis. I have mouse genome GRCm39 indexed by STAR/2.7.10b; rMATs was installed by "conda install bioconda::rmats";The Conda environment were configured with no error. But when running rMATs I got errors.  The command I have used and the error as below: 

rmats.py --s1 s1.txt  --s2 s2.txt  --gtf GRCm39.gtf  --bi GRCm39/star_index  -t paired --readLength 100 --nthread 16 --od Comp1  --tmp tmp_output_Comp1

mapping the first sample

mapping sample_0, Raw/Ctrl_NT.1_R1.fastq.gz Raw/Ctrl_NT.1_R2.fastq.gz is done with status 102

error in mapping sample_0, Raw/Ctrl_NT.1_R1.fastq.gz Raw/Ctrl_NT.1_R2.fastq.gz: 102

error detail: Jul 28 14:07:58 ..... started STAR run

Jul 28 14:07:58 ..... loading genome

EXITING: FATAL INPUT ERROR: unrecoginzed parameter name "genomeType" in input "genomeParameters.txt"

SOLUTION: use correct parameter name (check the manual)

Jul 28 14:07:58 ...... FATAL ERROR, exiting

Can you help me to take a look and let me know what's causing the error? Thank you!

Best,

Yan

[kutsc...@gmail.com]

When rMATS is run with --s1 it will run STAR to align the reads: https://github.com/Xinglab/rmats-turbo/blob/v4.3.0/rmats.py#L66

The error is from STAR. This issue from the STAR github suggests that the error could be due to using one version of STAR to create the index (--bi GRCm39/star_index) and then a different STAR version when running from rMATS: https://github.com/alexdobin/STAR/issues/1221

In the --tmp directory there should be a file like {date}_bam1_1/Log.out that should include the STAR version. You could use that version of STAR to create a new --bi index

Eric

[Yan Zhou]

Thank you, Eric! this fixed the problem.

[Yan Zhou]

Hi,Eric,

I finished the rMATs. can you help me to take a look at the log file below? there's no event identified. the Used reads for some reason is 0; although the read length is 100bp, it says NOT_EXPECTED_READ_LENGTH: 1088509283; Can you help me to take a look and let me know what you think might be going on? Thank you for your kind help!

 summary.txt 

EventType EventTypeDescription TotalEventsJC TotalEventsJCEC SignificantEventsJC SigEventsJCSample1HigherInclusion SigEventsJCSample2HigherInclusi

on SignificantEventsJCEC SigEventsJCECSample1HigherInclusion SigEventsJCECSample2HigherInclusion

SE skipped exon 0 0 0 0 0 0 0 0

A5SS alternative 5' splice sites 0 0 0 0 0 0 0 0

A3SS alternative 3' splice sites 0 0 0 0 0 0 0 0

MXE mutually exclusive exons 0 0 0 0 0 0 0 0

RI retained intron 0 0 0 0 0 0 0 0

gtf: 10.69956374168396

There are 78298 distinct gene ID in the gtf file

There are 278375 distinct transcript ID in the gtf file

There are 43834 one-transcript genes in the gtf file

There are 1298756 exons in the gtf file

There are 31588 one-exon transcripts in the gtf file

There are 24329 one-transcript genes with only one exon in the transcript

Average number of transcripts per gene is 3.555327

Average number of exons per transcript is 4.665491

Average number of exons per transcript excluding one-exon tx is 5.134663

Average number of gene per geneGroup is 9.397106

statistic: 0.03495025634765625

read outcome totals across all BAMs

USED: 0

NOT_PAIRED: 0

NOT_NH_1: 220144650

NOT_EXPECTED_CIGAR: 10378939

NOT_EXPECTED_READ_LENGTH: 1088509283

NOT_EXPECTED_STRAND: 0

EXON_NOT_MATCHED_TO_ANNOTATION: 0

JUNCTION_NOT_MATCHED_TO_ANNOTATION: 0

CLIPPED: 0

total: 1319032872

outcomes by BAM written to: tmp_output_Comp1/2025-07-29-11_35_51_260777_read_outcomes_by_bam.txt

novel: 443.2769544124603

The splicing graph and candidate read have been saved into tmp_output_Comp1/2025-07-29-11_35_51_260777_*.rmats

save: 0.01794600486755371

loadsg: 0.013273239135742188

==========

Done processing each gene from dictionary to compile AS events

Found 53721 exon skipping events

Found 3988 exon MX events

Found 20935 alt SS events

There are 12218 alt 3 SS events and 8717 alt 5 SS events.

Found 8014 RI events

==========

ase: 1.272951602935791

count: 0.2669370174407959

Processing count files.

Done processing count files.

[kutsc...@gmail.com]

It could be that your read length is not exactly 100. You can look at some individual alignments to pick a value for --readLength. You can also use --variable-read-length if your reads have different lengths

See this post: https://github.com/Xinglab/rmats-turbo/issues/84#issuecomment-831226986

Eric