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Error during rMATS analysis in the nextflow #442

Open Motoufiq opened 5 days ago

Motoufiq commented 5 days ago

Hi,

I am running a nextflow pipeline and rMATS is part of the pipeline. All the steps run well except the rMATS step. How should I overcome this errror? See the attached log below for reference. splicing.log.txt rmats_pairs.txt

EricKutschera commented 5 days ago

It looks like this is the error:

 Error in `$<-.data.frame`(`*tmp*`, "Event_type", value = "CA") :
    replacement has 1 row, data has 0
  Calls: get_postprocessing_table -> $<- -> $<-.data.frame

That error happens after rMATS completes. However it looks like most of the reads were filtered out by rMATS:

USED: 182296943
NOT_PAIRED: 5149055
NOT_NH_1: 256246142
NOT_EXPECTED_CIGAR: 21947137
NOT_EXPECTED_READ_LENGTH: 0
NOT_EXPECTED_STRAND: 0
EXON_NOT_MATCHED_TO_ANNOTATION: 688568009
JUNCTION_NOT_MATCHED_TO_ANNOTATION: 592092171
CLIPPED: 0
total: 1746299457

Only 10% (182296943/1746299457) of reads were USED, while 73% ((688568009 + 592092171) / 1746299457) were filtered for NOT_MATCHED_TO_ANNOTATION

I'm not familiar with the pipeline you are running, but my guess is that either the alignment step in the pipeline used different reference files than what was given to rMATS, or your reads just don't align well

Motoufiq commented 18 hours ago

@EricKutschera thank you. It was something to do with the setting true or false paired_stats. My samples were unpaired.