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gagneurlab / drop

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
MIT License
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Aberrant Splicing: error in 01_1_countRNA_splitReads_samplewise.R, [,j] index out of bounds #514

Closed kdewispelaere closed 4 months ago

kdewispelaere commented 5 months ago

Hi, Thanks for the great package. I'm running into an issue in the Aberrant splicing module. All my samples were analyzed using the nf-core rnaseq pipeline. 1 batch of files is causing problems which are not solved by re-analyzing them. The error lies in the 01_1_countRNA_splitReads_samplewise.R function. This is the error:

Loading required package: rtracklayer
Thu Feb  1 22:17:00 2024: Count split reads for sample: D000002plt
Error in h(simpleError(msg, call)) :
  error in evaluating the argument 'file' in selecting a method for function 'idxstatsBam': error in evaluating the argument 'object' in selecting a method for function 'bamFile': <RangedSummarizedExperiment>[,j] index out of bounds: D000002plt
Calls: countSplitReads ... .class1 -> [ -> [ -> .SummarizedExperiment.charbound
Execution halted
[Thu Feb  1 22:17:00 2024]
Error in rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R:
    jobid: 23
    output: /rds/project/rds-yWykMIGjpDE/data/PATH/Output/processed_data/aberrant_splicing/datasets/cache/raw-local-Platelets/sample_tmp/splitCounts/sample_D000002plt.done
    log: /rds/project/rds-yWykMIGjpDE/data/PATH/.drop/tmp/AS/Platelets/splitReads/D000002plt.Rds (check log file(s) for error message)

config.yaml.txt

I've tried to solve this problem for a while now and wanted to ask for your input on where this might come from? Any help is greatly appreciated.

kdewispelaere commented 4 months ago

This has been solved, there was no tab behind the last column of each row in the sample annotation for these files.