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scottzijiezhang / MeRIPtools

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issue when run countReads #22

Open JeremyQuo opened 1 year ago

JeremyQuo commented 1 year ago

Error in { : task 1 failed - "error in evaluating the argument 'x' in selecting a method for function 'reduce': subscript is out of bounds"

JeremyQuo commented 1 year ago

Reading gtf file to obtain gene model Filter out ambiguous model... Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... Warning in .get_cds_IDX(mcols0$type, mcols0$phase) : some CDS phases are missing or not between 0 and 2 Warning in .get_cds_IDX(mcols0$type, mcols0$phase) : The "phase" metadata column contains non-NA values for features of type exon. This information was ignored. Warning in makeTxDbFromGRanges(gr, metadata = metadata) : The following transcripts were dropped because their exon ranks could not be inferred (either because the exons are not on the same chromosome/strand or because they are not separated by introns): gnl|b0470|mrna.CDS492, gnl|b0484|mrna.CDS507, gnl|b4623|mrna.CDS=4503 OK Gene model obtained from gtf file... counting reads for each genes, this step may takes a few hours.... Hyper-thread registered: TRUE Using 6 thread(s) to count reads in continuous bins... Error in { : task 1 failed - "error in evaluating the argument 'x' in selecting a method for function 'reduce': subscript is out of bounds"

scottzijiezhang commented 1 year ago

It looks like the problem of GTF annotation file. Could be wrong match between chromosome names in the REFERENCE genome and GTF file.