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estepi / ASpli

Analysis of alternative splicing using RNAseq
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BAI Index file: Error in value[[3L]](cond) : 'Realloc' could not re-allocate memory (125829120 bytes) #21

Open vandesm opened 2 years ago

vandesm commented 2 years ago

Hello I am running into issues with gbcounts. I think the error is stating the BAI index files arent present but not sure. My input is below. I think I have misunderstood the PDF document explaining how to incorporate the BAI files

INPUT

Load all Bamfiles and make into data frame

bamFiles <- c("1 V1H9_24hr_DMSO_Replicate_1.bam", "1 V1H9_24hr_DMSO_Replicate_2.bam", "1 V1H9_24hr_DMSO_Replicate_3.bam", "2 V1H9_48hr_DMSO_Replicate_1.bam", "2 V1H9_48hr_DMSO_Replicate_2.bam", "2 V1H9_48hr_DMSO_Replicate_3.bam", "3 V1H9_24hr_S1_Replicate_1.bam", "3 V1H9_24hr_S1_Replicate_2.bam", "3 V1H9_24hr_S1_Replicate_3.bam", "4 V1H9_48hr_S1_Replicate_1.bam", "4 V1H9_48hr_S1_Replicate_2.bam", "4 V1H9_48hr_S1_Replicate_3.bam")

targets <- data.frame(bam = bamFiles, treatment = c('DMSO', 'DMSO', 'DMSO', 'DMSO', 'DMSO', 'DMSO', 'S1', 'S1', 'S1', 'S1', 'S1', 'S1'), time = c('24', '24', '24', '48', '48', '48', '24', '24', '24', '48', '48', '48' ), stringAsFactors = FALSE) getConditions(targets) gbcounts <- gbCounts(features = features, targets = targets, minReadLength = 100, maxISize = 50000, strandMode= 2)

Output Error Summarizing DMSO_24_FALSE_1 Error in value[3L] : 'Realloc' could not re-allocate memory (125829120 bytes) file: 1 V1H9_24hr_DMSO_Replicate_1.bam index: NA

dzijlmans commented 2 years ago

Hi, I am running into the same issue, though mine is compounded by a different issue altogether. I think you are running into a memory issue, which can be resolved by clearing the unused R memory. https://github.com/chernolab/ASpli/issues/4#issue-1147835246