BAI Index file: Error in value[[3L]](cond) : 'Realloc' could not re-allocate memory (125829120 bytes)

[vandesm]

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]

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.
chernolab/ASpli#4 (comment)