[E::hts_open_format] Failed to open file

[ntsopoul]

Hi,

I am trying to start FindPeaks and I get the following error multiple times till the system crashes: [E::hts_open_format] Failed to open file /Users/tsopoulidis/temp/young_2F.bam

The bam files were generated with cellranger and the path to them is correct.

This is the code:

import bed files (Peak Calling) for young_2F

extdata_path <- getwd() reference.file <- paste0(extdata_path,"/genes.gtf") junctions.file <- paste0(extdata_path,"/junction_files/young_2F_splice_junction_possorted_genome_bam.bed") bamfile <- c(paste0("/Users/tsopoulidis/temp/","young_2F.bam")) whitelist.bc.file <- c(paste0(extdata_path,"/young_2F/filtered_feature_bc_matrix/barcodes.tsv")) peak.output.file <- "young_2F_peaks.txt"

FindPeaks(output.file = peak.output.file, # output filename gtf.file = reference.file, # gene model as a GTF file bamfile = bamfile, # BAM alignment filename. junctions.file = junctions.file, # BED filename of splice junctions exising in BAM file. ncores = 4) # number of cores to use

[ntsopoul]

Ok I figured out the problem: the .bai file was in another folder