I am using the HiCUP pipeline to process my Hi-C data and am having some trouble. I am not sure if the error I am getting is related to the pipeline or my input file and would appreciate if anyone might have any idea of what may be causing this error. The code runs fine on test dataset provided with the pipeline. These are the last few lines of the error message i am getting:
Pairing KO_2_S9_L002_R1_001.map.sam and KO_2_S9_L002_R2_001.map.sam Pairing KO_2_S9_L001_R1_001.map.sam and KO_2_S9_L001_R2_001.map.sam Pairing complete Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input Calls: read.delim -> read.table Execution halted Could not produce hicup_mapper summary bar chart: /scratch/gencore/.local/easybuild/software/gencore_rnaseq/1.0/bin/Rscript /scratch/srm632/HiCUP/HiCUP-master/r_scripts/hicup_mapper_summary.r /scratch/HiCUP/results/ /scratch/HiCUP/results/hicup_mapper_summary_IOQBfKpcjf_21-49-36_25-05-2019.txt: Inappropriate ioctl for device at /scratch/HiCUP/HiCUP-master/hicup_mapper line 240.