Hi Thomas, I am trying to use the epiGBS pipeline you have created. I'm using a computer with CPU: 8, Mem: 64 GB, Disk: 480 GB root. My fastq.gz files have 25Gb each (illumina paired-end, Hi-seq). The demultiplex script runs for more than 12 hours and then gives an error: no space left on the device. It seems to have stoped on "nomatches". Nothing is saved on the output directory. Do you know how much space I would need for this dataset with compressed fastq.gz files with 25Gb each (R1 and R2), in case it is running correctly? Another question: do I need to clean up reads before running the demultiplex script? When should I take out contaminant reads, before or after demultiplexing? Thanks!
Hi Thomas, I am trying to use the epiGBS pipeline you have created. I'm using a computer with CPU: 8, Mem: 64 GB, Disk: 480 GB root. My fastq.gz files have 25Gb each (illumina paired-end, Hi-seq). The demultiplex script runs for more than 12 hours and then gives an error: no space left on the device. It seems to have stoped on "nomatches". Nothing is saved on the output directory. Do you know how much space I would need for this dataset with compressed fastq.gz files with 25Gb each (R1 and R2), in case it is running correctly? Another question: do I need to clean up reads before running the demultiplex script? When should I take out contaminant reads, before or after demultiplexing? Thanks!