Hello, I'm currently running some RNA-seq experiment alignments on a server with STAR. After about two hours, looking at the head of the Log.progress.out file, I am getting a result like this:
My total read count for the sample is ~80,000,000 reads. Does this mean that judging by the progress in the 'Read number' column my alignment is going to take over a week? It feels like this is abnormally long. When I submitted the bash script to the queue, the script started as follows:
#!/bin/bash #SBATCH --job-name=star #SBATCH --ntasks=1 #SBATCH --cpus-per-task=16 #SBATCH --time=0-64:00:00 #SBATCH --output=outfile.%j #SBATCH --error=errfile.%j module load STAR/2.7.4 STAR --genomeDir mm39starindex/mm39starindex/index --readFilesIn WTCHG_894903_72185194_1.fastq.gz WTCHG_894903_72185194_2.fastq.gz --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outFileNamePrefix alignments/WTCHG_894903_72185194
Should I have specified a longer time or more CPUs? Any advice will be really appreciated! Many thanks.