I am trying to generate the mouse genome to use for mapping my RNAseq data, however it has been running for over 4 days and still appears to be running. This seems to be too long, so I'm not sure if I have made a mistake or if I should stop the program, or what next.
I am using the Linux command line and have 100 GB free and am allocating 4 cores to run STAR. I used the following command and have gotten as far as it shows below. Now the command line just has a blinking white cursor.
STAR --runMode genomeGenerate --genomeDir /home/riva/Desktop/RNAseqPLN/genomeDir --genomeFastaFiles /home/riva/Desktop/RNAseqPLN/GRCm38.p4.genome.fa --sjdbGTFfile /home/riva/Desktop/RNAseqPLN/gencode.vM10.chr_patch_hapl_scaff.annotation.gtf --sjdbOverhang 100 --runThreadN 4
Oct 06 10:00:10 ..... Started STAR run
Oct 06 10:00:10 ... Starting to generate Genome files
Oct 06 10:00:56 ... starting to sort Suffix Array. This may take a long time...
Oct 06 10:01:09 ... sorting Suffix Array chunks and saving them to disk...