Hi, I am new to STAR, and I am trying to align sequences. First, I moved the reference genome into my new project directory; this reference genome was one .fa file that was created after the .fa files of each chromosome were concatenated. I then created a genome directory, called genomeDir, with the path to this reference genome file; my path started from the root of the project directory, although I did try to just give it the direct path to the reference genome, which I don't believe makes a difference. After making the genomeDir file, I was getting an "unable to access and write to file" error, which I learned could be solved by creating a STAR file within the genome directory. The command that I used to actually create the index was
STAR --runMode genomeGenerate --genomeDir genomeDir --genomeFastaFiles hg19.fa --runThreadN 4. This process kept on getting killed without a clear error message, so I tried two things: calling the make command from the STAR source directory and running the commands from the same folder and adding --genomeSAsparseD 2 to the command. None of these worked. Do you know if this is simply a RAM issue, or why else this might be happening?
Thank you so much for your help!