Indexing the reference genome

Question

[Yasemin]

nohup STAR \
  --runMode genomeGenerate \
  --genomeDir /Users/yasi/mockexp/genome/genome_index/ \
  --genomeFastaFiles /Users/yasi/mockexp/genome/GCF_000001405.39_GRCh38.p13_genomic.fna \
  --sjdbGTFfile /Users/yasi/mockexp/genome/genomic.gtf --sjdbOverhang 80 > star_genome_generate.log 2>&1

What I am missing or doing wrong while trying to index the reference genome with STAR?

[GenoMax]

What I am missing or doing wrong while trying to index the reference genome with STAR?

You need to tell us more. The command looks OK. Is the command not working? Are you getting errors?

[Mensur Dlakic]

You didn't tell us the error message or the contents of the log file. Tough to help you without proper information.

[Ram]

Note: Don't use nohup, it interferes with writing to STDOUT/STDERR. Use a proper utility like screen or tmux instead to run a process that you want to protect from interruption. See: https://unix.stackexchange.com/a/192973/135331