RAM for genome index with STAR

Question

[Fizzah]

Hello there, I am trying to index Gossypium hirsutum reference genome with STAR but the command stays for 2 days at " starting to sort Suffix Array. This may take a long time...". later I found out this problem is due to RAM allocation. I have 32 GB RAM in total.

1.Please address this issue and tell me how much RAM allocation would be enough for STAR indexing.

1. How can I allocate RAM by giving parameters in the command given below

Note: this the command I used

STAR --runMode genomeGenerate --genomeDir indexes/Gh \
            --genomeFastaFiles /home/pg/Fizzah/reference_genome/genome_assemblies_genome.fasta/ncbi-genomes-2021-12-15/GCF_007990345.1_Gossypium_hirsutum_v2.1_genomic.fna \
            --sjdbGTFfile /home/pg/Fizzah/reference_genome/genome_assemblies_genome.gtf/ncbi-genomes-2021-12-15/GCF_007990345.1_Gossypium_hirsutum_v2.1_genomic.gtf \
            --sjdbOverhang 149 --outFileNamePrefix Gh_RefIndex

[Hamid Ghaedi]

Have you tried --runThreadN? Ref

[jv]

Please share your additional information that has lead you to conclude that this issue is due to RAM allocation.

a previous Biostars post has addressed a similar issue STAR genome generate memory requirements looks like the issue was the input file that was being specified but other answers suggest setting the --limitGenomeGenerateRAM parameter

[jv]

also depending on how large the G. hirsutum genome is, 32 GB may not be enough memory