STAR ERROR: could not open genomeParameters.txt / How to increase RAM?

Question

[salamandra]

I generated genome index in STAR without problem, but when aligning reads to the genome got this error:

EXITING because of FATAL ERROR: could not open genome file /Volumes/PereiraLab/Tania/genomes/ensembl/Homo_sapiens_GRCh38_dna_primary_assembly/with_indices_Homo_sapiens_GRCh38_dna_primary_assembly/genomeParameters.txt
SOLUTION: check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permsissions

I checked in index genome directory and the file genomeParameters.txt does not exist there or in the whole computer.

Then, I saw this post. It seems there was not enough RAM for generating the index genome files, although no error was record. But how can I increase RAM when generating the index?

I'm new bioinformatics so have no idea how to do this. The commands for indexing the genome were:

GENOME=/Volumes/PereiraLab/Tania/genomes/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly/Homo_sapiens.GRCh38.dna.primary_assembly.fa
ANOTATION=/Volumes/PereiraLab/Tania/annotations/ensembl/Homo_sapiens.GRCh38.92/Homo_sapiens.GRCh38.92.gtf
GENOME_Index=/Volumes/PereiraLab/Tania/genomes/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly/with_indices_Homo_sapiens.GRCh38.dna.primary_assembly/
STAR --runThreadN 4 --runMode genomeGenerate --genomeFastaFiles $GENOME --sjdbGTFfile $ANOTATION --sjdbOverhang 99 --genomeDir $GENOME_Index

and for aligning:

READS=/Volumes/PereiraLab/Tania/Reprogram_HSC/Bioinformatics/RNA_seq_analysis_Newmethods/Results/BJs/WithoutAdaptersFastq/1A_ATCACG_withoutadapters.fastq
ALIGNMENTS=/Volumes/PereiraLab/Tania/Reprogram_HSC/Bioinformatics/RNA_seq_analysis_Newmethods/Results/BJs/STAR_alignments/
INDEX=/Volumes/PereiraLab/Tania/genomes/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly/with_indices_Homo_sapiens.GRCh38.dna.primary_assembly
STAR --runThreadN 12 --genomeDir $INDEX --readFilesIn $READS --outFileNamePrefix $ALIGNMENTS --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts

The genome index folder has these files only:

$ cd /Volumes/PereiraLab/Tania/genomes/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly/with_indices_Homo_sapiens.RCh38.dna.primary_assembly 
$ ls
    chrLength.txt           exonGeTrInfo.tab        sjdbList.fromGTF.out.tab
    chrName.txt         exonInfo.tab            sjdbList.out.tab
    chrNameLength.txt       geneInfo.tab            transcriptInfo.tab
    chrStart.txt            sjdbInfo.txt

[GenoMax]

How much RAM do you have? STAR requires 30G+ of free RAM to generate indexes and run alignments for human genome. If you don't have that much RAM available, you will need to find alternate hardware.

Alex Dobin makes pre-made STAR indexes available, if you want to save time. But above limit still applies.

[salamandra]

My pc has 16GB of RAM total. If use the pre-made indexes you suggest do I still need another computer to do the alignment? And to get those indexes I have to download each of the files in the link you provided into the same folder on my pc or just one of them?

[Eric Lim]

Yes. Memory footprint remains relatively large. You might need to try other alternatives, like hisat.

[GenoMax]

Yes you have to get all the files for the build you choose and they will have to be placed in the same folder on your local machine.

[salamandra]

Thanks. just to check: if I have a computer with 4 cores and each has 4GB (16 GB in total), the number I should put in front of the option '--runThreadN' is 4 and not 16...

[GenoMax]

Correct. 16 G is shared by all cores. There is no assignment of 4 G per core.