FATAL ERROR: Could not open genome file genomeParameters.txt

[MasashiAzuma]

Hello,

I am trying to align some RNA Seq data using the STAR aligner. I get the error of could not open genome file genomeParameters.txt. I have referenced this https://github.com/alexdobin/STAR/issues/292 thread without much success. I am unsure if it's due to my lack of RAM as I am trying to run this on my 8gb RAM laptop.

Additional information: I am also trying to run the MusMuscularis data

Here is my log.out file Log.out.txt

I hope I can gain some insight into this problem.

[alexdobin]

Hi @MasashiAzuma

STAR cannot open /mnt/c/Users/seraz/Research RNA-Seq/GenDir/genomeParameters.txt file that should be present if genome generation was successful. Generally, I do not recommend using paths with spaces in them.

[MasashiAzuma]

Thanks for you quick reply @alexdobin

I'm sorry if my understanding of this is limited as I am not experienced in RNA-seq, but how do I check if the genome generation was successful? Is this referring to my fastq file?

I will fix my file path promptly.

[MasashiAzuma]

Hello @alexdobin

I understand that I have to generate the genome in order to process the files; however, it seems that I have run into another error. I keep encountering the STD::bad_alloc error. I have tried limiting the amount of RAM but I still get the error.

Here is the new log.out Log.out.txt

[alexdobin]

Hi @MasashiAzuma

you need to use the primary dna FASTA from ENSEMBL: https://ftp.ensembl.org/pub/release-108/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz not the cdna FASTA.