STAR Indexing Diference for Small and Large Genome File Output I have a quick doubt on the output of the Genome Indexing, I have used the STAR program along with genome .fasta file and GFF file.

Genome size is 3GB, here is the file output

chrLength.txt
chrNameLength.txt
chrName.txt
chrStart.txt
genomeParameters.txt


I have another small Genome 60MB in size, I did the genome indexing, here is the file output

chrLength.txt
chrNameLength.txt
chrName.txt
chrStart.txt
exonGeTrInfo.tab
exonInfo.tab
geneInfo.tab
Genome
genomeParameters.txt
SA
SAindex
sjdbInfo.txt
sjdbList.fromGTF.out.tab
sjdbList.out.tab
transcriptInfo.tab


My point here is that, why I got the extra information for my small genome size, but I didn't get the same for the big size genome. I do apply the same procedure for the both.

here is the below information. Only difference I made for the large Genome size is (--sjdbOverhang 99 --genomeChrBinNbits 15) to reduce the memory, but the rest of things are same for small genome.

#!/bin/bash
NUM_THREADS=12
mkdir DB
STAR --runMode genomeGenerate --genomeDir DB \
    --runThreadN $NUM_THREADS \
    --genomeFastaFiles XL9_2.fa \
    --sjdbGTFfile XENLA_Frog.gtf+gff3 \
    --sjdbOverhang 99 \
    --genomeChrBinNbits 15


Could anyone give an idea, why there is different, I am new to this field, so I am wondering about the difference in this.

Thanks in advance.

Cheer
San
You didn't get extra information with the small genome, the index for the larger one just wasn't made. My guess is that you ran out of RAM. For mammalian sized genomes ensure you have at least 30GB of RAM, likely more like 60GB. Also, make sure to look for error messages.