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RNA indexing using STAR error

Hi, I am trying to index using STAR for reference genome but it is showing me this error repeatedly. I have checked the permissions and it is executable.

*EXITING because of INPUT ERROR: could not open genomeFastaFile: /home/sj384/hg38genome/GCA_000001405.15_GRCh38_genomic.fa
Mar 06 22:33:51 ...... FATAL ERROR, exiting*

My code is:

#Loading the STAR module
module load star

#Defining the path to the genome fasta file
genome_fasta_file="/home/sj384/hg38genome/humangenome.fa" #GCA_000001405.15_GRCh38_genomic.fa original file name 

#Defining the path to the annotation file (GTF format)
annotation_file="/home/sj384/hg38genome/hg38.refGene.gtf"

# output directory path
cd /scratch/sctnbc/sj384/hg38refg

#Main indexing
STAR --runThreadN 16 \
     --runMode genomeGenerate \
     --genomeDir /scratch/sctnbc/sj384/hg38refg \
     --genomeFastaFiles "$genome_fasta_file" \
     --sjdbGTFfile "$annotation_file" \
     --sjdbOverhang 100

Could someone please help me with this?

rna-seq star
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updated by Ram Ram • written by Shay • Shay

Looks like you either re-named the file after creating the code above or simply used the wrong the name.

Error says /home/sj384/hg38genome/GCA_000001405.15_GRCh38_genomic.fa file does not exist/is not readable. But your code is referring to /home/sj384/hg38genome/humangenome.fa name.

• 0 views • link
written by GenoMax GenoMax

Sorry, I changed the name after the error message. I ran it again and the same error pops up.

EXITING because of INPUT ERROR: could not open genomeFastaFile: /home/sj384/hg38genome/humangenome.fa
Mar 06 23:09:45 ...... FATAL ERROR, exiting
• 0 views • link
updated by Ram Ram • written by Shay • Shay

Can you make sure the file has data in it by posting output of head -4 humangenome.fa? Is the file of expected size? Human genome fasta file should be about 3 GB in size.

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written by GenoMax GenoMax

The size is 3.2GB

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written by Shay • Shay

1 answer

There is a chance that your home directory (where this genome is stored) is not available from worker nodes where you are submitting this job. Can you move the file to genomeDir /scratch/sctnbc/sj384/ and try from there?

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written by GenoMax GenoMax

I think that was the issue! It managed to work after being transferred to genomeDir /scratch/sctnbc/sj384 but the log.out file seems rather short. Is this normal?

Thank you so much for your help!

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written by Shay • Shay

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