STAR Genome index could not open genomeFastaFile

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2.8 years ago

bs58 ▴ 10

I'm trying to align a genome for the first time ever.

I downloaded the hg38.fa reference genome (from here wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz) and unziped it.

When I try building the Genome index with star using this command:

./STAR/source/STAR --runMode genomeGenerate --runThreadN 24 --genomeDir ./GenomeIndex --genomeFastaFiles hg38.fa

I get the following error:

EXITING because of INPUT ERROR: could not open genomeFastaFile: hg38.fa

I tried downloading the hg38.fa files from other sources (like ENSEMBL) and I get the same error.

What am I doing wrong?

RNAseq genome alignment STAR • 1.7k views

ADD COMMENT • link 2.8 years ago by bs58 ▴ 10

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a) how did you unzip it and b) what is the output of ls?

ADD REPLY • link 2.8 years ago by ATpoint 81k

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a) >tar -wzf hg38.fa.gz

b)

>ls

GenomeIndex STAR

ADD REPLY • link 2.8 years ago by bs58 ▴ 10

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Something is not right. Where is the hg38.fa file? Are you not in the directory where you uncompressed the file. Normally I would use tar -xzf (don't recall what w option is edit: that is just verify option).

ADD REPLY • link 2.8 years ago by GenoMax 141k

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gzip-compressed files should be decompressed with gzip -d, but I am pretty sure, despite not being a STAR user, that it will accept gzipped files, does it?

ADD REPLY • link 2.8 years ago by ATpoint 81k

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The fasta file is in ./GenomeIndex, i thought the option --genomeDir was where I should put the genome path and then --genomeFastaFiles the name of the file. Is it not like this?

ADD REPLY • link 2.8 years ago by bs58 ▴ 10

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