Problem when generating hg38 genome indexes using STAR

Question

[Sara]

I am trying to generate index files for hg38 genome using STAR using this command:

STAR --runThreadN 24 --runMode genomeGenerate --genomeDir /data/star_38/star --genomeFastaFiles hg38.fasta 

the process while running seems to be normal as it is shown here:

STAR --runThreadN 24 --runMode genomeGenerate --genomeDir /data/star_38/star --genomeFastaFiles hg38.fasta
    STAR version: 2.7.9a   compiled: 2021-05-04T09:43:56-0400 vega:/home/dobin/data/STAR/STARcode/STAR.master/source
Dec 28 11:23:53 ..... started STAR run
!!!!! WARNING: Could not move Log.out file from ./Log.out into /data/star_38/star/Log.out. Will keep ./Log.out

Dec 28 11:23:53 ... starting to generate Genome files
Dec 28 11:25:23 ... starting to sort Suffix Array. This may take a long time...
Dec 28 11:25:50 ... sorting Suffix Array chunks and saving them to disk...

Killed

I tried different locations to make sure it's not due to memory but got the same error. do you know what the problem could be?

[ATpoint]

I tried different locations to make sure it's not due to memory

This statement makes little sense. Disk location (is that what you mean?) has nothing to do with memory. What is on the machine the output of free -hm?

[Sara]

ATpoint here is the output:

              total        used        free      shared  buff/cache   available
Mem:           125G         11G         15G        510M         98G        112G
Swap:          8.0G        2.7G        5.3G

[cpad0112]

can you try this along with other parameters: --limitGenomeGenerateRAM 100000000000 (100 gb) . Make sure that you have write permissions to the index folder and enough HDD space.

[Sara]

@cpad0112, I got the same error!

[GenoMax]

Could not move Log.out file from ./Log.out into /data/star_38/star/Log.out.

This indicates that you are not able to write to /data/star_38 using the account this job is running under. That is the location you have chosen to put the index in.

[cpad0112]

Hi Sara try furnishing gtf file for your reference build and retry the command.(--sjdbGTFfile <input.gtf>)