Indexing the Reference Genome is not done in STAR

[helenine]

Hello, I tried to generate ref index using STAR with this code;

_#!/bin/bash

/truba/home/user/STAR-2.7.7a/source/STAR --runThreadN 16
--runMode genomeGenerate
--genomeSAsparseD 2
--limitGenomeGenerateRAM 20000000000
--genomeDir /truba/home/user/index
--genomeFastaFiles /truba/home/user/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa
--sjdbGTFfile /truba/home/user/Homo_sapiens.GRCh38.111.gtf
--genomeSAindexNbases 12_

But it gave error;

-bash-4.2$ ./generate_index.sh
Apr 17 10:17:17 ..... started STAR run
Apr 17 10:17:17 ... starting to generate Genome files
Apr 17 10:21:17 ..... processing annotations GTF
Apr 17 10:21:48 ... starting to sort Suffix Array. This may take a long time...
Apr 17 10:22:00 ... sorting Suffix Array chunks and saving them to disk...
./generate_index.sh: line 11: 73189 CPU time limit exceeded (core dumped) /truba/home/user/STAR-2.7.7a/source/STAR --runThreadN 16 --runMode genomeGenerate --genomeSAsparseD 2 --limitGenomeGenerateRAM 20000000000 --genomeDir /truba/home/user/index --genomeFastaFiles /truba/home/user/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa --sjdbGTFfile /truba/home/user/Homo_sapiens.GRCh38.111.gtf --genomeSAindexNbases 12

And ref is not completed;
Log.out chrName.txt chrStart.txt exonInfo.tab sjdbList.fromGTF.out.tab
chrLength.txt chrNameLength.txt exonGeTrInfo.tab geneInfo.tab transcriptInfo.tab

What should I do?

Thanks.

[Danilo Tatoni]

Read the error message

./generate_index.sh: line 11: 73189 CPU time limit exceeded

If you're inside a HPC unit, you're likely running this command in the login node, which is a bad practice. If not, ask your sysadmin about the walltime limit for a user process. This has nothing to do with STAR.