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alexdobin / STAR

RNA-seq aligner
MIT License
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Hg38 release 107 #1674

Open david-lazaro-gimeno opened 2 years ago

david-lazaro-gimeno commented 2 years ago

Hi Alex,

I am trying to generate the indexes for the release 107 on the human genome. I have previously used STAR with other species, but did not experienced this problem.

The code:

STAR --runMode genomeGenerate --genomeDir human38/ --genomeFastaFiles Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa --sjdbGTFfile Homo_sapiens.GRCh38.107.gtf --runThreadN 16 /usr/lib/rna-star/bin/STAR-avx2 --runMode genomeGenerate --genomeDir human38/ --genomeFastaFiles Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa --sjdbGTFfile Homo_sapiens.GRCh38.107.gtf --runThreadN 16 STAR version: 2.7.10a compiled: 2022-01-16T16:35:44+00:00 Oct 08 16:12:23 ..... started STAR run Oct 08 16:12:23 ... starting to generate Genome files Oct 08 16:13:02 ..... processing annotations GTF Oct 08 16:13:25 ... starting to sort Suffix Array. This may take a long time... Oct 08 16:13:35 ... sorting Suffix Array chunks and saving them to disk... Oct 08 18:41:52 ... loading chunks from disk, packing SA... Oct 08 18:43:03 ... finished generating suffix array Oct 08 18:43:03 ... generating Suffix Array index Oct 08 18:47:07 ... completed Suffix Array index /usr/bin/STAR: line 7: 9555 Killed "${cmd}" "$@"

The Log.out arrives to indicates in the last line:

Oct 08 18:47:07 ... completed Suffix Array index

I'm using 32 GB RAM 16 threads and have enough space to store all the intermediate files.

alexdobin commented 2 years ago

Hi @david-lazaro-gimeno

you may be running out of memory, for instance, if other apps use some of the RAM. If you cannot get more free RAM, one option to try would be --genomeSAindexNbases 12