failed building genome index with gffs annotation file

[zhusih...@gmail.com]

Hi,guys,

I've tried to build genome index with commands below:

/opt/software/STAR/bin/Linux_x86_64/STAR --runThreadN 12 --runMode genomeGenerate -genomeDir ./GenomeDir/ --genomeFastaFiles  ../database/Dendrobium.v2.fa --sjdbGTFfile  Dendrobium.gene.new.revise.gff3 --sjdbGTFtagExonParentGene Parent  --sjdbGTFtagExonParentTranscript Parent --sjdbGTFfeatureExon CDS

here is first 10 lines in  my gff3 file:

##gff-version   3

Scaffold100295  GLEAN   gene    386     807     0.784   -       .       ID=Dendrobium_GLEAN_10000751.g;Name=Dendrobium_GLEAN_10000751.g;

Scaffold100295  GLEAN   mRNA    386     807     0.784   -       .       ID=Dendrobium_GLEAN_10000751;Name=Dendrobium_GLEAN_10000751;Parent=Dendrobium_GLEAN_10000751.g;

Scaffold100295  GLEAN   CDS     386     514     .       -       0       ID=Dendrobium_GLEAN_10000751.CDS.1;Name=Dendrobium_GLEAN_10000751.CDS.1;Parent=Dendrobium_GLEAN_10000751;

Scaffold100295  GLEAN   CDS     604     807     .       -       0       ID=Dendrobium_GLEAN_10000751.CDS.2;Name=Dendrobium_GLEAN_10000751.CDS.2;Parent=Dendrobium_GLEAN_10000751;

Scaffold100581  GLEAN   gene    320     682     0.995   +       .       ID=Dendrobium_GLEAN_10000749.g;Name=Dendrobium_GLEAN_10000749.g;

Scaffold100581  GLEAN   mRNA    320     682     0.995   +       .       ID=Dendrobium_GLEAN_10000749;Name=Dendrobium_GLEAN_10000749;Parent=Dendrobium_GLEAN_10000749.g;

Scaffold100581  GLEAN   CDS     320     682     .       +       0       ID=Dendrobium_GLEAN_10000749.CDS.3;Name=Dendrobium_GLEAN_10000749.CDS.3;Parent=Dendrobium_GLEAN_10000749;

Scaffold101385  GLEAN   gene    261     659     1       +       .       ID=Dendrobium_GLEAN_10000744.g;Name=Dendrobium_GLEAN_10000744.g;

Scaffold101385  GLEAN   mRNA    261     659     1       +       .       ID=Dendrobium_GLEAN_10000744;Name=Dendrobium_GLEAN_10000744;Parent=Dendrobium_GLEAN_10000744.g;  

And my error message is like this:

###########

terminate called after throwing an instance of 'std::bad_alloc'

  what():  std::bad_alloc

Is there something I did wrong ? Or STAR just can't applied for gff3 annotation without exon attribution ?

Any thoughts ?

Cheers

[Alexander Dobin]

Hi @zhusihui1992

this error means that STAR run out of RAM.

How much RAM do you have? What is the size of the FASTA file and and the number of scaffolds?

Cheers

Alex