STAR indexing error: terminate called after throwing an instance of 'std::out_of_range'

Question

[khf0008]

Hi all,

This is my first time posting on Biostars, and first time doing any sort of bioinformatics project, so please be gentle! I have searched similar posts but I don't think they answer my question.

I'm using STAR to index the Drosophila genome. I ran the following as a script with 48gb of RAM:

STAR --runMode genomeGenerate --genomeDir /home/aubkhf/diet_mating/test_align --genomeFastaFiles /home/aubkhf/diet_mating/test_align/dmel-all-chromosome-r6.44.fasta --sjdbGTFfile /home/khf/diet_mating/test_align/filtered-dmel-all-r6.44.gtf --sjdbGTFtagExonParentTranscript Parent --sjdbOverhang 71 --runThreadN 2

And get the following error:

 ..... started STAR run
 ... starting to generate Genome files
 ... starting to sort Suffix Array. This may take a long time...
 ... sorting Suffix Array chunks and saving them to disk...
 ... loading chunks from disk, packing SA...
 ... finished generating suffix array
 ... generating Suffix Array index
 ... completed Suffix Array index
 ..... processing annotations GTF
 terminate called after throwing an instance of 'std::out_of_range'
 what():  vector::_M_range_check: __n (which is 0) >= this->size() (which is 0)
 ./index.sh: line 5: 28290 Aborted

I've already removed lines that don't have transcript_id and have tried with multiple files (eg. fasta and .gtf from ENSEMBL, fasta and .gff from Flybase) and neither worked. Any help would be greatly appreciated!

Thanks!

[Ram]

48gb should suffice for Drosophila genome. Have you tried tweaking the sjdbOverhang parameter? Try running STAR without that parameter.

[khf0008]

Same error :( But this time I got a file I haven't gotten before - exonGeTrInfo.tab:

[Ram]

Can you go up in RAM - maybe 64 or even 128 GB?