Genome generate BUG: next index is smaller than previous, EXITING

[Zachary Burkett]

Hello all,

I'm running into an error when building a genome index:

star --runThreadN 8 --runMode genomeGenerate --genomeDir /Users/Shared/finch/ensembl/indices --genomeFastaFiles /Users/Shared/finch/ensembl/Taeniopygia_guttata.taeGut3.2.4.dna.toplevel.fa --sjdbGTFfile /Users/Shared/finch/ensembl/Taeniopygia_guttata.taeGut3.2.4.84.chr.gff3 --sjdbGTFtagExonParentTranscript Parent=transcript: --sjdbOverhang 49

Jul 14 12:27:04 ..... Started STAR run

Jul 14 12:27:04 ... Starting to generate Genome files

Jul 14 12:27:27 ... starting to sort  Suffix Array. This may take a long time...

Jul 14 12:27:33 ... sorting Suffix Array chunks and saving them to disk...

Jul 14 12:40:12 ... loading chunks from disk, packing SA...

Jul 14 12:40:50 ... Finished generating suffix array

Jul 14 12:40:50 ... Generating Suffix Array index

BUG: next index is smaller than previous, EXITING

I'm doing this using STAR_2.5.1b on Mac OSX 10.11.5 with 32 gb RAM. I'm not sure how to proceed. Any help is greatly appreciated!

Thank you.

[Alexander Dobin]

Hi Zachary,

this is an internal problem that is quite rare. Please send me the links to the FASTA/GFF3 files you are using and I will try to reproduce it on my system.

Cheers

Alex

[Zachary Burkett]

Hello Alex,

Thanks for the reply. I was just this minute able to get around this problem using a different machine, albeit one with more RAM, so I'm assuming this must have been a RAM issue. Still, if you wish to investigate, the files can be found at the following locations:

Genome: ftp://ftp.ensembl.org/pub/release-84/fasta/taeniopygia_guttata/dna/

GFF3: ftp://ftp.ensembl.org/pub/release-84/gff3/taeniopygia_guttata

Thank you for your help (and the excellent software!)

Best,

Zach