FATAL problem while generating the suffix array

[Christoph Hafemeister]

Hi all,

STAR fails to generate a genome file. This is my output:

Jul 25 10:47:27 ..... Started STAR run

Jul 25 10:47:27 ... Starting to generate Genome files

Jul 25 10:47:40 ... starting to sort  Suffix Array. This may take a long time...

Jul 25 10:47:44 ... sorting Suffix Array chunks and saving them to disk...

Jul 25 10:49:00 ... loading chunks from disk, packing SA...

EXITING because of FATAL problem while generating the suffix array

The number of indices read from chunks = 7351296 is not equal to expected nSA=748611972

SOLUTION: try to re-run suffix array generation, if it still does not work, report this problem to the author

Jul 25 10:49:00 ...... FATAL ERROR, exiting

The problem is reproducible. I am running STAR version 2.3.0e. The command line call is 

STAR --runMode genomeGenerate --genomeDir MSU_Pseudomolecules/for_STAR_no_annotation --genomeFastaFiles MSU_Pseudomolecules/all.con --runThreadN 12

The fasta file that I am using can be downloaded here: ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/all.con

I'd appreciate any advice on what might be causing the error and what i could do to generate the genome file.

Best,

Christoph

[Alexander Dobin]

Hi  Christoph,

this error is most likely caused by the lack of disk space inside the genome directory to store all of the genome files. I have had a few users reporting this error and in all cases it was explained by the lack of disk space.

You need probably around ~10GB for storing the genome files. If this does not resolve your problem, please send me the Log.out file as well as the contents ("ls -l") of your genome directory after the failed run.

Cheers

Alex

[Joshua Arribere]

Were you trying to generate multiple genomes in parallel? If you have two windows open and are making genomes from the same genomeDir, I think the temporary files can also conflict and cause problems.