I am running my genome indexing STAR code in a company's cluster:
STAR --runThreadN 1 --runMode genomeGenerate --genomeDir /home/id/ --genomeFastaFiles /home/id/GRCm38.primary_assembly.genome.fa --sjdbGTFfile /home/id/gencode.vM24.primary_assembly.annotation.gtf --sjdbOverhang 100
But, I keep running into the same error saying,
Apr 01 08:44:03 ..... started STAR run Apr 01 08:44:03 ... starting to generate Genome files Apr 01 08:45:09 ... starting to sort Suffix Array. This may take a long time... Apr 01 08:45:25 ... sorting Suffix Array chunks and saving them to disk... Apr 01 09:10:06 ... loading chunks from disk, packing SA...
EXITING because of FATAL problem while generating the suffix array The number of indices read from chunks = 2269570266 is not equal to expected nSA=5305567000 SOLUTION: try to re-run suffix array generation, if it still does not work, report this problem to the author
Apr 01 09:10:49 ...... FATAL ERROR, exiting
After I googled about the problem, I thought the low number of thread could be a problem so I already increased to 4. Also, I assigned 36GB to the cluster to run STAR. But still I got the same error message.. Could you help me know how to resolve this issue? Thank you so much.