alexdobin
commented
3 years ago Hi @Ronika19
please try the following:
- Use the GTF from ensemble: http://ftp.ensembl.org/pub/current_gtf/danio_rerio/Danio_rerio.GRCz11.103.chr.gtf.gz
and remove
--sjdbGTFtagExonParentTranscript Parent --sjdbGTFfeatureExon exon - Switch to a newer version of STAR, preferrably the latest 2.7.8a: https://github.com/alexdobin/STAR/releases/tag/2.7.8a
Cheers Alex
Hi Alex I have been trying to generate index for Danio rerio using these fasta and gff3 file: http://ftp.ensembl.org/pub/current_gff3/danio_rerio/Danio_rerio.GRCz11.103.chr.gff3.gz http://ftp.ensembl.org/pub/current_fasta/danio_rerio/dna/Danio_rerio.GRCz11.dna.toplevel.fa.gz
I got an error using the following command: STAR --runThreadN 54 --runMode genomeGenerate --genomeDir /storage/scratch2/rd0331/Weam_Zebrafish_Project --genomeFastaFiles Danio_rerio.GRCz11.dna.fa --sjdbGTFfile Danio_rerio.GRCz11.103.gff3 --sjdbGTFtagExonParentTranscript Parent --sjdbGTFfeatureExon exon --genomeChrBinNbits 10 --limitGenomeGenerateRAM=200000000000
Error Message: Mar 09 21:32:48 ..... started STAR run Mar 09 21:32:48 ... starting to generate Genome files Mar 09 21:44:53 ... starting to sort Suffix Array. This may take a long time... Mar 09 21:47:16 ... sorting Suffix Array chunks and saving them to disk... Mar 09 23:56:15 ... loading chunks from disk, packing SA... Mar 09 23:59:12 ... finished generating suffix array Mar 09 23:59:12 ... generating Suffix Array index Mar 10 00:03:16 ... completed Suffix Array index Mar 10 00:03:16 ..... processing annotations GTF danio_star.sh: line 1: 80097 Segmentation fault STAR --runThreadN 54 --runMode genomeGenerate --genomeDir /storage/scratch2/rd0331/Weam_Zebrafish_Project --genomeFastaFiles Danio_rerio.GRCz11.dna.fa --sjdbGTFfile Danio_rerio.GRCz11.103.gff3 --sjdbGTFtagExonParentTranscript Parent --sjdbGTFfeatureExon exon --genomeChrBinNbits 10 --limitGenomeGenerateRAM=200000000000