BUG: next index is smaller than previous, EXITING
cyberPhage opened this issue · comments
Jan 30 09:37:01 ..... started STAR run
Jan 30 09:37:01 ... starting to generate Genome files
Jan 30 09:37:38 ... starting to sort Suffix Array. This may take a long time...
Jan 30 09:37:49 ... sorting Suffix Array chunks and saving them to disk...
Jan 30 09:45:37 ... loading chunks from disk, packing SA...
Jan 30 09:46:19 ... finished generating suffix array
Jan 30 09:46:19 ... generating Suffix Array index
BUG: next index is smaller than previous, EXITING
Jan 30 09:46:52 ...... FATAL ERROR, exiting
This is the error I am getting when I run this command, STAR --runThreadN 30 --runMode genomeGenerate --genomeDir . --genomeFastaFiles *fna --sjdbGTFfile *gtf --sjdbOverhang 100
with or without overhang.
head of .fna file is a follows
NC_033660.1 Microcebus murinus isolate mixed chromosome 1, Mmur_3.0, whole genome shotgun sequence
GGGCTCACTCTCTAAGTGATTCGAATGCACAGCCAGCCGAGAGCCACTGATTTAGGCCGTTTTAGGTGAAAATGAACAGA
GACGCTCAAGTTGCTTAAGGAGATGGGGTTACTGCAGGTTTACCCTGGAAATAAGCCAGGAGCAGGGAGCTGCCCAGGTA
AGACtggaggaaggggacaggagggagagtCCAACCACGGTTCCTCTGGGGACAGGGCCTTCATGACATCCTTCAGCAGC
AGGTGTCCCAGCACCTGCTCAAGTGTTCTGCCCCCGCGTCACCTTGCCTCCTATCATCTGGCCGCTAACAACCACTGCCC
TCGACTCAAGCTGTGGTCCAGGGACCAACCAACAGCATCAGTATTGCCCGGGAGCTCAGTGGAAATGCGGAATCTGGGGC
CCTGCCCAAGATTTCGGAGAGCCCCTGCAAAGGCATGCGCCTTTTGTGACCTGTGTCCGCTGACAGAATGGCAGGCTGGC
AGCATCTGCCTCAGCTGCAGACTCCAGCCCTGTGCTCCTTCTCTGTCCTCCGTGAGCTCCTTTAGCCAGTCCTCCAAGGG
CTCATCTCCAGGCTTGTCCCAGCCCTAAAAGTTGGTATTCCCAAGGCGAGTCCCACCGATTACAGACAAGTGAGGCTGAA
CACTGGGATTTTCTTATAATGTAGGAACTCGGCTCTATGGTATTACCCTCCTGTTAATAGTGACAACCAGCCTATACCTT
and head of .gtf file is:-
#gtf-version 2.2
#!genome-build Mmur_3.0
#!genome-build-accession NCBI_Assembly:GCF_000165445.2
#!annotation-source NCBI Microcebus murinus Annotation Release 101
NC_033660.1 Gnomon gene 139953 149493 . + . gene_id "RBP2"; transcript_id ""; db_xref "GeneID:105862656"; gbkey "Gene"; gene "RBP2"; gene_biotype "protein_coding";
NC_033660.1 Gnomon transcript 139953 149493 . + . gene_id "RBP2"; transcript_id "XM_012749110.1"; db_xref "GeneID:105862656"; gbkey "mRNA"; gene "RBP2"; model_evidence "Supporting evidence includes similarity to: 10 mRNAs, 11 ESTs, 9 Proteins, and 90% coverage of the annotated genomic feature by RNAseq alignments"; product "retinol binding protein 2"; transcript_biotype "mRNA";
NC_033660.1 Gnomon exon 139953 139971 . + . gene_id "RBP2"; transcript_id "XM_012749110.1"; db_xref "GeneID:105862656"; gene "RBP2"; model_evidence "Supporting evidence includes similarity to: 10 mRNAs, 11 ESTs, 9 Proteins, and 90% coverage of the annotated genomic feature by RNAseq alignments"; product "retinol binding protein 2"; transcript_biotype "mRNA"; exon_number "1";
NC_033660.1 Gnomon exon 140119 140297 . + . gene_id "RBP2"; transcript_id "XM_012749110.1"; db_xref "GeneID:105862656"; gene "RBP2"; model_evidence "Supporting evidence includes similarity to: 10 mRNAs, 11 ESTs, 9 Proteins, and 90% coverage of the annotated genomic feature by RNAseq alignments"; product "retinol binding protein 2"; transcript_biotype "mRNA"; exon_number "2";
NC_033660.1 Gnomon exon 147573 147674 . + . gene_id "RBP2"; transcript_id "XM_012749110.1"; db_xref "GeneID:105862656"; gene "RBP2"; model_evidence "Supporting evidence includes similarity to: 10 mRNAs, 11 ESTs, 9 Proteins, and 90% coverage of the annotated genomic feature by RNAseq alignments"; product "retinol binding protein 2"; transcript_biotype "mRNA"; exon_number "3";
NC_033660.1 Gnomon exon 149211 149493 . + . gene_id "RBP2"; transcript_id "XM_012749110.1"; db_xref "GeneID:105862656"; gene "RBP2"; model_evidence "Supporting evidence includes similarity to: 10 mRNAs, 11 ESTs, 9 Proteins, and 90% coverage of the annotated genomic feature by RNAseq alignments"; product "retinol binding protein 2"; transcript_biotype "mRNA"; exon_number "4";
Hi @cyberPhage
Please switch to the latest version of STAR.
If it does not help, please send me the Log.out file.