Comments (1)
Update: this error persists when the GTF is provided during alignment:
STAR --genomeDir ../../reference.tmp/T2Tv2_index_v2.7.11a.star --readFilesIn read1.fastq.gz read2.fastq.gz --sjdbGTFfile annotation.gtf --limitSjdbInsertNsj 6000000 --quantMode TranscriptomeSAM --outFileNamePrefix sample. --outSAMtype BAM SortedByCoordinate --runThreadN 8
STAR version: 2.7.11a compiled: 2023-09-15T03:04:06+0000 :/opt/conda/conda-bld/star_1694746407721/work/source
Jul 11 11:33:41 ..... started STAR run
Jul 11 11:33:41 ..... loading genome
Jul 11 11:36:25 ..... processing annotations GTF
Jul 11 11:40:55 ..... inserting junctions into the genome indices
EXITING because of FATAL GENOME INDEX FILE error: transcriptInfo.tab is corrupt, or is incompatible with the current STAR version
SOLUTION: re-generate genome index
Jul 11 12:00:20 ...... FATAL ERROR, exiting
from star.
Related Issues (20)
- Abberant splicing between genes
- multimapper doesnt output a matrix HOT 1
- error codes HOT 1
- EXITING because of FATAL ERROR in reads input: short read sequence line: 0 and Read Name is the read sequence HOT 1
- How does STAR handle V(D)J sequences (TCR/BCR)? HOT 4
- GeneFull priority vs Ex50pAS
- Pseudo gnes having higher mapping scores than the actual gene
- Running STARsolo for pico kit reads
- STARsolo output-Summary.csv
- Segmentation fault (core dumped)
- STAR alignments generate different counts: Full genome vs Split genome
- fatal error, cannot create output file for unmapped.out.mate1.thread0
- Possible to implement special treatment of multi-gene reads for BCR/TCR genes?
- [Version 2.7.11b] - Error running 'make' command HOT 3
- killed after "...starting to generate Genome files"
- Problem with reading FASTQ files
- secondary alignment bit in flag not set for unmapped mate of a pair with the other mate mapped
- Parameters for 10x 5' alignment
- Chimeric reads very high
- soloUMIfiltering distribution tracking?
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from star.