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I've found a thread on this from 2020/2021 that seems to indicate that this is the result of an incomplete index generation, or mismatching chromosomes in the transcriptome annotation/genome reference, but that is not the case in my data. The indexing and attempted alignment were both done with the same version (2.7.11a).
STAR error log:
STAR --genomeDir reference.tmp/T2Tv2_index_v2.7.11a.star --readFilesIn read1.fq.gz read2.fq.gz --quantMode TranscriptomeSAM --outFileNamePrefix sample_name. --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --runThreadN 1
STAR version: 2.7.11a compiled: 2023-08-15T11:38:34-04:00 :/home/dobin/data/STAR/STARcode/STAR.master/source
Jul 10 18:38:11 ..... started STAR run
Jul 10 18:38:12 ..... loading genome
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 10 18:39:47 ...... FATAL ERROR, exiting
Command exited with non-zero status 105
res memory (KB) 46868680
time (HH:mm:ss) 1:40.57
Genome indexing log:
STAR --runMode genomeGenerate --genomeDir T2Tv2_index_v2.7.11a.star --genomeFastaFiles genome.fa --sjdbGTFfile annotation.gtf --sjdbOverhang 149 --limitSjdbInsertNsj 6000000 --runThreadN 1
STAR version: 2.7.11a compiled: 2023-08-15T11:38:34-04:00 :/home/dobin/data/STAR/STARcode/STAR.master/source
Jul 09 23:12:30 ..... started STAR run
Jul 09 23:12:30 ... starting to generate Genome files
Jul 09 23:13:44 ..... processing annotations GTF
Jul 09 23:16:27 ... starting to sort Suffix Array. This may take a long time...
Jul 09 23:17:27 ... sorting Suffix Array chunks and saving them to disk...
Jul 10 06:47:04 ... loading chunks from disk, packing SA...
Jul 10 06:50:23 ... finished generating suffix array
Jul 10 06:50:23 ... generating Suffix Array index
Jul 10 06:57:38 ... completed Suffix Array index
Jul 10 06:57:55 ..... inserting junctions into the genome indices
Jul 10 17:37:09 ... writing Genome to disk ...
Jul 10 17:37:15 ... writing Suffix Array to disk ...
Jul 10 17:38:04 ... writing SAindex to disk
Jul 10 17:38:11 ..... finished successfully
res memory (KB) 152013596
time (HH:mm:ss) 18:26:39
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
I've found a thread on this from 2020/2021 that seems to indicate that this is the result of an incomplete index generation, or mismatching chromosomes in the transcriptome annotation/genome reference, but that is not the case in my data. The indexing and attempted alignment were both done with the same version (2.7.11a).
STAR error log:
Genome indexing log:
Chromosomes listed in annotation:
Chromosomes listed in reference genome:
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