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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 #978
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Hi @Kusimeena please regenerate the genome and check that your drive has not run out of space after genome generation, which could lead to the corruption of the output files. Cheers |
Hi, I'm seeing this same error message. Steps to reproduceLoad STAR environment
(Edit: I can also confirm this occurs on version Generate STAR index
where I retrieved the hg38 chromosome 21 FASTA and the hg38 gtf file from:
This ran sucessfully:
Run STARsolo on test data 1K PBMC v2 dataThe datasets I retrieved from here, and the barcodes file from here and attempted to map only the first lane
and the error message I recieve is:
Attached are the |
It looks like STAR does not like the fact that the GTF file specified more chromosomes than the FASTA After constraining the GTF file just to chromosome 21, it seems to progress to the mapping stage
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Hi alex,
I am sending you the log.out files for both genome generation and mapping. I believe the index generation went smoothly without any error. For the mapping, if i use "--quantMode GeneCounts" instead of "--quantMode TranscriptomeSAM GeneCounts", it runs successfully.
Thanking you for your kind support.
Regards
Meena Kusi
PhD candidate
Integrated Biomedical Sciences (IBMS) Graduate Program
University of Texas Health Science Center at San Antonio
7703 Floyd Curl Drive
San Antonio, TX 78229-3900
Email Address: kusim@livemail.uthscsa.edu<https://bobcatmail.txstate.edu/owa/redir.aspx?C=xyhz86wHSxPyJxsxML9Gu0umC3uzf0JdaW9FP77j26fMqeIocsXTCA..&URL=mailto%3aamr125%40txstate.edu>
…________________________________
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Sent: Monday, July 27, 2020 9:48 AM
To: alexdobin/STAR <STAR@noreply.github.com>
Cc: Kusimeena <kusim@uthscsa.edu>; Mention <mention@noreply.github.com>
Subject: Re: [alexdobin/STAR] 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 (#978)
Hi @Kusimeena<https://github.com/Kusimeena>
please regenerate the genome and check that your drive has not run out of space after genome generation, which could lead to the corruption of the output files.
If this does not help, please send me the Log.out files for both the genome generation and mapping.
Cheers
Alex
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Hi Meena, the files did not get attached - they cannot be attached in a reply, you would need to do it via GitHub site. Cheers |
Hi Alex, Here are the files: |
Hi Meena, Mehmet, Mehmet is right - this issue occurs when the GTF files contains extra chromosome not present in the FASTA file. Cheers |
…or cases where GTF file contains extra chromosomes not present in FASTA files.
Hi Meena, Mehmet, This bug is fixed in 2.7.5c, please try it out. Cheers |
Hello Alex, I found the error again in version 2.7.7a, could you please take a look? |
Hi David, I do not see this problem in my tests in 2.7.7a. Cheers |
Dear Alex, As I am experiencing similar problems. I was doing 2 pass alignment with intermediary genome files generation for pass 2 using the mouse genome from Ensembl (Mus_musculus.GRCm39.104.gtf and Mus_musculus.GRCm39.dna.primary_assembly.fa). After the first pass with STAR 2.7.1a I got this output while generating the intermediary reference genome: EXITING because of FATAL error, the sjdb chromosome 20 is not found among the genomic chromosomes Based on the discussion above, I compiled and used STAR 2.7.9a but I still get: EXITING because of FATAL error, the sjdb chromosome 20 is not found among the genomic chromosomes I do not know what to do at this stage. Thanks for your help. Best, |
Hi Jacques, it looks like the file with splice junctions contains chromosomes that are not present in the genome. Cheers |
Dear Alexander,
Thank you for replying. There is a first bunch of “pass1” alignments each obtained with:
2021-09-05 23:37:46 executing /share/apps/STAR/bin/Linux_x86_64/STAR --genomeDir/share/apps/STAR/indexes/Mus_musculus --readFilesIn /data/jcolinge/LUAD/ICM-03-2021/Fastq/341-1CAF_R1.fastq /data/jcolinge/LUAD/ICM-03-2021/Fastq/341-1CAF_R2.fastq --runThreadN 7 --outFileNamePrefix /data/jcolinge/LUAD/ICM-03-2021/alignment/STAR/341-1CAF_align/pass1/
Then a project specific genome is generated with:
2021-09-06 13:06:47 failed /share/apps/STAR/bin/Linux_x86_64/STAR --runThreadN 10 --runMode genomeGenerate --limitSjdbInsertNsj 2500000 --genomeDir /data/jcolinge/LUAD/ICM-03-2021/alignment/STAR/project-genome/ --genomeFastaFiles /share/apps/STAR/indexes/Mus_musculus/Mus_musculus.GRCm39.dna.primary_assembly.fa --sjdbFileChrStartEnd /data/jcolinge/LUAD/ICM-03-2021/alignment/STAR/341-1CAF_align/pass1/SJ.out.tab /data/jcolinge/LUAD/ICM-03-2021/alignment/STAR/341-1CD31_align/pass1/SJ.out.tab /data/jcolinge/LUAD/ICM-03-2021/alignment/STAR/341-1CD45_align/pass1/SJ.out.tab <plenty of other files here> --sjdbGTFfile /share/apps/STAR/indexes/Mus_musculus/Mus_musculus.GRCm39.104.gtf
Then pass2 alignment starts (though I am stuck at the genome generation for this project). I have use this pipeline on hundreds of files with different versions of STAR and different genomes. No problem so far (and thank you, we like STAR a lot!).
Best regards,
Jacques
De : Alexander Dobin ***@***.***
Envoyé : jeudi, 7 octobre 2021 18:34
À : alexdobin/STAR ***@***.***>
Cc : jcolinge ***@***.***>; Comment ***@***.***>
Objet : Re: [alexdobin/STAR] 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 (#978)
Hi Jacques,
it looks like the file with splice junctions contains chromosomes that are not present in the genome.
What are the STAR commands that you are using?
Cheers
Alex
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Hi Jacques, was the /share/apps/STAR/indexes/Mus_musculus genome index generated with the same Please send me the output of the failed run. Thanks! |
Hi, I am trying to align RNA-seq data using STAR version 2.7.5a using the following codes:
STAR --genomeDir /Users/Home/Desktop/STAR_RNAseq/NCBI_GRCh39_index --readFilesIn 01.fastq.gz --runThreadN 2 --readFilesCommand gunzip -c --outFileNamePrefix 01A --quantMode TranscriptomeSAM GeneCounts
and it ended up with,
XITING because of FATAL GENOME INDEX FILE error: transcriptInfo.tab is corrupt, or is incompatible with the current STAR version
SOLUTION: re-generate genome index
I checked the Log.out and it ends like "finished successfully
DONE: Genome generation, EXITING", so I believe there was no error with index generation. Could you help me how to fix this issue? Thanks.
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