Open benostendorf opened 3 months ago
From what I understand from the issue you linked, this is a bug in STAR and we will have to wait for the fix that the maintainer of STAR has already created (and links to in the bug report) is properly released (in the main STAR repository, not the separate pre-release repository). You could ask the maintainer in the issue to create a new release, noting that you also need this. Once he does this, I am glad to help with the necessary follow-up, which will be:
The only other possibility I see, if the maintainer doesn't create a release soon, would be to patch up the bioconda recipe with bugfix. This could be very straightforward, but I don't currently have the bandwidth to investigate this further. But feel free to ping me with questions regarding this, if you want to pursue that solution further.
Thanks for the prompt reply! I asked for creation of a new release, hopefully this will happen soon.
Maybe, just to be sure, a two more questions:
gene_id
tag? The maintainer was mentioning this as a requirement in the issue you linked to:
https://github.com/alexdobin/STAR/issues/1953#issuecomment-1727749459Because you never know, the error could be triggered by something different than the bug reported there. And also, the GitHub Actions continuous integration tests here just ran through these past days with a little fix to the STAR rules. So it's a bit funny that this fails on your end.
Yes, I used the automatic GTF download and there is a column where entries start with the gene_id
tag.
These are the first few lines from the gtf file:
#!genome-build GRCm38.p6
#!genome-version GRCm38
#!genome-date 2012-01
#!genome-build-accession NCBI:GCA_000001635.8
#!genebuild-last-updated 2020-02
1 havana gene 3073253 3074322 . + . gene_id "ENSMUSG00000102693"; gene_version "1"; gene_name "4933401J01Rik"; gene_source "havana"; gene_biotype "TEC"; havana_gene "OTTMUSG00000049935"; havana_gene_version "1";
On 7. Jun 2024, at 10:25, David Laehnemann @.***> wrote:
Maybe, just to be sure, a two more questions:
Did you just use the automatic GTF download that the workflow does, or did you manually put in place a GTF file. I guess that mismatches due to a manually added GTF might lead to issues. And in either case, could you check that the GTF file contains the gene_id tag? The maintainer was mentioning this as a requirement in the issue you linked to: alexdobin/STAR#1953 (comment) https://github.com/alexdobin/STAR/issues/1953#issuecomment-1727749459 Because you never know, the error could be triggered by something different than the bug reported there. And also, the GitHub Actions continuous integration tests here just ran through these past days with a little fix to the STAR rules. So it's a bit funny that this fails on your end.
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OK, at least this is not broken, then... :sweat_smile:
So it is probably some weird interaction of this bug with the software stack... :shrug:
Fingers crossed, that the release of the bug fix makes this go away.
Otherwise, we more regularly use the rna-seq-kallisto-sleuth
workflow ourselves, and maintain and improve it constantly. So maybe this is an alternative you might want to try for your RNAseq Analysis:
https://snakemake.github.io/snakemake-workflow-catalog/?repo=snakemake-workflows/rna-seq-kallisto-sleuth
I have deployed the latest version of this workflow (v2.1.2) and only adjusted the config files. I use the ENSEMBL GRCm38 mouse reference genome (release 102).
Unfortunately, the mapping step fails with the following error:
This seems to be the same error as reported here. Thank you for looking into this!