Closed mdozmorov closed 2 weeks ago
It also occurs when run with TAIR10; on the slack there has been some discussion on it, but I did not see a solution yet.
I was one of them. Started talking in Slack, and then transitioned to this GitHub discussion. Long chats. But, this is it: https://github.com/nf-core/rnasplice/issues/151.
Hi @mdozmorov ,
It looks like the genome annotation you're using might be Ensembl-based, which includes gene version identifiers. If that's the case, you'll need to specify the gene identifiers along with the version number. You can refer to my discussion with @tud03125 for an example of a working solution that addresses this.
Hope this helps!
Thanks, @jma1991, it worked. I hope this will help others:
gene_id "ENSG00000186092"; gene_version "7";
. Or, select any Ensembl ID.--miso_genes ENSG00000186092.7
. This should prevent the error and the pipeline will complete.It appears. --miso_genes
would be good a good required setting. The error message from the pipeline is not very informative.
Description of the bug
This issue appears in various forms in other issues, but I could not find a workable solution. This error occurs when running the pipeline with
--genome GRCh38
or with manually provided--fasta
and--gtf
(I use those from 10x Genomics).A workaround is to set
--sashimi_plot false
. But is there a better solution?Command used and terminal output
Relevant files
No response
System information
nextflow version 23.10.0.5891, run on HPC in local mode, Singularity, Rocky Linux 9.4, nf-core/rnasplice: 1.0.4