Hi, I am getting this error when trying to run RNA-STAR, how can I resolve it? Thank you. Fatal error: Matched on FATAL ERROR Transcriptome.cpp:48:Transcriptome: exiting because of INPUT FILE error: could not open input file /cvmfs/data.galaxyproject.org/managed/rnastar_index2/hg38/dataset_950901_…

Hello, You need to supply a reference annotation GFT dataset from the history at runtime. The GTF should be based on the UCSC “hg38” genome build. Some choices: For Gencode, copy the link to the GTF and paste it into the Upload tool. Hg38 data is here https://www.gencodegenes.org/ . After it i…

I did, but it was in gtf.gz format. I will reupload in gtf format in case this was why the annotation file could not be accessed. Thanks.

[image] Lena_Ho: I will reupload in gtf format That should work. The datatype gtf.gz is not supported. I wondering how this was loaded – gtf data in compressed format will uncompress upon Upload when “auto-detect” is used (for “type”). And, gtf.gz cannot be assigned directly. I’d be interes…

Linking in FAQ: Extended Help for Differential Expression Analysis Tools

I keep having the following error while running RNA Star : I cut the first five rows of the GTF file but I got the same error message as I got in last time. Fatal error: Matched on FATAL ERROR !!! WARNING: --genomeSAindexNbases 14 is too large for the genome size=375049285, which may cause seg-fau…

Hi @aaak This may be the root problem (not all jobs that were executing when the downtime started ended gracefully). Please see: UseGalaxy.org scheduled maintenance downtime October 13, 2020 – status and updates Once the server is back up, try a rerun. If you are still having problems: Please send…

Galaxy Community Help

RNA-STAR and hg38 GTF reference annotation

usegalaxy.org support

troubleshooting, transcriptomics, reference-annotation, rna_star

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