# RNA star job is not fully executed and still running **URL:** \ **Category:** usegalaxy.org support\ **Tags:** rna\_star\ **Created:** [August 12, 2024, 6:07am UTC](https://help.galaxyproject.org/t/rna-star-job-is-not-fully-executed-and-still-running/13200 "2024-08-12T06:07:04Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![bpathak](https://avatars.discourse-cdn.com/v4/letter/b/b487fb/32.png) [@bpathak](https://help.galaxyproject.org/u/bpathak)\ **Post date:** [August 12, 2024, 6:07am UTC](https://help.galaxyproject.org/t/rna-star-job-is-not-fully-executed-and-still-running/13200/1 "2024-08-12T06:07:04Z")
Hi, I am running RNA star alignment on [usegalaxy.org](http://usegalaxy.org) public server. The job has been running for over 24 hours and has not finished yet. Previously, it did not run properly citing the following error An error occurred while running the tool toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna\_star/2.7.11a+galaxy0. Details Execution resulted in the following messages: Fatal error: Matched on FATAL ERROR Tool generated the following standard error: Fatal INPUT FILE error, no valid exon lines in the GTF file: /jetstream2/scratch/main/jobs/59721549/inputs/dataset\_d6e78e25-8487-42c2-a2f5-d3c419ad5a11.dat Solution: check the formatting of the GTF file. One likely cause is the difference in chromosome naming between GTF and FASTA file. Aug 10 04:49:35 … FATAL ERROR, exiting However, in the first run- it showed the error in 20 minutes itself, but in the current run it is still orange and continuing. Does it mean that parameters have been fixed, but due to busy server, it is taking longer? ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [August 12, 2024, 7:35pm UTC](https://help.galaxyproject.org/t/rna-star-job-is-not-fully-executed-and-still-running/13200/2 "2024-08-12T19:35:31Z")
Welcome, @bpathak The error you had first indicates a reference genome and reference annotation mismatch problem. You will need to address that first before the job will run successfully. We have guides that help with solving this kind of problem. Start with this one to set up your reference data (genome + annotation). Even if you are using an index on the server, the guide and those it links to are relevant – see the “TIP” items at the bottom. [FAQ: How to use Custom Reference Genomes?](https://training.galaxyproject.org/training-material/faqs/galaxy/reference_genomes_custom_genomes.html) Then, this guide helps with spotting and correcting content problems in reference data. Even if you are not doing this kind of analysis, the help for the three reference data types will usually matter. Focus on the Reference Annotation section near the end. [FAQ: Extended Help for Differential Expression Analysis Tools](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_differential_expression_help.html) So, for this part of your question > [@bpathak](#): > > However, in the first run- it showed the error in 20 minutes itself, but in the current run it is still orange and continuing. Does it mean that parameters have been fixed, but due to busy server, it is taking longer? You will need to correct the inputs for a successful run. If you didn’t change anything and just used the rerun button, the new job will eventually fail with the same message. And, when a job executes (how “fast” it runs) includes two parts: the queue time and the execution time. The queue times varies depending on how busy the server is at that time. The execution time will be about the same. It sounds like your first job queued fast, then executed. You second job queued longer, and may still be queued or might be executing still. More details about how jobs execute are in this other guide → > [@Troubleshooting resources for errors or unexpected results](https://help.galaxyproject.org/t/troubleshooting-resources-for-errors-or-unexpected-results/42/1): > > ⏰ When working at [UseGalaxy.org](http://UseGalaxy.org), [UseGalaxy.eu](http://UseGalaxy.eu), or [UseGalaxy.org.au](http://UseGalaxy.org.au), your analysis jobs execute [at large scale academic clusters](https://training.galaxyproject.org/training-material/faqs/galaxy/#analysis). Hundreds of thousands of jobs process each month! > > - Use a [Workflow](https://training.galaxyproject.org/training-material/search2?query=workflow) for batch work. > - Allow [queued (grey color) and executing (yellow-orange) datasets](https://training.galaxyproject.org/training-material/faqs/galaxy/datasets_job_status.html) to finish processing. > - Deleting and rerunning puts your job back _at the end_ of the queue again! > - Job priority is the exactly the same for everyone. > - **Be patient**. Galaxy is a free service, when a lot of people are using it, [you may have to wait longer than usual](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_jobs_not_running.html) (especially for ‘big’ jobs, e.g. alignments). * * * There are a few moving parts but hopefully I’ve explained the overall context Ok? You can ask more questions about any of it. I would suggest focusing on fixing the reference data. We can help with that here if you get stuck. We’ll need some details about the job. How to do that is in the banner at this forum, or see directly here → [How to get faster help with your question](https://help.galaxyproject.org/docs?topic=11469) You can even delete-then-purge that job still executing if you want to. Then just ignore it, since it won’t provide you with any new information. Let us know how this works out! 🙂