Hi,
I am running RNA star alignment on 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?
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?
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
So, for this part of your question
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 →
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
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.
