RNA STAR not running!

[jennaj]

Hi @Mohammed_Thangameera

For the jobs at usegalaxy.org:

1. When working at any public Galaxy server, you are using a shared resource. That means that some of your jobs will run, then some of other people’s jobs will run, then more of yours, repeat. During the training last week, all servers had extra limits on concurrent jobs plus the usegalaxy.* servers overall were very busy. This week everything is back to normal but still busy, and processing a large number of jobs will still take time.

2. For the RNA STAR jobs that already failed, that is due to an input problem. The reference GTF used is labeled with Ensembl chromosome names. The built-in rn5 index is sourced from UCSC and uses a different chromosome naming format/label. The mismatch triggers a failure.

Try using a GTF from UCSC instead. The Q&A below discusses where to get a human reference annotation in GTF format, but the URL to the rat annotation is similar (replace “hg38” with “rn5”). The same is true for every genome with an annotation track that is hosted by UCSC and indexed in Galaxy.

@jennaj

The hg38 reference annotation GTF is now best sourced from UCSC. Not from the Table Browser but from the Downloads area here . There are a few Gene tracks to choose from. You can review what each of those represents then upload the selected GTF to Galaxy with the Upload tool. Just copy and paste in the URL and leave all other settings at the default. The correct datatype will be assigned.

The solution is

1. get the correct GTF into Galaxy
2. rerun all of your jobs using that GTF instead

Those new jobs will execute as resources become available. The jobs already queued up will also fail, so be sure to purge those to clear them from your queue.

Hope that helps!