Trinity is running since from one week for 20GB file??? is it ok???

1

Dear Sir,

Kindly help in this regards I was trying to make a de novo contig using trinity and it is running since from one week.
Is it ok??? or did I out something wrong
Kindly help

1 Like
2

Hello @Sachin_Srivastava

If the job is running (yellow/peach dataset), it is usually best to allow it to run. The same is true for queued jobs (grey dataset). This applies to jobs (any tool) executed at a public Galaxy server.

20 GB of fastq data – uncompressed – creates a very large assembly job. If it fails later on for exceeding resources (red dataset), you’ll need to do one or more of these:

  • Try a rerun to eliminate cluster issues
  • More QA/QC on the input reads (always recommended)
  • Consider downsampling the reads (tool: Seqtk)
  • Possibly need to move to your own Galaxy server where more resources can be allocated. The GVL version of Cloudman is one option: https://launch.usegalaxy.org/catalog

I added some tags to your post that will find prior Q&A about the above actions. Or, you can search the forum with those keywords (not all posts get tagged).

You didn’t state where you are working. But, if by chance at Galaxy Main https://usegalaxy.org, I can let you know that the cluster that runs Trinity (and Unicycler + RNA-Star) is very busy. Longer queue times are expected. If you delete the current job and rerun, that will only place your job back at the end of the queue again, extending wait time.

Thanks!

1 Like