Details
-
Type:
Task
-
Status: Closed (View Workflow)
-
Priority:
Minor
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: None
-
Labels:None
-
Story Points:2
-
Epic Link:
-
Sprint:Spring 10, Summer 1
Description
The goal here is to test both Trinity and the Blat scripts from our reference free alignment pipeline.
There are 4 Trinity jobs.
There are 4 blat jobs.
To test this, Brandon will tackle running these scripts to see if he can recreate the results.
Need to decide a test area.
The scripts reside on the cluster at the following location:
/projects/tomato_genome/fnb/dataprocessing/trinity
Script names:
trinity-hei.slurm
trinity-mal.slurm
trinity-nag.slurm
trinity-tam.slurm
blat-hei.slurm
blat-mal.slurm
blat-nag.slurm
blat-tam.slurm
These scripts also need to be cleaned up as well. Remove line comments that are no longer relevant, etc.
Attachments
Activity
Error has been found and the scripts have been fixed accordingly. Scripts are running, I will spend some time this weekend to BLAT the results.
Assigning to Brandon now that he is in the environment.
This is ongoing and once done the jobs complete, we will close this ticket.
2 of the trinity runs are still ongoing. 2 are complete. Fickle tool when run on the cluster!
But the current blat scripts worked fine.
The process will continue via ticket IGBF-3741 where we will run blat against 2bit format SL4 and SL5 and have more parameters.
I found out that Trinity v2.13 has a bug that prevents the creation of the output fasta files. I rewrote the script to use Trinity v2.14.0, but it is in the queue for Draco. Trying a test run on Orion with Trinity v2.14.0, will run the others using Orion if this one completes successfully. Scripts are located in /projects/tomato_genome/fnb/dataprocessing/brandon_work/nag/temp_trinity/trinity-nag.slurm
Patch notes for trinity updates: https://github.com/trinityrnaseq/trinityrnaseq/releases