Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Minor
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:2
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Epic Link:
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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
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Description |
The goal here is to test both Trinity and the Blat scripts from our reference free alignment pipeline. Details to come in comments. |
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. |
| Assignee | Robert Reid [ robertreid ] | Brandon Benkick [ bbendick ] |
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.
| Sprint | Spring 10 [ 194 ] | Spring 10, Summer 1 [ 194, 195 ] |
| Rank | Ranked higher |
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
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
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-3741where we will run blat against 2bit format SL4 and SL5 and have more parameters.