Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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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:1
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Epic Link:
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Sprint:Fall 6, Fall 7, Winter 1
Description
GOAL: Run the DBR1 raw sequences through the NCBI filtering tools.
Attachments
Issue Links
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Removed duplicates and wrote them to their own file (Variety_dupes.fa). The new files are located in /projects/tomato_genome/fnb/dataprocessing/TSA-transcriptomeShotgunAssembly/kelsieData/FCS_tools/FCS_GX/tom_runs/fin_results
They follow this pattern (Variety_contaminant3_removed.fa), We should be ready for another submission. Python script is fix_contam3_v2.py and is in same directory
| Assignee | Brandon Bendickson [ bbendick ] | Robert Reid [ robertreid ] |
I think this comment is in the wrong task! I'll copy it over to the TSA task.
| Sprint | Fall 6 [ 207 ] | Fall 6, Fall 7 [ 207, 208 ] |
| Rank | Ranked higher |
| Sprint | Fall 6, Fall 7 [ 207, 208 ] | Fall 6, Fall 7, Fall 8 [ 207, 208, 209 ] |
| Rank | Ranked higher |
FCS adaptor keeps dying due to BLAST step using up too much memory. I have gone up to 350gb per run and still running out of memory. Trying to find a way around this.
Checked troubleshooting page on github and found this:
Can FCS-adaptor run on sequencing reads?
FCS-adaptor is developed to operate on assembled genomes and is not intended to replace adaptor trimming on reads. There are various tools for read trimming; tools that are specialized for sequencing technologies may have a more expansive adaptor catalogue relative to FCS-adaptor.
This could be why my jobs are dying no matter how much memory I give them, the tool cant blast the reads.
OK, good to know. Let's stop trying to filter the reads!
R
This ticket can be closed as we now know that these tools are not suitable for large raw reads.
| 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 ] |
Location of results
/projects/tomato_genome/fnb/dataprocessing/TSA-transcriptomeShotgunAssembly/kelsieData/FCS_tools/FCS_GX/tom_runs/fin_results
Brandon has run a python script to remove the last 11 sequences that TSA people complained about.
And in addition, this script also addresses any sequences that are duplicated.
remove_Ns.py