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:3
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Epic Link:
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Sprint:Fall 6, Fall 7, Winter 1
Description
GOAL:
To recreate what was done by others.
But we have better filtering to begin with.....
Once IGB-3998 is complete, run the filtered sequences through NEXTFLOW in the same manner as Molly's tomato runs..
Different reference of course, now we use human.
Once we get salmon table, we can move to a DESEq2 run.
Attachments
Issue Links
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Sprint | Fall 6 [ 207 ] | Fall 6, Fall 7 [ 207, 208 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
solved our singularity problems and was able to rerun the commands successfully on hpc9. Now just need to wait until clusters are back up to launch the jobs.
Problem was with the tmp singularity folder, had to switch it to a local tmp directory.
| Sprint | Fall 6, Fall 7 [ 207, 208 ] | Fall 6, Fall 7, Fall 8 [ 207, 208, 209 ] |
| Rank | Ranked higher |
| Comment | [ 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. ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Nextflow ran successfully, results found in: /projects/tomato_genome/fnb/sidegig/dbr1-nextflow/NEXTFLOW
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Brandon Bendickson [ bbendick ] | Robert Reid [ robertreid ] |
Salmon counts file looks good.
We should share this with Tiffany from Kausik's lab and have her inspect it further. She can compare the counts here with what she has from the outside contractor.
This ticket is complete!
| 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 ] |
submitted help ticket to solve this error: INFO: Mounting image with FUSE.
/usr/bin/fusermount3: failed to unmount /projects/tomato_genome/fnb/dataprocessing/brandon_work/tmp_singularity/rootfs-4067999465/root: Permission denied
Tried rerunning old commands from tomato data that worked fined on hpc8, but is now yielding the same error. New testing directory is located in:
/projects/tomato_genome/fnb/dataprocessing/TSA-transcriptomeShotgunAssembly/kelsieData/FCS_tools/FCS_adaptor/temp_success
Waiting on response to help ticket, plus HPC will be out 12/18 to 12/20, which further slows us down