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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Activity
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.
Nextflow ran successfully, results found in: /projects/tomato_genome/fnb/sidegig/dbr1-nextflow/NEXTFLOW
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!
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