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  1. IGB
  2. IGBF-4001

NEXTFLOW on Kausik's DBR1 sequences

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          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.

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              Task - A task that needs to be done. IGBF-3998 DBR1 gene filtering

              • Major - Major loss of function.
              • Closed

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                bbendick Brandon Bendickson added a comment -

                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

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                bbendick Brandon Bendickson added a comment - 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
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                bbendick Brandon Bendickson added a comment -

                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.

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                bbendick Brandon Bendickson added a comment - 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.
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                bbendick Brandon Bendickson added a comment -

                Problem was with the tmp singularity folder, had to switch it to a local tmp directory.

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                bbendick Brandon Bendickson added a comment - Problem was with the tmp singularity folder, had to switch it to a local tmp directory.
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                bbendick Brandon Bendickson added a comment -

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

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                bbendick Brandon Bendickson added a comment - Nextflow ran successfully, results found in: /projects/tomato_genome/fnb/sidegig/dbr1-nextflow/NEXTFLOW
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                robofjoy Robert Reid added a comment -

                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!

                Show
                robofjoy Robert Reid added a comment - 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!

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                  • Assignee:
                    robofjoy Robert Reid
                    Reporter:
                    robofjoy Robert Reid
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                    • Created:
                      Updated:
                      Resolved: