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  1. IGB
  2. IGBF-3499

Complete evaluation of RNA-Seq dataset submissions

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          2
        • Epic Link:
        • Sprint:
          Fall 6, Spring 1, Spring 2, Spring 3, Spring 9, Summer 1, Summer 2, Summer 3, Summer 4, Summer 5, Summer 6, Summer 7, Fall 1

          Description

          Directory: /projects/tomato_genome/fnb/dataprocessing
          Review the SRA re-runs on the cluster for Muday, Johnson, mature pollen, and Ravi lab data. Once bam, junction, and coverage graph files have been produced and checked deploy data to IGB Quickload hotpollen host.

          NOTE: This ticket changed in scope and focus a bit! The new goal is:

          • Complete comparative evaluation of pre- and post-submission RNA-Seq data using multiqc results and special code written for this purpose.

          This goal builds on the final work that Molly Davis did for us, before her appointment ended. We need to complete this work this sprint because we need to recover the large amount of disk space used up by running nf-core/rnaseq pipeline.

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3500 Re-run mark-2022-timeseries data with data downloaded from SRA

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3544 Re-run mature pollen and seedling pipeline with SL4 using data newly submitted to SRA

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3545 Re-run nextflow Mark pollen tube data for SL4 and SL5 with data dowloaded from SRA

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3589 Re-run nextflow Ravi 30-681594536 data for SL4 and SL5 with data dowloaded from SRA

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3590 Re-run nextflow Ravi 30-804059537 data for SL4 and SL5 with data dowloaded from SRA

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3591 Re-run nextflow Ravi 30-605730043 data for SL4 and SL5 with data dowloaded from SRA

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3406 Re-run Nextflow Muday time course data with SL5 data downloaded from SRA

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3424 Re-run mature pollen and seedling pipeline with SL5 using data newly submitted to SRA

              • Major - Major loss of function.
              • Closed

                Activity

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                8 older comments
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                bbendick Brandon Bendickson added a comment -

                The one that generated an error for me is for SL4 (2019), Muday Lab/pollen tube, anthocyanin reduced (are) heat stress, 15 - 75 min (SRP460750)/anthocyanin reduced (are) 28 Celsius 15 min, rep A.28.15.7 (SRR25478302) alignments.

                I am on a Windows laptop, and I am connected to the Eduroam network

                Show
                bbendick Brandon Bendickson added a comment - The one that generated an error for me is for SL4 (2019), Muday Lab/pollen tube, anthocyanin reduced (are) heat stress, 15 - 75 min (SRP460750)/anthocyanin reduced (are) 28 Celsius 15 min, rep A.28.15.7 (SRR25478302) alignments. I am on a Windows laptop, and I am connected to the Eduroam network
                Hide
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                ann.loraine Ann Loraine added a comment -

                Thank you for the info Brandon Bendickson!

                I have looked into what the problem was. It turns out that I had forgotten to make all the files world-readable. I have made that change on the server and checked a few of the files from the Muday lab datasets. It looks good from my end.

                Please re-commence testing Brandon Bendickson when ready!

                Show
                ann.loraine Ann Loraine added a comment - Thank you for the info Brandon Bendickson ! I have looked into what the problem was. It turns out that I had forgotten to make all the files world-readable. I have made that change on the server and checked a few of the files from the Muday lab datasets. It looks good from my end. Please re-commence testing Brandon Bendickson when ready!
                Hide
                Permalink
                bbendick Brandon Bendickson added a comment -

                Ran into the same problem again, with the same file from the previous comment. (Muday Lab/pollen tube, anthocyanin reduced (are) heat stress, 15 - 75 min (SRP460750)/anthocyanin reduced (are) 28 Celsius 15 min, rep A.28.15.7 (SRR25478302) alignments)

                The error message was: The feature http://igbquickload.org/hotpollen/S_lycopersicum_Sep_2019/SRP460750-SL4/SRR25478302.bam is not reachable. moving ticket back to To do

                Show
                bbendick Brandon Bendickson added a comment - Ran into the same problem again, with the same file from the previous comment. (Muday Lab/pollen tube, anthocyanin reduced (are) heat stress, 15 - 75 min (SRP460750)/anthocyanin reduced (are) 28 Celsius 15 min, rep A.28.15.7 (SRR25478302) alignments) The error message was: The feature http://igbquickload.org/hotpollen/S_lycopersicum_Sep_2019/SRP460750-SL4/SRR25478302.bam is not reachable. moving ticket back to To do
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment - - edited

                Thank you Brandon Bendickson! Sorry, I thought I had fixed the problem. Now I have - I think!

                I modified permissions using:

                find . -type f | xargs chmod a+r

                and noticed there were some other problems with the permissions, which I fixed using commands like:

                find . -type d | xargs chmod a+x
find . -type f | xargs chmod a-x
find . | xargs chmod o-w

                Viewing and checking permissions for the entire file tree with:

                find . -type d | xargs ls -ld # check directory permissions
find . -type f | xargs ls -l # checking file permissions

                Brandon Bendickson please check again and thank you for noticing the problem!

                Show
                ann.loraine Ann Loraine added a comment - - edited Thank you Brandon Bendickson ! Sorry, I thought I had fixed the problem. Now I have - I think! I modified permissions using: find . -type f | xargs chmod a+r and noticed there were some other problems with the permissions, which I fixed using commands like: find . -type d | xargs chmod a+x find . -type f | xargs chmod a-x find . | xargs chmod o-w Viewing and checking permissions for the entire file tree with: find . -type d | xargs ls -ld # check directory permissions find . -type f | xargs ls -l # checking file permissions Brandon Bendickson please check again and thank you for noticing the problem!
                Hide
                Permalink
                bbendick Brandon Bendickson added a comment -

                All SL4 is good and all SL5 is good. I ran into no further errors, moving this to done!

                Show
                bbendick Brandon Bendickson added a comment - All SL4 is good and all SL5 is good. I ran into no further errors, moving this to done!

                  People

                  • Assignee:
                    bbendick Brandon Bendickson
                    Reporter:
                    Mdavis4290 Molly Davis
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                    Dates

                    • Created:
                      Updated:
                      Resolved: