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  1. IGB
  2. IGBF-135

investigate potential problem with QL samtools access

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          0.5

          Description

          I noticed today that this samtools query doesn't work on IGBQuickLoad or our backup site on Bioviz:

          $ samtools view -H http://bioviz.org/quickload/A_thaliana_Jun_2009/LFYChIPSeq/LFY.bam chr1 > chr1.sam
          [knet_seek] SEEK_END is not supported for HTTP. Offset is unchanged.
          $ samtools view -H http://igbquickload.org/quickload/A_thaliana_Jun_2009/LFYChIPSeq/LFY.bam chr1 > chr1.sam
          [knet_seek] SEEK_END is not supported for HTTP. Offset is unchanged.

          This may affect IGB.

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              ann.loraine Ann Loraine created issue -
              ann.loraine Ann Loraine made changes -
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              ann.loraine Ann Loraine made changes -
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              ann.loraine Ann Loraine made changes -
              Epic Link IGBF-236 [ 15233 ]
              mason Mason Meyer (Inactive) made changes -
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              mason Mason Meyer (Inactive) made changes -
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              mason Mason Meyer (Inactive) made changes -
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              ann.loraine Ann Loraine made changes -
              Assignee David Norris [ dcnorris ]
              ann.loraine Ann Loraine made changes -
              Summary investigate potential problem with QL random access investigate potential problem with QL samtools access
              ann.loraine Ann Loraine made changes -
              Story Points 0.5
              ann.loraine Ann Loraine made changes -
              Epic Link IGBF-236 [ 15233 ]
              ann.loraine Ann Loraine made changes -
              Workflow Loraine Lab Workflow [ 14718 ] Fall 2019 Workflow Update [ 18720 ]
              ann.loraine Ann Loraine made changes -
              Workflow Fall 2019 Workflow Update [ 18720 ] Revised Fall 2019 Workflow Update [ 20842 ]
              Status Open [ 1 ] In Progress [ 3 ]
              nfreese Nowlan Freese made changes -
              Assignee David Norris [ dcnorris ] Nowlan Freese [ nfreese ]
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              nfreese Nowlan Freese added a comment -

              Bam files have been moved off of the IGB Quickload site (mostly to scidas).

              I tested using samtools 1.9 Using htslib 1.9 on Mac.

              samtools view -H http://lorainelab-quickload.scidas.org/rnaseq/A_thaliana_Jun_2009/SRP059384/SRR2060634.bam

              The above command worked.

              Closing issue.

              Show
              nfreese Nowlan Freese added a comment - Bam files have been moved off of the IGB Quickload site (mostly to scidas). I tested using samtools 1.9 Using htslib 1.9 on Mac. samtools view -H http://lorainelab-quickload.scidas.org/rnaseq/A_thaliana_Jun_2009/SRP059384/SRR2060634.bam The above command worked. Closing issue.
              nfreese Nowlan Freese made changes -
              Assignee Nowlan Freese [ nfreese ]
              nfreese Nowlan Freese made changes -
              Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
              nfreese Nowlan Freese made changes -
              Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
              nfreese Nowlan Freese made changes -
              Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
              nfreese Nowlan Freese made changes -
              Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
              nfreese Nowlan Freese made changes -
              Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
              nfreese Nowlan Freese made changes -
              Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
              nfreese Nowlan Freese made changes -
              Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
              nfreese Nowlan Freese made changes -
              Resolution Done [ 10000 ]
              Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                People

                • Assignee:
                  Unassigned
                  Reporter:
                  ann.loraine Ann Loraine
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                  Dates

                  • Created:
                    Updated:
                    Resolved: