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  1. UGENE
  2. UGENE-8072

[safe_point, pdb] Empty sequence

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    • Tests Type:
      GUI automatic
    • Affect Type:
      Userdefined

      Description

      The file from the issue 7953 opens with an empty chain B sequence. This causes the sequence to be incorrectly identified as DNA.

      Moreover, the following SAFE_POINTs occur:
      0. Make sure the currently selected sequence is the "chain B sequence".
      1. Open the OP "Statistics" tab.
      Trying to recover from error: U2Region::sumLength(regions) != 0 at C:\BuildAgent\work\release\ugene\src\corelibs\U2View\src\ov_sequence\sequence_info\DNAStatisticsTask.cpp:350
      2. Open the OP "In Silico PCR" tab. Insert "AAAAAAAAAAAAAAA" as Forward and Reverse primers. Click "Find product(s) anyway".
      Trying to recover from error: Invalid sequence length at C:\BuildAgent\work\release\ugene\src\plugins\pcr\src\InSilicoPcrProductsTable.cpp:63
      3. Main menu->Actions->Analyze->Find high DNA flexibility regions... In the "DNA Flexibility" dialog that appears, click "Search".
      Trying to recover from error: Internal error: a user is not allowed to input such window step at C:\BuildAgent\work\release\ugene\src\plugins\dna_flexibility\src\FindHighFlexRegionsAlgorithm.cpp:43
      4. In the Project View, right-click on chain B sequence->Export/Import->Export sequences... In the "Export Selected Sequences" dialog that appears, click "Save both strands", then Export.
      Trying to recover from error: Invalid DBI reference at C:\BuildAgent\work\release\ugene\src\plugins\dna_export\src\ExportSequenceTask.cpp:138
      5. In the Annotations Editor, expand chain B annotation [multi_model_with_ter.pdb]- >chain_info (0, 1)- >chain_info. Then right-click on chain_info->Export->Export sequence of selected annotations... Confirm the "Export Sequence of Selected Annotations" dialog that appears.
      Trying to recover from error: Invalid DBI reference at C:\BuildAgent\work\release\ugene\src\plugins\dna_export\src\ExportSequenceTask.cpp:138
      Trying to recover from error: Got an empty object name, type: OT_SEQUENCE at C:\BuildAgent\work\release\ugene\src\corelibs\U2Core\src\models\GObject.cpp:41
      6. Open any annotation file (for example, data/samples/Genbank/CVU55762.gb) and drag the annotation object from the Project View into the 3D Structure Viewer window.
      Trying to recover from error: Invalid sequence length provided! at C:\BuildAgent\work\release\ugene\src\corelibs\U2Core\src\gobjects\AnnotationTableObject.cpp:255
      7. Open any chromatogram file (for example, data/samples/ABIF/A01.abi). Drag the "chain B sequence" object from the Project View to the chromatogram window. Then click "Lock scales". The Chromatogram Viewer becomes empty. Try holding the mouse button inside this viewer and moving it.
      Trying to recover from error: Last mouse press position is out of visible range! at C:\BuildAgent\work\release\ugene\src\corelibs\U2View\src\ov_sequence\GSequenceLineView.cpp:170
      8. Build dotplot with the bad sequence.
      Task Searching repeats finished with error: Subtask Find Repeats is failed: Repeat length is too large: 2, sequence size: 0
      Try to move the plot.
      Trying to recover from error: Failed to update visible range. Range is out of the sequence range! at C:\BuildAgent\work\release\ugene\src\corelibs\U2View\src\ov_sequence\GSequenceLineView.cpp:470
      9. Build the GC Content graph.
      Trying to recover from error: Illegal sequence length at C:\BuildAgent\work\release\ugene\src\corelibs\U2View\src\ov_sequence\ADVGraphModel.cpp:410

      In addition, all dialogs that require entering a region (region 0-0 is invalid, and any other is more than a sequence), NCBI queries (GET https://blast.ncbi.nlm.nih.gov/Blast.cgi?&CMD=Put&PROGRAM=blastn&EXPECT=10&HITLIST_SIZE=20&DATABASE=nr&FILTER=L&GAPCOSTS=5 2&NUCL_REWARD=2&NUCL_PENALTY=-3&WORD_SIZE=11&TOOL=ugene&EMAIL=ugene-ncbi-blast@unipro.ru&QUERY=), export as alignment, and many other components stopped working.

      My suggestions: correctly read the amino acid sequence of the second chain of the second model. It should be equal to M (check how the second model is displayed at https://www.rcsb.org/3d-view). Otherwise, if the sequence is incorrect according to the PDB format, don't display the sequence at all (skip it as is done for the FASTA format).

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              Assignee:
              biserova Evelina
              Reporter:
              biserova Evelina
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                Dates

                Created:
                Updated: