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Type: Bug
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Status: Open
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Priority: Minor
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Resolution: Unresolved
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Affects Version/s: None
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Fix Version/s: None
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Component/s: None
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Labels:None
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Sprint:DEV-51-3, DEV-51-4, DEV-51-5, DEV-51-RELEASE, DEV-52-1
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Affect Type:Userdefined
Scenario1: If the path to the reference contains a semicolon, then the alignment will start but fail with an error.
- Create folder with this name "Sanger;output".
- Put attached reference in this folder.
- Select Tools-> Sanger data analysis->Maps reads to reference.. menu item
- Add reference from "Sanger;output" folder.
- Add 2 attached reads
- Click Map button
Process is not finished successfully.
[ERROR][11:42] process:12824>Task
{Workflow run from cmdline}finished with error: Map to Reference: 'D:/sanger' is not a file Map to Reference: File not found: 'D:/ugene/src/ugeneui/outpit/reference.gb' see 'ugene --help=align-to-reference' for details
Scenario2: If the path to the reference does not contain a semicolon, but the reads do, then the alignment will start, but reads whose path contains a semicolon will not participate in it.
- Create folder with this name "Sanger;output".
- Copy 2 attached reads in this folder.
- Select Tools-> Sanger data analysis->Maps reads to reference.. menu item
- Add reference from attachment
- Add read from Sanger;output folder
- Click Map button
Process is not finished successfully.
[ERROR][12:21] process:9700>The trimming was skipped for the sequences without quality information.
[ERROR][12:21] process:9700>The trimming was skipped for the sequences without quality information.
[[ERROR][12:12] process:3316>Subtask
{Compose alignment} is failed: The related chromatogram not found[ERROR][12:12] process:3316>Subtask {Map to reference} is failed: Subtask {Compose alignment}
is failed: The related chromatogram not found
[ERROR][12:12] Task
finished with error: Subtask
{Compose alignment}is failed: The related chromatogram not found
Scenario3: Sanger data analysis in Worklow Designer
- Put all 3 attached files in "Sanger;output" folder.
- Open WD
- Open workflow sample Trim and map Sanger reads.
- Select Read Sequence item and add one read from "Sanger;output" folder.
- Select Map to reference item and add reference from "Sanger;output" folder.
Error dialog appears, see attachment shapshort1.png
One more issue: no Russian translation for this dialog.
- relates to
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UGENE-5291 WD can't work with files with ; in name
- Tested