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Type:
Bug
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Status: Closed
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Priority:
Major
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Resolution: Fixed
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Affects Version/s: 1.29
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Fix Version/s: 1.30
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Component/s: Basic-MSA, Basic-Nucl
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Story Points:1
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Epic Link:
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Sprint:DEV-30-3
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Affect Type:Userdefined
Possible values of CAP3 parameters are set incorrent in the "Contig Assembly with CAP3" dialog, for example, try to set value of the "Overlap percent identity cutoff" to "65". As a result UGENE returns an error notification:
CAP3 tool exited with code 1
In the TRACE log it is written that:
Value for overlap percent identity cutoff must be > 65
Correct the possible values as follows (use maximum/minimum possible values for not specified values):
| № | Parameter | Min value | Max value |
|---|---|---|---|
| 1 | Band expansion size | 10 | Not specified |
| 2 | Base quality cutoff for differences | 16 | 99 |
| 3 | Base quality cutoff for clipping | 6 | 99 |
| 4 | Max qscore sum at differences | 21 | Not specified |
| 5 | Max gap length in any overlap | 2 | Not specified |
| 6 | Gap penalty factor | 1 | Not specified |
| 7 | Match score factor | 1 | Not specified |
| 8 | Mismatch score factor | Not specified | -1 |
| 9 | Overlap length cutoff | 16 | Not specified |
| 10 | Overlap percent identity cutoff | 66 | Not specified |
| 11 | Overlap similarity score cutoff | 251 | Not specified |
| 12 | Max number of word matches | 31 | Not specified |
| 13 | Clipping range | 6 | Not specified |
- relates to
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UGENE-5991 Modify the CAP3 dialog
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- Closed
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