[UGENE-5533] WD: Crash in "Trim and align Sanger reads" when reference contains wrong symbols Created: 02/Mar/17  Updated: 31/May/18  Resolved: 26/Jun/17

Status: Closed
Project: UGENE
Component/s: Basic-MSA, Basic-Nucl, Workflow
Affects Version/s: 1.26.1
Fix Version/s: 1.26.3

Type: Bug Priority: Major
Reporter: Svetlana Samoilenko Assignee: Aleksey Tiunov [X] (Inactive)
Resolution: Fixed  
Labels: crash, sanger, stability
Remaining Estimate: Not Specified
Time Spent: Not Specified
Original Estimate: Not Specified
Environment:

Windows 64

Issue Links:
Relates
relates to UGENE-5620 Message when input reference alphabet... Closed
relates to UGENE-5667 Error in log when workflow is execute... Closed
Story Points: 1
Assigned Tester: Dmitrii Sukhomlinov
Epic Link: Sanger
Sprint: DEV-27-5, DEV-27-6, DEV-27-7
Affect Type: Userdefined

 Description   

Reproducible on 1.26.1 release

1. Select "Trim and аlign Sanger reads" in Workflow Designer
2. Set Reference =.../test/general/_common_data/alphabets/standards_rna_1000.gb where first symbols changed with illegal value ="*".
3. Set correct reads from .../test/general/_common_data/sanger
4. Push Run on Results page
Crash

 Comments   
Comment by Denis Kandrov [ 02/May/17 ]

I get a bellow error message:

(1) No reference sequence in the file: /home/dkandrov/ugene/trunk_new/test/general/_common_data/alphabets/standard_rna_1000_copy1.gb

I checked on commit https://github.com/ugeneunipro/ugene/commit/6a4e188b198c57b436fd08b23a07203d61046c67

Comment by Denis Kandrov [ 02/May/17 ]

Please attach an incorrect file with reference. It maybe help to reproduce.

Comment by Yuliya Algaer [ 15/May/17 ]

Reviewed.

Comment by Aleksey Tiunov [X] (Inactive) [ 24/May/17 ]

It is reproducable on the release branch. It should be fixed for the minor release.
Check, that everything is OK for modified reference in FASTA format.
Ensure, that error messages are meaningful in master branch.

Comment by Dmitrii Sukhomlinov [ 06/Jun/17 ]

Error message is not meaningful for user

Subtask

Unknown macro: {Align reads with BLAST & SW task}

is failed: Subtask

Unknown macro: {Align one read with BLAST & SW task}

is failed: Subtask

Unknown macro: {Run NCBI BlastAll task}

is failed: [blastall 2.2.26] FATAL ERROR: Database C:/Users/dsukhomlinov/AppData/Local/Temp/ugene_tmp/p9804/align_to_ref/d_0 was not found or does not exist

Comment by Aleksey Tiunov [X] (Inactive) [ 26/Jun/17 ]

The error message fix should be done in UGENE-5620.

Comment by Yuliya Algaer [ 28/Jun/17 ]

Reviewed.

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