MUSCLE align fails with an meaningless error in GUI and crashes in WD

Scenario to reproduce 1:

1. Open "data/samples/CLUSTALW/ty3.aln.gz".
2. Select {Align -> Align sequences to profile with MUSCLE...}

   item in the context menu.

3. Wait for a task finish.
4. Select {Align -> Align with MUSCLE...}

   item in the context menu.
   Expected state: the msa is successfully aligned.
   Current state: the task fails with an error:

   [ERROR][18:39] Task {MUSCLE align 'ty3.aln.gz'} finished with error: Subtask {Workflow wrapper 'MUSCLE align 'ty3.aln.gz''} is failed: Subtask {Run workflow: align} is failed: Subtask {Read document: 'N87489.fasta'} is failed: Document is empty.

There is another error in debug build:

[ERROR][18:24] Task {MUSCLE align 'ty3.aln.gz'} finished with error: Subtask {Workflow wrapper 'MUSCLE align 'ty3.aln.gz''} is failed: Subtask {Run workflow: align} is failed: Subtask {Workflow process} is failed: The process '/Users/atiunov/root/projects/clear/clear_tr/installer/macosx/debug_bundle/ugeneuid.app/Contents/MacOS/ugenecld' crashed some time after starting successfully

Scenario 2:

1. Open an attached alignment
2. Align it with MUSCLE
   Current state: there is an error in the log

   Document is empty

3. Open WD sample "Align with MUSCLE" and set input data to the same file
4. Run the workflow
   Current state: UGENE crashes

Also we have crash report with same error: http://ugene.net/ugenecrashes?id=8306