Issue is reproducible in 39.0, 40.0 versions.
Scenario:
- Load workflow sample "Convert alignment to ClustalW"
- Select "Read alignment" and add input file attached file gap_column_subalign_subalign.aln
- Run workkflow
Trying to recover from error: Empty alignment passed for writing to C:/Users/ccv/workflow_output/2021.09.20_22-41/output.aln at C:\BuildAgent\work\release\ugene\src\plugins\workflow_designer\src\library\DocWorkers.cpp:851