Hello! Thanks for the detailed report and sorry for the late reply!
Regarding the first error, it seems that TopHat was not able to map the reads, so there were no output. Please do the following:
1) Make sure that the reference sequence, that you provided, is the correct one for the data.
2) Try to filter/trim/etc. your input NGS data (i.e. FASTQ files) BEFORE using the Tuxedo workflow. For example, use this workflow:
https://ugene.unipro.ru/wiki/display/WDD21/Raw+RNA-Seq+Data+Processing.
3) Check out any errors of TopHat in the log.
Also, see these NGS tutorials:
LINK. There are some sample data, you may run the workflow using them to make sure that it works in your environment.
As for the second error, we will follow your advice and fix this issue in the nearest future (see issue
UGENE-5255). And we will also correct the error message in the first case (
UGENE-5256). Thanks again for the report!