Tuxedo pipeline doesn't work on data drosophila data

An error occurs when Tuxedo pipeline is run on data specified in the Tuxedo article:

• Input paired-end reads datasets:
  1) GSM794483_C1_R1_1.fq.gz and GSM794483_C1_R1_2.fq.gz (i.e. C1_R1)
  2) GSM794484_C1_R2_1.fq.gz and GSM794484_C1_R2_2.fq.gz (i.e. C1_R2)
  3) GSM794485_C1_R3_1.fq.gz and GSM794485_C1_R3_2.fq.gz (i.e. C1_R3)
  4) GSM794486_C2_R1_1.fq.gz and GSM794486_C2_R1_2.fq.gz (i.e. C2_R1)
  5) GSM794487_C2_R2_1.fq.gz and GSM794487_C2_R2_2.fq.gz (i.e. C2_R2)
  6) GSM794488_C2_R3_1.fq.gz and GSM794488_C2_R3_2.fq.gz (i.e. C2_R3)

• Split datasets to samples: first three datasets to the first sample, last three datasets to the second sample.

• Bowtie index of drosophila_melanogaster: "BDGP5.25/Sequence/Bowtie2Index/genome.*" files from the iGenome package
• Known transcript file: file "BDGP5.25/Annotation/Archives/archive-2013-03-06-11-13-59/Genes/genes.gtf"

UGENE version used 4 threads.

Note: the data can found on the UGENE local file server in "data/tuxedo_paper_data" directory.