field missing, sequence preparation errors

I am a newbie here.

I am working on converting genome/gtf data to FASTA file format and using flux-simulator for that. The demo example from the flux-simulator works without any problem.
After that, I downloaded genome and gtf data from http://hgdownload.soe.ucsc.edu/downloads.html, https://genome.ucsc.edu/cgi-bin/hgTables?command=start.

But while running mouse(mm9) gtf, it does not work at all and shows the error:
[ERROR] Error while loading stats: Field 5 not found
java.lang.IllegalArgumentException: Field 5 not found


I also tried to run flux simulator for "fly" genome.

I got this error:
[INFO] Loading default PCR distribution
        preparing transcript sequences ** ERROR
[ERROR] Error while preparing sequences:
[ERROR] Error while fragmenting : Problems reading sequence chr2L: pos 22877860, len 82,
check whether chromosomal sequence exists / has the correct size
java.lang.RuntimeException: Problems reading sequence chr2L: pos 22877860, len 82,


Can you please tell how to solve these problems?