Error in MapSplice

[rbloom5]

Hello all,

I am using MapSplice to process RNA seq reads. I get the following output:

[Sun Mar 20 23:28:09 2016] Beginning Mapsplice run (v2.0)
-----------------------------------------------
bin directory: [/home/ubuntu/Packages/MapSplice_multithreads_12_07/bin/]
[Sun Mar 20 23:28:09 2016] Checking for files or directory
[Sun Mar 20 23:28:10 2016] Checking for files or directory
[Sun Mar 20 23:28:10 2016] Checking for files or directory
[Sun Mar 20 23:28:10 2016] Checking for Bowtie index files
[Sun Mar 20 23:28:11 2016] reads all chromo sizes
[Sun Mar 20 23:45:27 2016] check reads format
[Sun Mar 20 23:45:59 2016] Run MapSplice multi-thread
[0] return code
[Mon Mar 21 02:41:01 2016] combine to file 64FIOR4W-RiboZero/tmp/original/original.sam
[Mon Mar 21 02:41:04 2016] remove files ['64FIOR4W-RiboZero/tmp/original/original.sam.1', '64FIOR4W-RiboZero/tmp/original/original.sam.2', '64FIOR4W-RiboZero/tmp/original/original.sam.3', '64FIOR4W-RiboZero/tmp/original/original.sam.4', '64FIOR4W-RiboZero/tmp/original/original.sam.5', '64FIOR4W-RiboZero/tmp/original/original.sam.6', '64FIOR4W-RiboZero/tmp/original/original.sam.7', '64FIOR4W-RiboZero/tmp/original/original.sam.8']
[Mon Mar 21 02:41:18 2016] convert sam files to junctions
[FAILED]
Error: convert sam file to junctions failed


I can't find any other insight into what the error is or why the program failed. Any suggestions?