repeating the same analysis with different outputs

[leogg-github]

Hi everyone,

I have ran the same analysis twice with the same data. The first time I got a complete chloroplast and the second time I get three scaffolds. On the attached log files you will see the names of the files are changed but they correspond to exactly the same source files including a fasta seed file. The log seems to be pretty much the same until the program does the slimming. I have no idea why this is happening. Any help would be much appreciated. Thanks!!

get_org.log_run 1.txt
get_org.log_run2.txt