RNA-seQ trinityrnaseq-2.1.1 different runs get different transcripts!

[nufangdeshengming]

sorry,my title is wrong ,i mean that the same run gets the different transcripts!
I use trinityrnaseq-2.1.1 to assemble the reads to get the transcripts.First i try the following command "bash runMe.sh",using the sample data located in
trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly,and i get the result trinity.fasta which is located in the directory trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir.
Next,i try the following commands "Trinity -seqType fq -max_memory 2G -left reads.left.fq,reads2.left.fq -right reads.right.fq,reads2.right.fq -SS_lib_type RF -CPU 4",and i get the reasult trinity.fasta.But when i examine the two results above, i find that i get almostly the absolutely different results,i try to search
on google ,but cannot get the answer,is there some get the same result as mine?

[westerman]

Well, Trinity is non-deterministic. Because it chooses some running conditions randomly it will not run exactly the same between runs. But the differences should be minor.

[nufangdeshengming]

But the key point is that it is not just "a few minor differences",there are many differences between them , i donnot what is wrong ,shouldn't the two commonds get almostly the same results?