Summary
Trinity is a transcriptome de novo assembler exclusively for Illumina solexa data.
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1. There're three steps for Trinity assembly, inchworm, chrysalis, butterfly. If you have huge amount of reads, say over 50 million pair end reads, the backtracking step of butterfly might cause problems, the recursive calls consume so much memory that exceeds the default memory java can use (1G). The error you'll saw in the output is "java.lang.OutOfMemoryError: Java heap space".
The solution would be go into the output directory and find the file named "failed_cmds", rerun the command in it by changing "java -Xms1G ..." to "java -Xms5G ...".
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