I have been trying to get Trinity running for the last week I have two fastq files that I have been trying to run. One is a raw fastq (no trimming) about 17.5 GB (pre and post Fastq Groomer), one is a trimmed fastq about 15.8 GB (pre and post Fastq Groomer). I am trying to run single strand. I have tried F, R, and Not Set for direction. I have dumped all the data sets that were up previously to free up space. I have tried changing the data type from fastqsanger to fastq. I currently have one post Fastq Groomer file up (15.86 GB) and it is still hanging. Nothing I have tried seems to work.
RNA STAR worked fine, even on the raw data. However, I am trying to do a de novo assembly, so Trinity looks like the only option available. Any insights welcome.