I am unable to get trinity to complete assembly of even simple data sets. I fetch an SRA file from NCBI, run trimmomatic, and wind up with R1-paired and R2-paired files (8.5G each) which I use as inputs to trinity, and I get errors every time. I assembled many transcriptomes with a similar trinity workflow last year with no problems - I started to work with some new species just last month, and nothing completes. I backtracked to files that worked last year, they all crash. I tried every possible permutation of concatenating the input files, making them a collection, they all crash. I cannot get it to complete on anything.
I’m sure there’s been a new version of trinity since last year, so I am hopeful that there is some parameter or input format that is new, a simple fix, or perhaps I need to somehow reformat my data. But I am completely stumped - would appreciate any help, or any test files that I could try.