What happens to intermediate Trinity files when assembly terminated pre-completion

Question

[peri.tobias]

I am assembling de novo transcriptomes using Trinity 2.1.1 on high performance computer cluster at my institution. My initial assembly ran out of wall-time at 65 hours. I left the intermediate files/folders within the directory and re-ran the assembly which completed in 6 hours.

I would like to know this:

• When the assembly is stopped and then re-run, does Trinity look for intermediate files (from previous run) to continue the assembly.
• If not, is it adviseable to remove intermediate files to avoid corrupting the second run.

Answer 1

[Chris Fields]

Trinity stores intermediate files during the run, and should pick up at the last step successfully completed.

EDIT: it's a good idea to redirect the output to a log file when running, then using tail to make sure everything's fine.