This message repeating means that you have many reads that are too short to assemble.
Try filtering out reads that are too short to be used, then rerun. The job is seems to be running out of resources when attempting to sorting out usable read pairs from those that are not. Pre-filtering by length will address that. Use a QA tool that will remove/separate both ends of a pair if one of the paired reads fails the filter. Trinity expects intact pairs as an input.
If it seems like that length filter eliminates too many reads:
- prior QA steps may have been too strict
- you need to still run QA
- the reads were originally too short
- the read quality is actually low, and the QA steps are correct
The last two would be the most concerning re is this data even usable?
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Thanks!