I got twice the same error by running Trinity on Galaxy, that is:
Thread 1 terminated abnormally: Error, counts of reads in FQ: 40001112.25 (as per cat /pylon5/mc48nsp/xcgalaxy/main_staging//15659867/inputs/dataset_19697450.dat | wc -l) doesn't match fastool's report of FA records: 40001113 at /opt/packages/trinity/2.2.0/Trinity line 3087 thread 1.
As a consequence Trinity stops producing an empty file.
As far as I know that seems to be something related with the number of reads inside the loaded files but I have no idea how to deal with that (it looks more like a Trinity bug on Galaxy). That is, in my opinion, quite unusual because the same workflow has been running multiple times with many samples from the same experiment.
N.B. --> The same error is given independently from two samples processed separately.
Anyone can give me some tips?