A query to the source code of FASTX Toolkit shows that this error messages is printed when FASTX tools are given an empty file. Indeed:

$ touch empty # creates an empty file called "empty" (if there was no such file)

$ fastq_quality_trimmer -t 10 -i empty
fastq_quality_trimmer: Premature End-Of-File (filename ='empty')

$ echo -n | fastq_quality_trimmer -t 10
fastq_quality_trimmer: Premature End-Of-File (filename ='-')

Therefore, your input was most likely an empty file or an empty stream.