The size of the output FASTQ file is different when the -t argument is greater then 1.
I found that it might be caused by line 124 in kneaddata/trf_parallel.py
Since file_handle_write is always not None after the file is opened(line 124), only the first temporary file is appended to the tempfile_written_list and datfile_to_write_list (line 115~116). As a result, the trf command actually executes only one parallel temporary file.
Here is the PR fix: append all split FASTA files to the list for TRF execution by weichisyu · Pull Request #45 · biobakery/kneaddata · GitHub that aims to fix this issue.
Version: The commit of KneadData I am using is 90c05f3cd25a8c74a4d804f27dd0ce52718007d8