As hrhotz indicated, the reads in two fastq files are not in the same length in the paired-end data after filtering data with “filter by quality” tool. “Reruning” has not led to any solution. What I did not understand from the thread is what is meant “corrupt file” and how to fix it.
I am familiar with all tutorials given in the links. I revised them quickly and to be honest, No idea occurred to me regarding the problem.
I used SRA files and did not intervene into the any files except for running in turn “fastp + filter by quality” tools . I think something happens after using these two tools… Anyways thanks for your prompt response and help. I will not feed input files, obtained by “filter by quality” tool to Hisat2, since its single or combined usage(i.e, with other tools) creates the same problem…