Hi @elaheahmadi,
Thanks for posting your commands and file names. Your problem looks similar to this post here.
You are missing the 'source-format' parameter in your command and the default format of 'SingleLaneSamplePairedEndFastqDirFmt' is not right for your situation. Just override this by adding --source-format PairedEndFastqManifestPhred33 or --source-format PairedEndFastqManifestPhred64 depending on which format you have. This is described in the importing tutorial, at the bottom of the 'fastq-manifest-formats' section.
Lastly, make sure that either your --input path gives the correct path to your manifest file, or that you are entering the script from the directory in which it is in. Let us know if you are still running into any problems. Good luck!