Hi @Brigitta1,
thanks for the information! The main question then is if you have installed QIIME1 as well as you have its conda environment active while you running the python script.
The metadata file includes the information related to each sample you have processed, then you will have all the sequences produces for a sample in its fastq file.
Again, I would suggest to work with qiime2 and not qiime1 which may be more tricky to use.
In particular, I found thesethreads related to Ion Torrent data:
After you import the sequences inti qiime2, you will be able to export the number of sequences per each sample easily!
Hope that helps
Luca