I need to give the customary message that QIIME 1 is no longer being updated, and support/features are going to be found in QIIME 2: https://qiime2.org/
Unless you've got a particular reason to use QIIME 1 for this analysis, it would probably be better to switch to QIIME 2. As for your particular issue, you would have to resolve the problem of the sequences failing to align to the core alignment. Since apparently no sequences are aligning, that means something is making your reads not match 16S.
1. Are these reads bacteria/archael 16S ribosomal small subunit reads?
2. Is it possible that there are non-16S PCR or sequencing artifacts in your reads, e.g. Illumina adapters, spacers, or barcodes? You may have to manually inspect some of the reads to determine this.