conda install numpy=1.10.4
If successful, see if the prior commands will complete.
Is this supposed not enough to run any typical microbial diversity analyses?
How do you think whether it might be originated in the procedure of qiime1 during converting my Sanger fasta dataset to the one which can be used in qiime2 pipeline?
Considering this is from qiime2 process, let me consult this problem in qiime2 forum, too.
I'm sorry that I don't have an answer on this (i've not tried Sanger data in QIIME2). The 97% clustering approach (vsearch, I assume) seems appropriate to use for this data, since you can't use the denoising software (dada2 or deblur, made for Illumina error models).
When you first ran it, did it not make a tree with matching tips to the OTUs?
That's the only thing I can think of offhand that would give you an OTU counts object that worked (did it give reasonable clustering?) for, e.g. bray-curtis but not for UniFrac or PD in alpha diversity.