I believe you have multiread fast5 files, as generated by recent versions of MinKNOW. A conversion script is available to convert these to the older, one-read one-file format. AFAIK Albacore is being deprecated and no version will be made supporting the multiread fast5 files, as Albacore is being replaced by Guppy.
The command line to convert from multi read fast5s to single read fast5s is as follows:
$multi_to_single_fast5 -i /path/to/fast5/ -s /path/to/save/output/
