'block' gzip files (see page 10 here: http://samtools.github.io/hts-specs/SAMv1.pdf), are commonly used in bioinformatics. They are valid gzip files, but use the somewhat rare scheme of storing the data in many consecutive gzip blocks. System gunzip or zcat will yield all the data in all blocks, however flate2:GzDecoder will only yield data from the first block. I believe that correct behavior is to continue reading the steam to find another block until EOF.