I wouldn't claim Java is the best language, but I don't see obvious deficiencies in JVM, in comparison (good, well thought-out comparison) with alternatives. Same for language - not only Java runs a hard task of strong backward compatibility for the third decade, it actually managed to implement some afterthought additions tolerably.
So - while in the end the author might still be correct - arguments needed.
From APL point of view C could be conidered below "barely tolerable", which doesn't prevent its, C, widespread use. It's hard to have a language convenient for all kinds of problems, so I'd like to learn details in your case.
For the genomic data of a single human, we would model our sequencing data as one of (if i remember how i did it) 5 values, for each position in the roughly 3 billion bases we tracked. So the representation of a genome was required roughly 3 billion instances of 3 bits each, but this wasn't how Apache Spark was written to calculate, you end up wasting 2 bits per byte in any semi fast packing scheme, but every byte is being shuttled around endlessly over the network.
We fiddled around with various representation schemes but were always forced into wasting bits that we had no fast means (via processor intrinsics) of moving around.
That's somewhat vague, but hopefully conveys the essence of the frustration.