The new default settings for topaz (discussed here) are very helpful! But every time I use topaz on a large dataset, I invariably forget to split it beforehand and systematically run into this infamous Argument list too long error.
I can always work around this error by splitting the exposures into random subsets of 5000 exposures (I have not tried larger subsets, and I suspect the max number of arguments depends on the configuration of the underlying Linux system anyway). But this trips up every newcomer I teach how to use topaz from within CryoSPARC, and since the error message doesn’t suggest a solution these people remain puzzled until I explain what the problem is and how to fix it.
Some time ago, @nfrasser proposed a solution to this, see Support long argument list specified as file for all topaz commands by nfrasser · Pull Request #192 · tbepler/topaz · GitHub
So, for those of you around here experiencing the same frustration (still battling with this @olibclarke ?), maybe a thumbs up on this GitHub PR or even a message with a gentle nudge could help get the topaz developers’ attention on this.