Iva Veseli

Hey @Sirbius, let's see if we can figure out your problem :) It looks like the setup script was able to find the raw files you downloaded, which is great....

(Also @Sirbius - if you don't mind saying, what sort of issues are you having with the automatic download? If it is not a server-specific problem, we may be able...

@meren I tested it on my laptop, where I have the same sqlite version as @efogarty11: ``` $ sqlite3 --version 3.31.1 2020-01-27 19:55:54 3bfa9cc97da10598521b342961df8f5f68c7388fa117345eeb516eaa837bb4d6 ``` However, I am also on...

@meren, that was my only guess as to what had happened. We have all the proper calls to `disconnect()` as far as I can see in the migrate scripts, maybe...

>sounds like a race condition. Your I/O pressure is high or your CPU is busy? You see the problem. Makes sense. I was running `anvi-run-kegg-kofams -T 4` on several contigs...

I will take a look @meren :)

@dspeth and @meren, I have tested this in the development branch and it happily appears to be something we already fixed :) I was able to increase from 1 to...

I have added a warning ([commit](https://github.com/merenlab/anvio/commit/d22722ea598400c3996c0b61bb7eef1134784b44)), and now if you run anvi-get-sequences-for-hmm-hits on a database that does not have hits, you should see something like the following: ``` WARNING ===============================================...

The output from each thread gets put onto a queue after the thread finishes, and then each portion of the output is appended to a single file. This all happens...

>I'm afraid this is related to architecture depended differences how Python threads are handled Oh no :( The `multiprocessing` class (which is the one we use) is supposed to [run...