Open bluegenes opened 2 years ago
I can't replicate this on farm nodes c6-58
or bm10
- but I believe it happens ;). I've seen weird things happen with sqlite on the nodes on our HPC. I think it has to do with locking, but that's just a guess.
Next time you run across this problem, could you record the specific node and filesystem you're on? thanks!
I'm seeing some odd behavior, but not sure if this is server-related or sourmash related.
On a compute node,
tax prepare
will refuse to prepare a new lineages database, saying the table already exists. After running, a new file of that name exists but is empty.file:
512 -rw-r--r-- 1 ntpierce ctbrowngrp 0 Aug 15 15:14 gtdb-rs207.taxonomy.db
On the login node, running the exact same command seems to work, even without removing the empty file.
file:
15M -rw-r--r-- 1 ntpierce ctbrowngrp 54M Aug 15 15:17 gtdb-rs207.taxonomy.db
Running the command again once the file is non-empty produces the error seen above.