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epruesse / SINA

SINA - Reference based multiple sequence alignment
https://sina.readthedocs.io
GNU General Public License v3.0
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LC_ALL requirement #72

Closed geboro closed 4 years ago

geboro commented 5 years ago

Hi! SINa is terminating with the following error: This is SINA v1.2.11 (revision 21227). PT server index missing. Building... sh: warning: setlocale: LC_ALL: cannot change locale (C.UTF-8) arb_pt_server: arb_pt_server: no version information available (required by arb_pt_server) arb_pt_server: arb_pt_server: no version information available (required by arb_pt_server) arb_pt_server: arb_pt_server: no version information available (required by arb_pt_server) arb_pt_server: arb_pt_server: no version information available (required by arb_pt_server) arb_pt_server: relocation error: arb_pt_server: symbol , version not defined in file with link time reference terminate called after throwing an instance of 'sina::query_pt::exception' what(): Failed to (re)build PT server index! (out of memory?) Aborted

I can modify LC_ALL, but I'm not sure which locale is required by SINA... any ideas? Thanks!

epruesse commented 5 years ago

Hi @geboro!

Can you update to 1.6.0? It's available via Bioconda (highly recommended) as well as via the releases page here.

W.r.t. to your problem - you probably ran out of memory. The LC_ALL is just a warning, and actually issued from the shell. Don't worry about that. It terminated because the "ARB PT server" exited without building an index, which is usually because it didn't have enough memory. You could try shutting down all other applications, but I really recommend just updating from the (ancient) 1.2.11 to the 1.6.0. That one no longer uses the PT server by default, is some 10x faster, uses all your computer's cores, and needs much less memory.

epruesse commented 4 years ago

Closing due to inactivity