Log Messages
As SEISMIC-RNA runs, it writes messages to the terminal (standard error) and to a log file. Messages are ranked by level from most to least important:
Level |
Name |
Used for |
|---|---|---|
-2 |
Error |
Problem causing all or part of SEISMIC-RNA to fail |
-1 |
Warning |
Abnormal event from which recovery is possible |
0 |
Info |
Major normal events: helpful for monitoring progress |
1 |
Debug |
Minor normal events: helpful for monitoring more closely |
2 |
Trace |
Finer detail: helpful for troubleshooting |
Controlling terminal output
By default, Info (0) and more important messages appear in the terminal.
Use --verbose (-v) to see more; --quiet (-q) to see less.
Each additional -v or -q shifts the threshold by one level:
Flag |
Shows in terminal |
|---|---|
-vv |
Trace and above (everything) |
-v |
Debug and above |
(none) |
Info and above (default) |
-q |
Warning and above |
Error only |
These flags must go between seismic and the subcommand:
seismic -v cluster out/sars2-fse
Log files
By default, messages are also written to a log file at:
./log/seismic-rna_YYYY-MM-DD_hh-mm-ss.log
Use --log PATH (between seismic and the subcommand) to choose a
different path, or --log "" to disable log files.
The log file records messages at the same verbosity level as the terminal,
so -v enlarges both the terminal output and the log file.
Each line in the log file is prefixed with a timestamp:
2026-06-04 14:22:01.123456 Info 12345 Clustering sars2-fse / region fse
To view a log file, open it with less:
less -R log/seismic-rna_2024-04-08_15-20-09.log
The -R flag causes less to render the document in color (if the default
colored log messages are enabled); without it, less just prints the ANSI codes
for the colors, which makes the document harder to read.
To see new messages appear instantly as they are written to the log file, press Shift-F when less is open. Press Ctrl-C to stop the continuous updates, then q to quit less.