mothur

Make.contigs not written to log after seg fault error, v1.44.3

I noticed that in recent versions of Mothur (at least as far back as 1.44.1), if make.contigs command encounters a segmentation fault, no details are written to the log file. The make.contigs command itself is not written to the log file. Mothur simply exits with the error. In my log file, I have no record of what happened, and no record of the last command run (make.contigs).

However, when playing around with an older version (v1.42.1), I noticed that the segmentation fault error does appear in the log file. It has some helpful messages about the error as well. I think this functionality was ideal.

It would be nice if the log file gets updated at the start of the command given, and if the segmentation fault error could be written to the log before Mothur exits. Is it possible to bring this back?

Thanks for bringing this to our attention. We changed the logging features to buffer the log output. This allows the user to set a log file name or silence logs before the log is generated. The make.contigs command is failing before the buffer can be written. We will revisit the design of this feature. You can follow the progress here, Revisit buffered logs · Issue #760 · mothur/mothur · GitHub.