-q (--sequential) option seems to be not working

[annahake]

Hi,
I use phyml Version 3.3.20190321 (from bioconda) from the command line.
When I start phyml with a sequential alignment file like your example file and with the option -q or --sequential, the program starts with
Command line: phyml -i primatesNT.phy -m GTR --sequential
end never finishes or actually starts running or giving any error code.
If I change the format to interleaved everything works.

[stephaneguindon]

Indeed... The github version works fine with the --sequential and -q options but the bioconda one seems to fail miserably... Maybe @epruesse has an idea?

[epruesse]

No clue... what does the option do?

@annahake You could try running gdb --args phyml.... and then run in the prompt gdb opens and then after a while press Ctrl-C to get back into the debugger and then see with bt command where in the code it is. Repeat for sampling.

[stephaneguindon]

--sequential aka -q set the value of io->interleaved to NO (the default being YES). PhyML then calls Read_Seq_Interleaved(io) (in case io->interleaved == YES) or Read_Seq_Sequential(io) (when io->interleaved == NO). Those two functions have been here forever and I don't imagine there could be any serious issue with them. I'm perplexed...

[epruesse]

Can you reproduce it?

[epruesse]

And, is this osx or linux or both?

[stephaneguindon]

I was able to reproduce the bug on ubuntu 18.04. I haven't tried any other architecture.

[annahake]

I tested it also on a linux machine.