Getting gCF and sCF values

[Steve G]

I am using hybseq target capture dna sequence data and have been trying to get gene and site concordance factor values following this page (http://www.iqtree.org/doc/Concordance-Factor). 

I already ran my data through iqtree once to make standard bootstrap gene trees using this:

iqtree -s <input file> -nt AUTO -ntmax 4 -m TEST -bb 1000 -wbtl -czb

So I already have a species tree and a concatenated .treefile. But when I try and use these files in this command

iqtree2 -t <concat.treefile> --gcf <gene.treefile> --prefix concord

the gCF values I get don't match up with the bootstrap support values. 

So I want to start over following the commands on the page I linked above. I tried to use this command

iqtree2 -p ALN_DIR --prefix concat -B 1000 -T AUTO

Which worked according to the .log file, but I didn't get any output files other than a log file. So I have a few questions at this point. Is the command above the same thing as running this

iqtree2 -s ALN_FILE -p PARTITION_FILE --prefix concat -B 1000 -T AUTO

and if so why am I not getting any output files other than the .log file. If these commands do not do the same thing how do I make a partition nexus file to use with this command?

Thanks

[Bui Quang Minh]

Are there any error/warning message(s) from the log file. If yes, can
you paste them here?

(I tend to think that if only the log file is produced, then there may
some errors which makes IQ-TREE stopped prematurely)

Minh

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