Open aldendirks opened 7 months ago
If it's not too late, what was the command you used to run iqtree in the first place?
Hi @aldendirks, Thank you for using IQ-TREE/AliSim. Your bug report contains 3 questions, please find my answers below.
There is no ALISIM information in concat.log as the tutorial states (visible to my eyes with a manual checkover and also confirmed with cat concat.log | grep "ALISIM". I do see information on ALISIM in the concat.iqtree file visible with tail -n 100 concat.iqtree.
=> To improve the visibility, we changed to output AliSim command to the main output of IQ-TREE (i.e., .iqtree file) instead of the log file (i.e., .log, which captures everything from the console). I updated the relevant tutorial (on IQ-TREE wiki), which will be synchronized to IQ-TREE doc later.
Is this the information I can use in the likelihood sCF command? Do I specify -m trimmed_alignments.best_model.nex?
=> I need to discuss this with @bqminh @roblanf. Will come back to you once I've got the answer.
By the way, this file actually doesn't exist for me... maybe it is referring to concat.best_model.nex. The directory with the alignments is called trimmed alignments but prefix was set to "concat".
=> Yes, it should be concat.best_model.nex. This is a bug, which has been fixed. This bug fixed will be included in the next release of IQ-TREE.
There is no ALISIM information in
concat.log
as the tutorial states (visible to my eyes with a manual checkover and also confirmed withcat concat.log | grep "ALISIM"
. I do see information on ALISIM in the concat.iqtree file visible withtail -n 100 concat.iqtree
. This is the relevant section:Is this the information I can use in the likelihood sCF command? Do I specify
-m trimmed_alignments.best_model.nex
?By the way, this file actually doesn't exist for me... maybe it is referring to
concat.best_model.nex
. The directory with the alignments is called trimmed alignments but prefix was set to "concat".Thanks for your help!