identical sequences not added at the end with the --no-outfiles option

[Cecile Ane]

I got trees that were missing some tips when using the --no-outfiles option, but the problem is not systematic. The log says that the identical sequences that are ignored will be added back in the tree at the end, but there are not.

To reproduce the issue, I am attaching 2 alignment files: "a1" has 24 tips (many identical to each other) and 400 base pairs. The problem occurs on this data set. The other data set "a2" is a toy data set with just 5 tips (the last 2 are identical) and 10 base pairs. The problem does not occur on that second data set. Below are shell commands to run IQ-TREE without and with the --no-outfiles option, and then commands to count the number of commas in the output trees, which relates to the number of tips in these output trees. Tips are kicked out on the first data set with the --no-outfiles option.

iqtree -s a1.phy -djc -m HKY+G -pre trial11
iqtree -s a1.phy -djc -m HKY+G -pre trial12 --no-outfiles
grep -o "," trial11.treefile | wc -l # 23
grep -o "," trial12.treefile | wc -l # 5
iqtree -s a2.phy -djc -m HKY+G -pre trial21
iqtree -s a2.phy -djc -m HKY+G -pre trial22 --no-outfiles
grep -o "," trial21.treefile | wc -l # 4
grep -o "," trial22.treefile | wc -l # 4

Thanks!

Cécile.

[Minh Bui]

Hi Cecile,

Please do not use --no-outfiles. This option will turn off writing .log, .treefile and .iqtree file. So IQ-Tree is supposed not to print .treefile here. I don’t know why that still happened, quite likely just some intermediate (partial) tree. That’s the reason.

A couple of other options to turn off specific files:

--no-log disables .log file

--no-iqtree disables .iqtree file

--no-uniqueseq disables .uniqueseq.phy file

Cheers

Minh

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<a1.phy><a2.phy>

[Cecile Ane]

Thank you Minh!