ERROR: Too many threads for short alignments, please reduce number of threads or use -nt AUTO to determine it.

[Cacau Centurion]

I'm running iqtree 1.6.1 for phylogeny construction with about 50 partitions (that is 50 protein sequences with partition info) and 500 species. The command I'm using is

iqtree -s 1.aln -spp 1.partition -m MFP+MERGE -mset LG,WAG -mrate I,G -bb 1000 -nt AUTO

However, I was told the following and the analysis was distrupted.

ERROR: Too many threads for short alignments, please reduce number of threads or use -nt AUTO to determine it.

I've specified -nt AUTO already. Is there a solution? Do I have to specify the number of threads?

[Minh Bui]

Hi there,

This problem is known: the error message is not entirely correct, but the part "please reduce number of threads” gave the right hint. It happens when some partition is very short and -nt AUTO does not work properly. To resolve this issue we have to change the parallelisation scheme. But for now as a quick fix, please specify -nt with a number of threads smaller than the number of partitions for your data set. That should fix it.

Thanks,

Minh

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