--tree_method raxml and iqtree runtimes

[IanGBrennan]

Description of the bug

runtime for --tree_method iqtree is much much longer than --tree_method raxml.

I have run both tree estimation methods on the example data using singularity and docker.

Actual runtimes for the tree estimation programs are consistent (comparing iqtree/*.log and raxml/RAxML_info* files), e.g. AHE-L151 took 0.4s with IQTREE and 0.9s with RAxML.

But total pipeline runtimes differ:
total example data pipeline runtime w/IQTREE --> 8m 53s
total example data pipeline runtime w/RAxML --> 20s

Command used and terminal output

nextflow run ausarg/pipesnake -r v1.1 --input data/ToyData_SampleInfo_PRG.csv --outdir testing_PRG_iqtree --stage from-prg --blat_db data/ToyData_SqCL_25Targets.fasta --batching_size 2 -profile singularity --tree_method iqtree

and

nextflow run ausarg/pipesnake -r v1.1 --input data/ToyData_SampleInfo_PRG.csv --outdir testing_PRG_raxml --stage from-prg --blat_db data/ToyData_SqCL_25Targets.fasta --batching_size 2 -profile singularity --tree_method raxml

Relevant files

Execution_Report_Timeline_Comparison.zip
The above example was run with -profile singularity.

System information

No response

[IanGBrennan]

We have still not identified the source of this issue, but have temporarily changed the base.config file to default to tree_method = "raxml" to avoid the slowdown currently. Users can still specify --tree_method iqtree in the pipeline run command if they'd prefer to use IQTREE.

Will continue to look for the root cause.