ausarg/pipesnake is a bioinformatics best-practice analysis pipeline for phylogenomic reconstruction starting from short-read 'second-generation' sequencing data.
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
Description of the bug
runtime for
--tree_method iqtreeis 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/*.logandraxml/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
Relevant files
Execution_Report_Timeline_Comparison.zip The above example was run with
-profile singularity.System information
No response