0006838: MEGA-CC (v11.0.13) bootstrap error: "Invalid number of bootstrap replicates: 0"

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Date Submitted

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0006838

MEGA

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2025-08-07 00:58

2025-09-02 10:24

Reporter

guest

Assigned To

gstecher

Priority

normal

Severity

minor

Reproducibility

have not tried

Status

resolved

Resolution

won't fix

Platform

Linux

Debian/Ubuntu

Product Version

MEGA 11

Target Version

Fixed in Version

Summary

0006838: MEGA-CC (v11.0.13) bootstrap error: "Invalid number of bootstrap replicates: 0"

Description

I've recently joined my team as the new bioinformatician in Spain and I am currently working on a Python pipeline to automate phylogenetic analysis of certain nucleotide sequences using MEGA-CC (v11.0.13).

In this pipeline, the user selects a reference matrix of aligned sequences, and the pipeline calls MEGA-CC to perform the phylogenetic reconstruction with bootstrap support. However, I keep encountering the following error: Message = Oh no! An error occurred when finalizing the calculation: Invalid number of bootstrap replicates: 0

The strange thing is that I have explicitly specified: Bootstrap Replicates = 2000 in the .mao file. I’m not sure if this is a silly mistake on my part or possibly a bug, so I would really appreciate any help or clarification.

If anyone has encountered this issue before or has suggestions on how to ensure the bootstrap replicates are correctly passed and recognized by MEGA-CC, I would be very grateful.

Thanks in advance for your time and support!

Best regards,
Adrián

Steps To Reproduce

mao file (snippet)
[ ProcessTypes ]
ppInfer = true
ppNJ = true
ppUPGMA = false
ppBootstrap = true

[ AnalysisSettings ]
Analysis = Phylogeny Reconstruction
Scope = All Selected Taxa
Statistical Method = Neighbor-joining
Test of Phylogeny = Bootstrap method
Bootstrap Replicates = 2000
Substitution Model = ====================
Substitutions Type = Nucleotide
Model/Method = Tamura-Nei
...

MEGA-CC Error Output
Status : Conducting Bootstrap Test
Current Progress : 0%
Bootstrap Rep # : 0/-1 [ remaining]
...
Message = Oh no! An error occurred when finalizing the calculation: Invalid number of bootstrap replicates: 0

Python Code Snippet That Generates the .mao
bootstrap = parametros.get('bootstrap', True)
replicas = int(parametros['replicas']) if bootstrap else 0
pp_bootstrap = "true" if bootstrap else "false"

contenido = f"""
[ ProcessTypes ]
ppInfer = true
ppNJ = {pp_nj}
ppUPGMA = {pp_upgma}
;ppBootstrap = {pp_bootstrap}

[ AnalysisSettings ]
Bootstrap Replicates = {replicas}
...
"""

Notes
(0008089) gstecher (administrator) 2025-09-02 10:24	fixed in version 12 but won't fix in version 11

Issue History
Date Modified	Username	Field	Change
2025-08-07 00:58	guest	New Issue
2025-09-02 10:24	gstecher	Note Added: 0008089
2025-09-02 10:24	gstecher	Status	new => resolved
2025-09-02 10:24	gstecher	Resolution	open => won't fix
2025-09-02 10:24	gstecher	Assigned To	=> gstecher

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