0001381: stop at Computing distance matrix

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Date Submitted

Last Update

0001381

MEGA

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public

2019-08-27 06:59

2019-08-28 12:40

Reporter

guest

Assigned To

gstecher

Priority

normal

Severity

minor

Reproducibility

have not tried

Status

resolved

Resolution

no change required

Platform

Linux

Product Version

MEGA-CC 11 (command line version)

Target Version

Fixed in Version

Summary

0001381: stop at Computing distance matrix

Description

i use mega cc to build a phylogenetic tree.
i use the command :

./megacc -a /home/fmm/data/seq/infer_ML_amino_acid.mao -d ready.fasta -o home/fmm/data/seq/
but it stop at :

Executing analysis:

99% Computing distance matrix
i do not know why

Additional Information

MEGA-CC 10.1.1 Molecular Evolutionary Genetics Analysis
Build#: 10190812-x86_64
    0% Organizing sequence information
    0% 08/27/2019 09:41:37 PM
Using the following analysis options:
  No. of Taxa 518
  Analysis Phylogeny Reconstruction
  Statistical Method Maximum Likelihood
  Test of Phylogeny None
  No. of Bootstrap Replications Not Applicable
  Substitutions Type Amino acid
  Model/Method Jones-Taylor-Thornton (JTT) model
  Rates among Sites Uniform Rates
  No of Discrete Gamma Categories Not Applicable
  Gaps/Missing Data Treatment Use all sites
  Site Coverage Cutoff (%) Not Applicable
  ML Heuristic Method Nearest-Neighbor-Interchange (NNI)
  Initial Tree for ML Make initial tree automatically (Default - NJ/BioNJ)
  Branch Swap Filter None
  Number of Threads 11
  Has Time Limit False
  Maximum Execution Time -1
  datatype snProtein
  MissingBaseSymbol ?
  IdenticalBaseSymbol .
  GapSymbol -
Start time: 08/27/2019 09:41:37 PM
Executing analysis:

   99% Computing distance matrix

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First Name

ming

Last Name

fang

fmmljay@qq.com

Confirm Email

fmmljay@qq.com

Attached Files

ready.fasta (1,010,784 bytes) 2019-08-27 06:59

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Notes
(0004289) gstecher (administrator) 2019-08-28 12:40	Hi Ming, I am writing in response to the bug report you recently submitted regarding the MEGA software. I tested the ML construction analysis with the data set you uploaded and the analysis runs to completion but takes some time. For the data and settings you used, progress is very slow but eventually finishes. If you let it run, the analysis will complete (it took about an hour on my computer). -- Best regards, Glen Stecher Institute for Genomics and Evolutionary Medicine igem.temple.edu

Issue History
Date Modified	Username	Field	Change
2019-08-27 06:59	guest	New Issue
2019-08-27 06:59	guest	File Added: ready.fasta
2019-08-28 12:40	gstecher	Note Added: 0004289
2019-08-28 12:40	gstecher	Status	new => resolved
2019-08-28 12:40	gstecher	Resolution	open => no change required
2019-08-28 12:40	gstecher	Assigned To	=> gstecher