MantisBT - MEGA
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IDProjectCategoryView StatusDate SubmittedLast Update
0000357MEGACalculation Errorpublic2017-01-03 14:592023-04-14 18:38
Reporterguest 
Assigned To 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusnewResolutionopen 
PlatformPCOSLinuxOS VersionDebian
Product VersionMEGA-CC 11 (command line version) 
Target VersionFixed in Version 
First NameKsenia
Last NameSafina
Emailk.r.safina@gmail.com
Confirm Emailk.r.safina@gmail.com
Summary0000357: Unable to save ancestral states into file
DescriptionI'm trying to reconstruct the ancestral states for 13800 sequences. After several hours of calculation, the process ended up with Access violation error after "100% Analysis Complete" message. In the "Additional information" section I've provided megacc's output.

I'm not sure if it is the issue of megacc or computational system I'm using. I've relaunched it six times, and it crashed repeatedly.

It works fine on smaller subsets of my dataset, including a set of 12000 sequences.

Thanks.
Steps To Reproduce
Additional Information
MEGA-CC 7.0.20 Molecular Evolutionary Genetics Analysis
Build#: 7161007-x86_64
    0% Organizing sequence information a
    0% 2-1-17 10:57:15
Using the following analysis options:
  No. of Taxa 13832
  Analysis Ancestral Sequence Inference
  Tree to Use Use tree from file
  Statistical Method Maximum Likelihood
  Substitutions Type Nucleotide
  Model/Method General Time Reversible model
  Rates among Sites Gamma Distributed With Invariant Sites (G+I)
  No of Discrete Gamma Categories 4
  Gaps/Missing Data Treatment Use all sites
  Site Coverage Cutoff (%) Not Applicable
  Branch Swap Filter None
  Has Time Limit False
  Maximum Execution Time -1
  datatype snNucleotide
  containsCodingNuc False
  MissingBaseSymbol ?
  IdenticalBaseSymbol .
  GapSymbol -
Start time: 2-1-17 10:57:15
Executing analysis:

  100% Computing data coverage MEGA-CC has logged the following error:
  When = 3-1-17 03:07:19
  Data file = /export/home/ksafina/1_01_2017_reconstruct_ancestors_replica4/strains_wo_reassortants_nonredundant.fasta
  AnalysisFile = /export/home/ksafina/1_01_2017_reconstruct_ancestors_replica4/ancestral_seqs_ML_nucleotide.mao
  Tree File = /export/home/ksafina/1_01_2017_reconstruct_ancestors_replica4/tree_rooted.nwk
  Parameter = -f
  Parameter = Fasta
  Parameter = -t
  Parameter = /export/home/ksafina/1_01_2017_reconstruct_ancestors_replica4/tree_rooted.nwk
  Parameter = -o
  Parameter = /export/home/ksafina/1_01_2017_reconstruct_ancestors_replica4/ancestors
  Message = Access violation

  Please see the summary file for warnings/messages
  Please validate all your inputs and try again. If you think this is a
  bug, please report it at http://www.megasoftware.net [^]
       100% Analysis Complete
An unhandled exception occurred at $00000000006C13CA :
EInOutError:
EAccessViolation :
  $00000000006C13CA
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Attached Files
Issue History
Date ModifiedUsernameFieldChange
2017-01-03 14:59guestNew Issue
2017-01-18 13:40gstecherFile Deleted: HIV-CPZ-2000bootConrad.mts
2022-12-05 06:51guestNote Added: 0005854
2023-04-14 18:38guestNote Added: 0006486

Notes
(0000276)
gstecher   
1969-12-31 17:33   
The first bug is known and fixed for 3.1. For the second part I pointed the user to the appropriate section of the help file as well as chapter 9 of Nei and Kumar book
(0005854)
guest   
2022-12-05 06:51   
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(0006486)
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