MantisBT - MEGA
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IDProjectCategoryView StatusDate SubmittedLast Update
0000203MEGAAlignment Explorerpublic2016-06-29 03:502016-07-25 11:39
Reporterguest 
Assigned Togstecher 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusresolvedResolutionwon't fix 
PlatformPCOSLinuxOS Versionother
Product VersionMEGA-CC 11 (command line version) 
Target VersionFixed in Version 
First NameMahdi
Last NameGhanbari
Emailghanbari.msc@gmail.com
Confirm Emailghanbari.msc@gmail.com
Summary0000203: Error in alignment step
DescriptionI tried to run the mega_cc on a data set of 730 kb size to align the reads from 10 viruses. Here is the error I receive every time
 An error has occurred: External process finished with exit code 2. (/home/ngs/.config/megacc/MEGA7_7160617-x86_64/Private/MUSCLE/muscleUnix64.exe )
Steps To Reproduce
Additional InformationHere is the all commands and outputs:
.........:~/Desktop/AMA$ ./megacc -a ama/muscle_align_nucleotide.mao -d ama/test.fasta -o ama/
MEGA-CC 7.0.18 Molecular Evolutionary Genetics Analysis
Build#: 7160617-x86_64
Alignment settings:
                          : Gap Penalties : ====================
                          : Gap Open : -1.00
                          : Gap Extend : 0.00
                          : Memory/Iterations : ====================
                          : Max Memory in MB : 111872
                          : Max Iterations : 8
                          : Advanced Options : ====================
                          : Cluster Method (Iterations 1,2) : UPGMA
                          : Cluster Method (Other Iterations) : UPGMA
                          : Min Diag Length (Lambda) : 24
                          : datatype : snNucleotide
                          : containsCodingNuc : False
                          : missingBaseSymbol : ?
                          : identicalBaseSymbol : .
                          : gapSymbol : -
 
    0% 29-6-16 11:53:25
Executing multiple sequence alignment (MUSCLE)
15 MB(1%) Iter 1 1.82% K-mer dist pass 1 15 MB(1%) Iter 1 100.00% K-mer dist pass 1
100 MB(5%) Iter 1 11.11% Align node 6070 MB(100%) Iter 1 22.22% Align node 6097 MB(100%) Iter 1 33.33% Align node 7122 MB(100%) Iter 1 44.44% Align node 7190 MB(100%) Iter 1 55.56% Align node 7212 MB(100%) Iter 1 66.67% Align node 7236 MB(100%) Iter 1 77.78% Align node 7259 MB(100%) Iter 1 88.89% Align node 7282 MB(100%) Iter 1 100.00% Align node 7426 MB(100%) Iter 1 100.00% Align node
7427 MB(100%) Iter 1 20.00% Root alignment 7427 MB(100%) Iter 1 30.00% Root alignment 7427 MB(100%) Iter 1 40.00% Root alignment 7427 MB(100%) Iter 1 50.00% Root alignment 7427 MB(100%) Iter 1 60.00% Root alignment 7427 MB(100%) Iter 1 70.00% Root alignment 7427 MB(100%) Iter 1 80.00% Root alignment 7427 MB(100%) Iter 1 90.00% Root alignment 7427 MB(100%) Iter 1 100.00% Root alignment 7427 MB(100%) Iter 1 100.00% Root alignment 7427 MB(100%) Iter 2 12.50% Refine tree 7427 MB(100%) Iter 2 25.00% Refine tree 7427 MB(100%) Iter 2 37.50% Refine tree 7427 MB(100%) Iter 2 50.00% Refine tree 7427 MB(100%) Iter 2 62.50% Refine tree 7427 MB(100%) Iter 2 75.00% Refine tree 7427 MB(100%) Iter 2 87.50% Refine tree 8673 MB(100%) Iter 2 100.00% Refine tree 8673 MB(100%) Iter 2 100.00% Refine tree
8673 MB(100%) Iter 2 20.00% Root alignment 8673 MB(100%) Iter 2 30.00% Root alignment 8673 MB(100%) Iter 2 40.00% Root alignment 8673 MB(100%) Iter 2 50.00% Root alignment 8673 MB(100%) Iter 2 60.00% Root alignment 8673 MB(100%) Iter 2 70.00% Root alignment 8673 MB(100%) Iter 2 80.00% Root alignment 8673 MB(100%) Iter 2 90.00% Root alignment 8673 MB(100%) Iter 2 100.00% Root alignment 8673 MB(100%) Iter 2 100.00% Root alignment 8673 MB(100%) Iter 2 100.00% Root alignment MEGA-CC has logged the following error:
  When = 29-6-16 12:42:12
  Data file = ama/test.fasta
  AnalysisFile = ama/muscle_align_nucleotide.mao
  Parameter = -o
  Parameter = ama/
  Message = An error has occurred: External process finished with exit code 2. (/home/ngs/.config/megacc/MEGA7_7160617-x86_64/Private/MUSCLE/muscleUnix64.exe )

  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 [^]
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Issue History
Date ModifiedUsernameFieldChange
2016-06-29 03:50guestNew Issue
2016-07-01 08:54gstecherAssigned To => gstecher
2016-07-01 08:54gstecherStatusnew => assigned
2016-07-01 08:54gstecherNote Deleted: 0000127
2016-07-01 08:55gstecherNote Deleted: 0000129
2016-07-01 08:55gstecherNote Deleted: 0000138
2016-07-01 08:55gstecherNote Added: 0003682
2016-07-25 11:39gstecherNote Added: 0003684
2016-07-25 11:39gstecherStatusassigned => resolved
2016-07-25 11:39gstecherResolutionopen => won't fix

Notes
(0003682)
gstecher   
2016-07-01 08:55   
Hi Mahdi,

I am writing in response to the bug report you recently submitted regarding the MEGA software. Could you send me the fasta file you were using when the error occurred so that I can duplicate the problem?

--
Best regards,

Glen Stecher
(0003684)
gstecher   
2016-07-25 11:39   
Hi Mahdi,

Sorry for the late response, I have been traveling on vacation. MEGA-CC is not actually doing the sequence alignment but rather it uses the MUSCLE software. It seems that MUSCLE is not able to handle your sequence data. My suggestion is that you download MUSCLE directly from its author's website and read the documentation for working with very large datasets. In the documentation you will find suggestions for fine-tuning the alignment to work with your data. If that still doesn't work, you can contact the author of MUSCLE directly.

On 07/08/2016 12:54 AM, Mahdi Ghanbari wrote:
> Hi Glen
> Thank you for your email. Please find the attached fasta file I used.
> Appreciate your help on this.
>
> Regards
> Mahdi