0001781: OS X 64 bit download broken

Notes
(0001545) agasky (reporter) 1969-12-31 17:33	Hello Amber Ha, In the bug report you submited about MEGA, you mentioned 3 files (test1.meg, test2.meg, excelfile.xls). Unfortunatley, I only recieved the file test2.meg, if you could email me test1.meg and the excel file, it would help me to better understand the issue. In your steps to reproduce the bug, you mention aligning the data; are you aligning test1 and test2 seperately? If so, different distance results are not unusual; since every sequence is taken into account during the alignment. Since test1 and test2 will likely have different alignments their distances will also be different. Thanks, Nick

(0001546) agasky (reporter) 1969-12-31 17:33	User only included 1 of the 3 files they mentioned in their bug report. Waiting to hear back from them with the other two files. I don't know why they didn't just zip up all 3 of the files and upload them with the bug report. It sounds like the user has an initial data set (test1), aligns it, and performs the pairwise distance analyis on it and finds a distance of 0.5 for the first two sequences, then goes back to the alignment of test1, adds in more sequences, re-aligns, and re-analyses the new file with pairwise distances and gets a distances of 0.4 for the first two sequences. They think that it must be a bug because of the difference, I THINK (not confirmed) that the difference is simply that the alignments are different which accounts for the pairwise distance difference.

(0001547) agasky (reporter) 1969-12-31 17:33	Dear Nick, Thank you for your prompt reply. I have attached another set of files which is our real data for your comments. Please ignore the attachement in previous mail. Test1 and test2 are aligned separately but the sequences no.1 to 30 and sample Test1 to 5 are the same in the two files. No.1 to 29 are reference sequences and no. 30 is outgroup sequence. In our analysis, we usually compared the genetic relationship in terms of the genetic distance of test sample ("Test1 to 7" in blue in excel file) among reference sequences (no.1 to 29). Reference sequences are fixed all the time in different analysis. We supposed that the relationship among reference sequences no.1 to 29 should remain unchanged in between different distance analysis. Is it right? However, recently, we observed that discrepancy (0000090:0000030% analysis) happened after entering Test samples. Please refer to the excel file for detail, discrepancy for the reference sequences that we are much concern are highlighted in red. In the past, we usually got distance value of 8% for (10,11), but when we analyse only Test sample 1 to 5. The distnace for (10,11) changed to 5.9%. All sequences in file test1 and test2 are same except two sequences (Test6 and Test7) more in file test1. We found that dicrepancy can turn back when any data set containing sequences of "Test6 & 7", the value will go back to 8.0%. I'm not sure anything we may get wrong because we are new user. We would be grateful if you could help us to solve this problem. Looking forward to your reply. Best regards, Amber

(0001548) agasky (reporter) 1969-12-31 17:33	Hello Amber, When I compared your two meg files (test1.meg & test2.meg) I noticed that the alignment for sequences 10-19, test1, test2, test3 were different between the files (see diff.png). Remember, using pairwise deletion, sites with gaps or ambiguities are removed (if necessary) so the alignment can effect which sites are used to determine the pairwise distance. The file test1.meg has 398 sites with no gaps while test2.meg has 396 sites with no gaps. For a reason of the discrepancy see distance_difference_explination.png. Thanks, Nick

Issue History
Date Modified	Username	Field	Change
1969-12-31 17:33	agasky	Note Added: 0001545
1969-12-31 17:33	agasky	Status	new => assigned
1969-12-31 17:33	agasky	Assigned To	=> agasky
1969-12-31 17:33	agasky	Note Added: 0001546
1969-12-31 17:33	agasky	Status	assigned => feedback
1969-12-31 17:33	agasky	File Deleted: test2.meg
1969-12-31 17:33	agasky	File Added: test2_origional.meg
1969-12-31 17:33	agasky	File Added: test1.meg
1969-12-31 17:33	agasky	File Added: test2.meg
1969-12-31 17:33	agasky	File Added: TN Distance.xls
1969-12-31 17:33	agasky	File Added: diff.png
1969-12-31 17:33	agasky	File Added: distance_difference_explination.PNG
1969-12-31 17:33	agasky	Note Added: 0001547
1969-12-31 17:33	agasky	Note Added: 0001548
1969-12-31 17:33	agasky	Status	feedback => resolved
1969-12-31 17:33	agasky	Resolution	open => fixed
2020-02-17 16:33	guest	New Issue
2020-02-24 07:58	gstecher	File Deleted: TN Distance.xls
2020-02-24 07:58	gstecher	File Deleted: test2.meg
2020-02-24 07:58	gstecher	File Deleted: test2_origional.meg
2020-02-24 07:58	gstecher	File Deleted: test1.meg
2020-02-24 07:59	gstecher	File Deleted: diff.png
2020-02-24 07:59	gstecher	File Deleted: distance_difference_explination.PNG
2020-03-06 08:12	gstecher	Status	new => resolved
2020-03-06 08:12	gstecher	Resolution	open => unable to reproduce
2020-03-06 08:12	gstecher	Assigned To	=> gstecher

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