We do our best to help you solve your problems with MEGAN and fix any bug that might be there.
We appreciate your help if you submit bug reports to this category.
To fix a bug, we have to understand and reproduce the problem. This is only possible, if you explain your problem both detailed and concise. This means please include all the information that you deem necessary to understand your problem, but do not include too much unnecessary context.
If you have found multiple problems, separate them into multiple bug reports. As the bugs will most likely have to be fixed separately, this makes it easier for us to update the community of the changes that have been made to fix each problem.
Try to provide a so-called minimal example. For example you could select the first 100 reads of your dataset, process them the same way you did for all of the reads and if this produces the same problem please attach the input and output files that you produced to you bug report. This way, we can exactly reproduce what happened.
State clearly, which operating system and MEGAN version you are using and if you are using any non-default mapping or taxonomy files.
Example bug report
You would start a separate topic for each bug, please do not post new bugs as a reply to old threads.
This bug report is an example and is already fixed in the current version of MEGAN.
TOPIC TITLE: weight/magnitude of reads is not used in quantification
I am using MEGAN6 Ultimate version 6.0.12alpha on MacOS (10.9.4). As I was using a subset of reads from my WGS metagenomic dataset assigned to one specific gene, I decided to simplify the data and delete all duplicate reads I had. To keep the quantitative information, I added the number of duplicates found to each remaining read.
I attached “magnitude=number” to the header.
Unfortunately, the magnitudes were not used to calculate the number of reads assigned to a node (which was what I expected). I did select the “Use read magnitudes” checkbox when loading my BLAST-XML file. (I only compared against Drosophilaceae, to get the results faster.) I get only the original five reads assigned to the Drosophila taxon, while I should have over 900 “weighted reads”.
In the Inspect Window, each of the reads has the correct weight assigned, but this did not influence the analysis.
I attached a fastA-file containing the first five reads to this post, as well as the BLAST-XML and the RMA6 file I generated with them.
SINAweighted.fasta (2.4 KB) SINAweighted-Alignment.xml (564.7 KB) SINAweighted-Alignment.rma6 (32.1 KB)