Unable to open extracted reads

User Questions
1

Hi there!

I am working on some metagenomic data. I have mapped my reads to host genome and removed host seqs but as expected there is a little bit of contamination, which I had planned to extract once I get to the MEGAN stage.

I have successfully run DIAMOND on the ‘unmapped’ reads using version /0.8.6 and an ncbi-nr db downloaded in June 2016 and obtained .daa files. I have also run DIAMOND separately using version /0.8.22 with a newer ncbi-nr db downloaded a few weeks ago to obtained .m8 files

I have successfully meganized .daa files obtained from version 0.8.6 and also created .rma6 files from the .m8 tab DIAMOND output.

I have gone ahead to extract reads of interests but I am unable to open the extracted reads for subsequent analysis. Below are the error messages I get when I try to open them

Error: opening extracted reads from .rma6 file
Command usage: open file= [readOnly={false|true}]; - Open a MEGAN file (ending on .rma, .meg or .megan)
File has unknown type: /scicomp/home/kui8/HiSeq_Peru/Extracted_bact_reads/BactUnexpL1
Error: Execute failed: java.io.IOException: File has unknown type: /scicomp/home/kui8/HiSeq_Peru/Extracted_bact_reads/BactUnexpL1
Executing: open file=’/scicomp/home/kui8/HiSeq_Peru/Extracted_bact_reads/BactUnexpL1.rma6’;
Executing: ‘open’‘file’’=’’/scicomp/home/kui8/HiSeq_Peru/Extracted_bact_reads/BactUnexpL1.rma6’;
Closing window…
Not an RMA file

Error: opening extracted reads from .daa file
Executing: open file=’/scicomp/home/kui8/HiSeq_Peru/Extracted_bact_reads/BactUnexpL1R12.daa’;
Executing: ‘open’‘file’’=’’/scicomp/home/kui8/HiSeq_Peru/Extracted_bact_reads/BactUnexpL1R12.daa’;
Closing window…
Input file is not a DAA file.
Command usage: open file= [readOnly={false|true}]; - Open a MEGAN file (ending on .rma, .meg or .megan)
Input file is not a DAA file.
Error: Execute failed: java.io.IOException: Input file is not a DAA file.

What files are they? and how do I open them to run downstream analysis in MEGAN?

With MEGAN 5, I was able to extract reads of interests and run downstream MEGAN analysis on those, I am not sure what I am doing wrong with MEGAN 6. Any help will be greatly appreciated.

thanks,
Nsa

2

I have gone ahead to extract reads of interests but I am unable to open the extracted reads for subsequent analysis. Below are the error messages I get when I try to open them

Did you use “File-> Extract Reads” to extract reads from a DAA or RMA6 file? If so, then the resulting files contain reads in FastA format and such files cannot be opened by MEGAN.

Or did you use “File->Extract to New Document…”? This will generate a new RMA6 file containing the reads associated with the nodes that you selected.

3

Thank you Daniel! I used 'Extract reads’
I forgot a few steps in my old workflow (…extract reads —> DIAMOND again —> extracted.m8 ----> …)

But I see now that I can remove these steps by simply extracting to a new document. Saves me a lot of trouble.
Thank you!

Cheers,
Nsa