Paired reads daa-meganizer daa2rma

User Questions
1

Hi Daniel,

I’m trying to analyze my Ilumina paired read data with MEGAN6. So followed this workflow:

Two fastq files: R1 and R2 --> diamond blastx -input RX -output file.daa -->
a) daa-meganizer: daa-meganizer -i FA3_h100_R1.daa FA3_h100_R2.daa -pr true -ps 23 -a2t prot_acc2tax-Nov2018X1.abin

Problem reported: Although I set the pair read option, it doesn’t recognize it and processes the data separately.

That’s what appear in command line when performing the analyses.
WARNING: Not an RMA6 file, will ignore paired read information

Obviously, when uploading the meganized file in MEGA6 appears every read assignation and not the combination of both reads (R1 and R2).

So then, I tried the second option:
b) daa2rma: daa2rma -i FA3_h100_R1.daa FA3_h100_R2.daa -pr true -ps 23 -a2t prot_acc2tax-Nov2018X1.abin -o salida/

It looks like everything it’s okay, but instead of obtaining two output files for each input file as it is mentioned in -help, I just have one output file, and when I upload it to MEGAN6 appears every single read assignation, again, and not the combination.

Can you help to solve any of both problems, please?

Thank you,

Belen

daa2rma
Opening file: prot_acc2tax-Nov2018X1.abin
In DAA files: FA3_h100_R1.daa, FA3_h100_R2.daa
Output file: salida/FA3_h100_R1.rma6
Classifications: Taxonomy
Parsing file: FA3_h100_R1.daa
10% 20% 30% 40% 50% 60% 70% 80% 90% Parsing file: …/…/METAGENOMA_FISABIO/RUN19_032_33/fastq/FA3_h100_R2.daa
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% (0.2s)
Total reads: 24
Alignments: 449
100% (0.0s)
100% (0.0s)
100% (0.0s)
Linking paired reads
Number of pairs: 11
Binning reads: Initializing…
Initializing binning…
Using paired reads in taxonomic assignment…
Using ‘Naive LCA’ algorithm for binning: Taxonomy
Binning reads…
Binning reads: Analyzing alignments
Total reads: 24
With hits: 24
Alignments: 449
Assig. Taxonomy: 24
MinSupport set to: 1
Binning reads: Applying min-support & disabled filter to Taxonomy…
Min-supp. changes: 0
Binning reads: Writing classification tables
Numb. Tax. classes: 3
Binning reads: Syncing
Class. Taxonomy: 3
100% (1.3s)
Total time: 7s
Peak memory: 1.3 of 7.3G

2

Dear beruv3,

Do you have already solved your problem? I’ve the same problem. Could you like to give a guide to solved the problem? Thank you so much

3
  1. daa-meganizer can combine paired reads (due to limitations of the file format)
  2. if you use daa2rma in paired read mode, then MEGAN does not “combine” the reads, but rather, it leaves reads separate, but uses the pair to improvement the assignment of the reads.