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bengtssonpalme / MetaxaQR

MetaxaQR: Accurate classification and curation of current and future DNA barcodes
GNU General Public License v3.0
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Inconsistent results between Metaxa2 and MetaxaQR taxonomic profiling #3

Open Anto007 opened 2 years ago

Anto007 commented 2 years ago

I conducted some tests using a small nematode gut metagenome assembly as the input (Note- I have uploaded here the fasta file in .txt format to comply with the upload format requirements). nematode_metagenome.txt

Below are the command-lines that I used to run Metaxa2 and MetaxaQR

metaxa2 -i nematode_metagenome.fasta -o test_metaxa2_nematode_metagenome -g SSU --plus T
metaxaQR -i nematode_metagenome.fasta -o test_metaxaQR_nematode_metagenome -g SSU

In the *taxonomy.txt output file from Metaxa2, the nematode SSU is clearly indicated while the same is strangely absent from the *taxonomy.txt output file of MetaxaQR. While *archaea.fasta from Metaxa2 is empty, the corresponding output file from MetaxaQR is populated with a large nematode rRNA sequence. I would appreciate it very much if you could offer some insights on this strange behavior? Thanks again

bengtssonpalme commented 2 years ago

This surely seems like a bug. If I look in the intermediate output, that sequence seems to end up in the completely wrong place in the final output – it does not at all look like it should be in Archaea in the intermediate files. I will look into this.