I'm trying to extract rRNA sequences from my metagenomic datasets in order to perform diversity analysis on qiime. The overall purpose is compare the microdiversity (one target species) pointed by MUMmer, using the entire dataset and the microdiversity pointed by qiime diversity analysis.
So I chose rRNASelector and Metaxa to extract the sequences.
I'm having trouble to run rRNASelector on unix server through ssh.
It starts, the dialog box opens on my screen, I choose the reads file (fasta), but then I get this error message:
"Starting hmmsearch for forward using lib/16s_bact_for3.hmm
Not right file format! -> Abort"
My hmmer is ok, when I type hmmsearch -h it gives to me the help information.
I've tried to run it choosing all possible paths for hmmsearch, but it just crashes. Besides this, the dialog box dynamics is so slow, I cant either change the length parameter...
In parallel, I'm running Metaxa, and it seems to work well, but for my metagenomic dataset it is finding too few sequences. Is a poor richness dataset, in fact, but even though I was expecting more. My output for bacteria sequences is 61 reads of a total of 110504 sequences. This sequences are from Illumina paired end, merged through Flash, with a average combine of 81% and average length of 293
The sequences used for rRNASelector are the same
If someone have experience with this kind of workflow, I appreciate every suggestion, because I dont have much experience, and maybe I am missing something, or doind something wrong.
Thank you so much!