Hi,
I am doing the pipeline of my Illumina paired end samples, but I got some unclear issues.
First, I don’t know why, but when I try to search for some topic in the forum and I go to Google, it shows me some results. However, I can’t access and it has been showing me the following message:
“Information
Sorry but you are not permitted to use the search system.”
So, basically I have to check page by page in order to check if I find a topic related to mine, but this is though.
Moving to my main issue… I am using the version v.1.39.4 and I amfollowing Myseq SOP tutorial. I ran align.seqs and in the end I got a lot of unclassified sequences.
This was the command I ran:
classify.seqs(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.count_table, reference=trainset14_032015.pds.fasta, taxonomy=trainset14_032015.pds.tax, cutoff=80)
When I openned the tax summary file, I got it:
taxlevel rankID taxon daughterlevels total Day_01 Day_12 Day_17 Day_29 Day_30 Day_38 Day_42 Day_56 Day_68 0 0 Root 1 392548 43739 44545 43862 43225 54282 43321 34222 39640 45712 1 0.1 Bacteria 3 392548 43739 44545 43862 43225 54282 43321 34222 39640 45712 2 0.1.1 Actinobacteria 1 487 19 188 132 40 64 21 7 12 4 3 0.1.1.1 Actinobacteria 2 487 19 188 132 40 64 21 7 12 4 4 0.1.1.1.1 Actinobacteria_unclassified 1 1 0 0 0 0 1 0 0 0 0 5 0.1.1.1.1.1 Actinobacteria_unclassified 1 1 0 0 0 0 1 0 0 0 0 6 0.1.1.1.1.1.1 Actinobacteria_unclassified 0 1 0 0 0 0 1 0 0 0 0 4 0.1.1.1.2 Actinomycetales 1 486 19 188 132 40 63 21 7 12 4 5 0.1.1.1.2.1 Actinomycetales_unclassified 1 486 19 188 132 40 63 21 7 12 4 6 0.1.1.1.2.1.1 Actinomycetales_unclassified 0 486 19 188 132 40 63 21 7 12 4 2 0.1.2 Bacteria_unclassified 1 391292 43632 44314 43666 43114 54118 43224 34143 39541 45540 3 0.1.2.1 Bacteria_unclassified 1 391292 43632 44314 43666 43114 54118 43224 34143 39541 45540 4 0.1.2.1.1 Bacteria_unclassified 1 391292 43632 44314 43666 43114 54118 43224 34143 39541 45540 5 0.1.2.1.1.1 Bacteria_unclassified 1 391292 43632 44314 43666 43114 54118 43224 34143 39541 45540 6 0.1.2.1.1.1.1 Bacteria_unclassified 0 391292 43632 44314 43666 43114 54118 43224 34143 39541 45540 2 0.1.3 Proteobacteria 1 769 88 43 64 71 100 76 72 87 168 3 0.1.3.1 Proteobacteria_unclassified 1 769 88 43 64 71 100 76 72 87 168 4 0.1.3.1.1 Proteobacteria_unclassified 1 769 88 43 64 71 100 76 72 87 168 5 0.1.3.1.1.1 Proteobacteria_unclassified 1 769 88 43 64 71 100 76 72 87 168 6 0.1.3.1.1.1.1 Proteobacteria_unclassified 0 769 88 43 64 71 100 76 72 87 168
I guess this is not normal 
What could I try to do? Is this a command error or a bug in this version?
Thank you!