amptk v1.2.5 taxonomy error about amptk

[nextgenusfs]

Is there any more information in the logfile? Can you verify that the file in your DB folder location called 16S.extracted.fa is not empty and it contains the sequences you expect? And then lastly the script for sintax should have been writing to file, is that file empty or what does it contain?

[AlexGaithuma]

Is there any more information in the logfile? Can you verify that the file in your DB folder location called 16S.extracted.fa is not empty and it contains the sequences you expect? And then lastly the script for sintax should have been writing to file, is that file empty or what does it contain?

Thanks for your prompt reply,

1. 16S.extracted.fa is not empty and it contains expected sequences,

2. Contents of the sintax script look as follows:
   ASV41 d:Bacteria(1.0000) + d:Bacteria
   ASV42 d:Bacteria(1.0000),p:"Proteobacteria"(0.4800),c:Gammaproteobacteria(0.4300),o:"Enterobacteriales"(0.3000),f:Enterobacteriaceae(0.3000),g:Biostraticola(0.1500) + d:Bacteria
   ASV57 d:Bacteria(0.9900),p:Firmicutes(0.2500),c:Clostridia(0.1200),o:Clostridiales(0.1200),f:"Nitrospiraceae"(0.0800),g:Nitrospira(0.0800) - d:Bacteria
   ASV45 d:Bacteria(1.0000),p:"Proteobacteria"(0.1700),c:Gammaproteobacteria(0.1300),o:"Enterobacteriales"(0.1100),f:Enterobacteriaceae(0.1100),g:Biostraticola(0.0800) + d:Bacteria
   ASV55 d:Bacteria(1.0000),p:"Proteobacteria"(0.1200),c:Gammaproteobacteria(0.1200),o:"Enterobacteriales"(0.0300),f:Enterobacteriaceae(0.0300),g:Aeromonas(0.0200) + d:Bacteria

3. log file looks like this:
   [01/07/19 18:11:11]: /home/bioadmin/packages/amptk-1.2.5/bin/amptk-assign_taxonomy.py --method hybrid -f ./Kafue_MG.lulu.otus.fa -i ./Kafue_MG.lulu.otu_table.txt -m ./Kafue_MG.mapping_file.txt -d 16S -o Kafue_MG

[01/07/19 18:11:11]: OS: linux2, 8 cores, ~ 8 GB RAM. Python: 2.7.15
[01/07/19 18:11:11]: Python Modules: numpy v1.15.2, pandas v0.23.4, matplotlib v2.2.3, psutil v5.4.7, natsort v5.4.0, biopython v1.68, edlib v1.2.3, biom-format v2.1.7
[01/07/19 18:11:11]: AMPtk v1.2.5, USEARCH v9.2.64, VSEARCH v2.9.0
[01/07/19 18:11:11]: Loading FASTA Records
[01/07/19 18:11:11]: 265 OTUs
[01/07/19 18:11:11]: Global alignment OTUs with usearch_global (USEARCH)
[01/07/19 18:11:11]: usearch9 -usearch_global ./Kafue_MG.lulu.otus.fa -db /home/bioadmin/packages/amptk-1.2.5/DB/16S.udb -userout Kafue_MG.usearch.txt -id 0.7 -strand both -output_no_hits -maxaccepts 0 -top_hits_only -userfields query+target+id -threads 8
[01/07/19 18:11:18]: usearch v9.2.64_i86linux32, 4.0Gb RAM (8.0Gb total), 8 cores
(C) Copyright 2013-16 Robert C. Edgar, all rights reserved.
http://drive5.com/usearch

License: [email protected]

[01/07/19 18:11:18]: 00:00 3.9Mb 0.0% Rows
00:00 78Mb 100.0% Rows
00:00 78Mb Read taxonomy info...done.
00:00 79Mb Reading pointers...done.
00:00 81Mb Reading db seqs...done.
00:00 133Mb 0.1% Searching Kafue_MG.lulu.otus.fa, 0.0% matched
00:01 223Mb 4.5% Searching Kafue_MG.lulu.otus.fa, 100.0% matched
00:02 261Mb 15.6% Searching Kafue_MG.lulu.otus.fa, 91.2% matched
00:03 270Mb 25.3% Searching Kafue_MG.lulu.otus.fa, 93.2% matched
00:04 286Mb 49.5% Searching Kafue_MG.lulu.otus.fa, 91.9% matched
00:05 286Mb 62.5% Searching Kafue_MG.lulu.otus.fa, 91.7% matched
00:06 287Mb 79.5% Searching Kafue_MG.lulu.otus.fa, 90.6% matched
00:07 301Mb 100.0% Searching Kafue_MG.lulu.otus.fa, 89.1% matched

[01/07/19 18:11:18]: Classifying OTUs with UTAX (USEARCH)
[01/07/19 18:11:18]: usearch9 -utax ./Kafue_MG.lulu.otus.fa -db /home/bioadmin/packages/amptk-1.2.5/DB/16S.udb -utaxout Kafue_MG.utax.txt -utax_cutoff 0.8 -strand plus -notrunclabels -threads 8
[01/07/19 18:11:18]: usearch v9.2.64_i86linux32, 4.0Gb RAM (8.0Gb total), 8 cores
(C) Copyright 2013-16 Robert C. Edgar, all rights reserved.
http://drive5.com/usearch

License: [email protected]

[01/07/19 18:11:18]: 00:00 3.8Mb 0.0% Rows
00:00 78Mb 100.0% Rows
00:00 78Mb Read taxonomy info...done.
00:00 79Mb Reading pointers...done.
00:00 81Mb Reading db seqs...done.
00:00 133Mb 0.1% 0 seqs, 0.0% at phylum, 0.0% genus (P > 0.00)
00:00 210Mb 100.0% 265 seqs, 63.8% at phylum, 16.2% genus (P > 0.80)

WARNING: Option -notrunclabels not used

[01/07/19 18:11:18]: Classifying OTUs with SINTAX (USEARCH)
[01/07/19 18:11:18]: usearch9 -sintax ./Kafue_MG.lulu.otus.fa -db /home/bioadmin/packages/amptk-1.2.5/DB/16S.extracted.fa -tabbedout Kafue_MG.sintax.txt -sintax_cutoff 0.8 -strand both -threads 8
[01/07/19 18:11:20]: usearch v9.2.64_i86linux32, 4.0Gb RAM (8.0Gb total), 8 cores
(C) Copyright 2013-16 Robert C. Edgar, all rights reserved.
http://drive5.com/usearch

License: [email protected]

[01/07/19 18:11:20]: 00:00 37Mb 0.1% Reading /home/bioadmin/packages/amptk-1.2.5/DB/16S.extracted.fa
00:00 61Mb 100.0% Reading /home/bioadmin/packages/amptk-1.2.5/DB/16S.extracted.fa
00:00 27Mb 0.1% Masking (fastnucleo)
00:00 27Mb 100.0% Masking (fastnucleo)
00:00 28Mb 0.1% Word stats
00:01 28Mb 40.2% Word stats
00:01 28Mb 100.0% Word stats
00:01 28Mb 100.0% Alloc rows
00:01 99Mb 0.1% Build index
00:02 99Mb 90.8% Build index
00:02 99Mb 100.0% Build index
00:02 99Mb 0.0% Initialize taxonomy data
00:02 99Mb 100.0% Initialize taxonomy data
00:02 99Mb 0.0% Building name table
00:02 99Mb 100.0% Building name table
00:02 99Mb 2778 names, tax levels min 1, avg 5.9, max 6
00:02 133Mb 0.1% Processing
00:02 202Mb 100.0% Processing

[AlexGaithuma]

Thank you for your Feedback.

I found out that the problem occured during database creation.
There was a problem with the format of the database input file "-i Extra_rdp_v16.fa" file.
There were some instances with a comma and others with a colon:

86332;tax=d:Bacteria,p:"Proteobacteria",c:Alphaproteobacteria,o:"Rickettsiales",f:Anaplasmataceae,g:Wolbachia;

and

86332;tax=d:Bacteria:p:"Proteobacteria",c:Alphaproteobacteria,o:"Rickettsiales",f:Anaplasmataceae,g:Wolbachia;

Once I resolved this, there was no error.

[nextgenusfs]

Great, glad you got it sorted!