Download and generate SILVA reference database

[najibveto]

hello,
I am working on 16s amplicon sequencing and I wanted to create a SILVA reference database using this tutorial:
https://constax.readthedocs.io/en/latest/tutorial3.html
so I created a script as follow:

`#!/bin/bash

constax
--input SILVA_138_SSURef_tax_silva.fasta
--select_by_keyword " Bacteria;"
--output silva_Db_bacteria.fasta

constax
--input SILVA_138_SSURef_tax_silva.fasta
--select_by_keyword " Archaea;"
--output silva_Db_archaea.fasta`

but i got the following error:

`Welcome to CONSTAX version 2.0.17 build 0 - The CONSensus TAXonomy classifier
This software is distributed under MIT License
© Copyright 2021, Julian A. Liber, Gian M. N. Benucci & Gregory M. Bonito
https://github.com/liberjul/CONSTAXv2
https://constax.readthedocs.io/

Please cite us as:
CONSTAX2: Improved taxonomic classification of environmental DNA markers
Julian Aaron Liber, Gregory Bonito, Gian Maria Niccolò Benucci
Bioinformatics, Volume 37, Issue 21, 1 November 2021, Pages 3941–3943; doi: https://doi.org/10.1093/bioinformatics/btab347
Using the user-supplied pathfile at /home/najib/miniconda3/opt/constax-2.0.17-0/pathfile.txt
/home/najib/miniconda3/opt/constax-2.0.17-0/constax_no_inputs.sh: line 185: [: /home/najib/miniconda3/bin/classifier: unary operator expected
Please specify --msu_hpcc if using it, otherwise specify paths for --sintax_path,
--rdp_path, --utax_path (if not using BLAST), and --constax_path
SINTAX: vsearch
RDP: classifier
/home/najib/miniconda3/opt/constax-2.0.17-0/constax_no_inputs.sh: line 204: [: /home/najib/miniconda3/bin/java: unary operator expected
UTAX:
UTAX not executable. Did you mean to use -b/--blast flag?
CONSTAX: /home/najib/miniconda3/opt/constax-2.0.17-0
CONSTAX directory not found
Welcome to CONSTAX version 2.0.17 build 0 - The CONSensus TAXonomy classifier
This software is distributed under MIT License
© Copyright 2021, Julian A. Liber, Gian M. N. Benucci & Gregory M. Bonito
https://github.com/liberjul/CONSTAXv2
https://constax.readthedocs.io/`

I already installed constax:

`
packages in environment at /home/najib/miniconda3:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
blast 2.5.0 hc0b0e79_3 bioconda
boost 1.77.0 py39h5472131_0 conda-forge
boost-cpp 1.77.0 h359cf19_1 conda-forge
brotlipy 0.7.0 py39h3811e60_1003 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2021.10.8 ha878542_0 conda-forge
certifi 2021.10.8 py39hf3d152e_1 conda-forge
cffi 1.15.0 py39hd667e15_1
charset-normalizer 2.0.12 pyhd8ed1ab_0 conda-forge
colorama 0.4.4 pyh9f0ad1d_0 conda-forge
conda 4.11.0 py39hf3d152e_2 conda-forge
conda-package-handling 1.7.3 py39h3811e60_1 conda-forge
constax 2.0.17 pyhdfd78af_0 bioconda
cryptography 36.0.1 py39h95dcef6_0 conda-forge
icu 69.1 h9c3ff4c_0 conda-forge
idna 3.3 pyhd8ed1ab_0 conda-forge
krb5 1.19.2 hcc1bbae_3 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
libarchive 3.5.2 hccf745f_1 conda-forge
libblas 3.9.0 13_linux64_openblas conda-forge
libcblas 3.9.0 13_linux64_openblas conda-forge
libcurl 7.81.0 h2574ce0_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.3 h58526e2_2 conda-forge
libgcc-ng 11.2.0 h1d223b6_12 conda-forge
libgfortran-ng 11.2.0 h69a702a_13 conda-forge
libgfortran5 11.2.0 h5c6108e_13 conda-forge
libgomp 11.2.0 h1d223b6_12 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 13_linux64_openblas conda-forge
libnghttp2 1.46.0 h812cca2_0 conda-forge
libopenblas 0.3.18 pthreads_h8fe5266_0 conda-forge
libsolv 0.7.19 h780b84a_5 conda-forge
libssh2 1.10.0 ha56f1ee_2 conda-forge
libstdcxx-ng 11.2.0 he4da1e4_12 conda-forge
libxml2 2.9.12 h885dcf4_1 conda-forge
libzip 1.8.0 h4de3113_1 conda-forge
libzlib 1.2.11 h36c2ea0_1013 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
lzo 2.10 h516909a_1000 conda-forge
mamba 0.15.3 py39h951de11_0 conda-forge
ncurses 6.3 h9c3ff4c_0 conda-forge
numpy 1.22.2 pypi_0 pypi
openjdk 8.0.312 h7f98852_0 conda-forge
openssl 1.1.1l h7f98852_0 conda-forge
pandas 1.4.1 pypi_0 pypi
pcre 8.45 h9c3ff4c_0 conda-forge
pip 22.0.3 pypi_0 pypi
pycosat 0.6.3 py39h3811e60_1009 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pyopenssl 22.0.0 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 py39hf3d152e_4 conda-forge
python 3.9.5 h12debd9_4
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.9 2_cp39 conda-forge
pytz 2021.3 pyhd8ed1ab_0 conda-forge
qax 0.9.5 hac521b0_1 bioconda
rdptools 2.0.3 hdfd78af_1 bioconda
readline 8.1 h46c0cb4_0 conda-forge
reproc 14.2.3 h7f98852_0 conda-forge
reproc-cpp 14.2.3 h9c3ff4c_0 conda-forge
requests 2.27.1 pyhd8ed1ab_0 conda-forge
ruamel_yaml 0.15.80 py39h3811e60_1006 conda-forge
seqfu 1.9.1 hbd632db_1 bioconda
seqkit 2.1.0 h9ee0642_0 bioconda
setuptools 60.9.3 py39hf3d152e_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sqlite 3.37.0 h9cd32fc_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tqdm 4.62.3 pyhd8ed1ab_0 conda-forge
tzdata 2021e he74cb21_0 conda-forge
urllib3 1.26.8 pyhd8ed1ab_1 conda-forge
vsearch 2.21.1 hf1761c0_1 bioconda
wheel 0.37.1 pypi_0 pypi
xz 5.2.5 h516909a_1 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zip 3.0 h7f98852_1 conda-forge
zlib 1.2.11 h36c2ea0_1013 conda-forge
zstd 1.5.2 ha95c52a_0 conda-forge
`

[liberjul]

Hi @najibveto ,

Thanks for reaching out about this issue. There is a temporary fix for you, but I will also update the main script to make this unnecessary. Add the flag -b to your command which will tell the script to ignore trying to find the UTAX path.

Also, can you make sure that your directory /home/najib/miniconda3/opt/constax-2.0.17-0/ contains several scripts (constax_no_inputs.sh, etc.)?

Let me know if this fixes your problem,

Julian

[najibveto]

thank you a lot for your help.
sorry for my late reply ^^.
I could work around it using your python script ^^.