##Install gblocks
wget http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_Linux64_0.91b.tar.Z
tar zxvf Gblocks_Linux_0.91b.tar.Z
Step 1: Download latest conda installer
$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
Log info
--2021-02-12 18:18:56-- https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
Resolving repo.continuum.io (repo.continuum.io)... 104.18.200.79, 104.18.201.79, 2606:4700::6812:c94f, ...
Connecting to repo.continuum.io (repo.continuum.io)|104.18.200.79|:443... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh [following]
--2021-02-12 18:18:56-- https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
Resolving repo.anaconda.com (repo.anaconda.com)... 104.16.131.3, 104.16.130.3, 2606:4700::6810:8203, ...
Connecting to repo.anaconda.com (repo.anaconda.com)|104.16.131.3|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 94235922 (90M) [application/x-sh]
Saving to: ‘Miniconda3-latest-Linux-x86_64.sh’
100%[=====================================================================================================================================================================>] 94,235,922 51.0MB/s in 1.8s
2021-02-12 18:18:58 (51.0 MB/s) - ‘Miniconda3-latest-Linux-x86_64.sh’ saved [94235922/94235922]
Step 2: Run the installer
$ bash Miniconda3-latest-Linux-x86_64.sh
Log info
Welcome to Miniconda3 py38_4.9.2
In order to continue the installation process, please review the license
agreement.
Please, press ENTER to continue
>>>
Press ENTER untill this message appear
Do you accept the license terms? [yes|no]
Type yes
Log info
Miniconda3 will now be installed into this location:
/home/kplee/miniconda3
- Press ENTER to confirm the location
- Press CTRL-C to abort the installation
- Or specify a different location below
[/home/kplee/miniconda3] >>> /home/kplee/program/miniconda3
I set /home/kplee/program/miniconda3 as the installation path and press ENTER
Log info
PREFIX=/home/kplee/program/miniconda3
Unpacking payload ...
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /home/kplee/program/miniconda3
added / updated specs:
- _libgcc_mutex==0.1=main
- brotlipy==0.7.0=py38h27cfd23_1003
- ca-certificates==2020.10.14=0
- certifi==2020.6.20=pyhd3eb1b0_3
- cffi==1.14.3=py38h261ae71_2
- chardet==3.0.4=py38h06a4308_1003
- conda-package-handling==1.7.2=py38h03888b9_0
- conda==4.9.2=py38h06a4308_0
- cryptography==3.2.1=py38h3c74f83_1
- idna==2.10=py_0
- ld_impl_linux-64==2.33.1=h53a641e_7
- libedit==3.1.20191231=h14c3975_1
- libffi==3.3=he6710b0_2
- libgcc-ng==9.1.0=hdf63c60_0
- libstdcxx-ng==9.1.0=hdf63c60_0
- ncurses==6.2=he6710b0_1
- openssl==1.1.1h=h7b6447c_0
- pip==20.2.4=py38h06a4308_0
- pycosat==0.6.3=py38h7b6447c_1
- pycparser==2.20=py_2
- pyopenssl==19.1.0=pyhd3eb1b0_1
- pysocks==1.7.1=py38h06a4308_0
- python==3.8.5=h7579374_1
- readline==8.0=h7b6447c_0
- requests==2.24.0=py_0
- ruamel_yaml==0.15.87=py38h7b6447c_1
- setuptools==50.3.1=py38h06a4308_1
- six==1.15.0=py38h06a4308_0
- sqlite==3.33.0=h62c20be_0
- tk==8.6.10=hbc83047_0
- tqdm==4.51.0=pyhd3eb1b0_0
- urllib3==1.25.11=py_0
- wheel==0.35.1=pyhd3eb1b0_0
- xz==5.2.5=h7b6447c_0
- yaml==0.2.5=h7b6447c_0
- zlib==1.2.11=h7b6447c_3
The following NEW packages will be INSTALLED:
_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main
brotlipy pkgs/main/linux-64::brotlipy-0.7.0-py38h27cfd23_1003
ca-certificates pkgs/main/linux-64::ca-certificates-2020.10.14-0
certifi pkgs/main/noarch::certifi-2020.6.20-pyhd3eb1b0_3
cffi pkgs/main/linux-64::cffi-1.14.3-py38h261ae71_2
chardet pkgs/main/linux-64::chardet-3.0.4-py38h06a4308_1003
conda pkgs/main/linux-64::conda-4.9.2-py38h06a4308_0
conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.7.2-py38h03888b9_0
cryptography pkgs/main/linux-64::cryptography-3.2.1-py38h3c74f83_1
idna pkgs/main/noarch::idna-2.10-py_0
ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7
libedit pkgs/main/linux-64::libedit-3.1.20191231-h14c3975_1
libffi pkgs/main/linux-64::libffi-3.3-he6710b0_2
libgcc-ng pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
ncurses pkgs/main/linux-64::ncurses-6.2-he6710b0_1
openssl pkgs/main/linux-64::openssl-1.1.1h-h7b6447c_0
pip pkgs/main/linux-64::pip-20.2.4-py38h06a4308_0
pycosat pkgs/main/linux-64::pycosat-0.6.3-py38h7b6447c_1
pycparser pkgs/main/noarch::pycparser-2.20-py_2
pyopenssl pkgs/main/noarch::pyopenssl-19.1.0-pyhd3eb1b0_1
pysocks pkgs/main/linux-64::pysocks-1.7.1-py38h06a4308_0
python pkgs/main/linux-64::python-3.8.5-h7579374_1
readline pkgs/main/linux-64::readline-8.0-h7b6447c_0
requests pkgs/main/noarch::requests-2.24.0-py_0
ruamel_yaml pkgs/main/linux-64::ruamel_yaml-0.15.87-py38h7b6447c_1
setuptools pkgs/main/linux-64::setuptools-50.3.1-py38h06a4308_1
six pkgs/main/linux-64::six-1.15.0-py38h06a4308_0
sqlite pkgs/main/linux-64::sqlite-3.33.0-h62c20be_0
tk pkgs/main/linux-64::tk-8.6.10-hbc83047_0
tqdm pkgs/main/noarch::tqdm-4.51.0-pyhd3eb1b0_0
urllib3 pkgs/main/noarch::urllib3-1.25.11-py_0
wheel pkgs/main/noarch::wheel-0.35.1-pyhd3eb1b0_0
xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
yaml pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0
zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3
Preparing transaction: done
Executing transaction: done
installation finished.
Do you wish the installer to initialize Miniconda3
by running conda init? [yes|no]
[no] >>>
I typed yes
Log info
no change /home/kplee/program/miniconda3/condabin/conda
no change /home/kplee/program/miniconda3/bin/conda
no change /home/kplee/program/miniconda3/bin/conda-env
no change /home/kplee/program/miniconda3/bin/activate
no change /home/kplee/program/miniconda3/bin/deactivate
no change /home/kplee/program/miniconda3/etc/profile.d/conda.sh
no change /home/kplee/program/miniconda3/etc/fish/conf.d/conda.fish
no change /home/kplee/program/miniconda3/shell/condabin/Conda.psm1
no change /home/kplee/program/miniconda3/shell/condabin/conda-hook.ps1
no change /home/kplee/program/miniconda3/lib/python3.8/site-packages/xontrib/conda.xsh
no change /home/kplee/program/miniconda3/etc/profile.d/conda.csh
modified /home/kplee/.bashrc
==> For changes to take effect, close and re-open your current shell. <==
If you'd prefer that conda's base environment not be activated on startup,
set the auto_activate_base parameter to false:
conda config --set auto_activate_base false
Thank you for installing Miniconda3!
Please close and reopen the terminal, to complete the installation.
After closing and re-opening the shell/terminal, we should be able to use the conda command:
$ conda update --yes condaLog info
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /home/kplee/program/miniconda3
added / updated specs:
- conda
The following packages will be downloaded:
package | build
---------------------------|-----------------
_openmp_mutex-4.5 | 1_gnu 22 KB
ca-certificates-2021.1.19 | h06a4308_0 121 KB
certifi-2020.12.5 | py38h06a4308_0 141 KB
cffi-1.14.4 | py38h261ae71_0 226 KB
chardet-4.0.0 |py38h06a4308_1003 194 KB
cryptography-3.3.1 | py38h3c74f83_0 566 KB
idna-2.10 | pyhd3eb1b0_0 52 KB
ld_impl_linux-64-2.35.1 | h2b15070_1 627 KB
libgcc-ng-9.3.0 | h9cbead1_17 7.8 MB
libgomp-9.3.0 | h9cbead1_17 377 KB
libstdcxx-ng-9.3.0 | h2ae2ef3_17 4.0 MB
openssl-1.1.1i | h27cfd23_0 2.5 MB
pip-20.3.3 | py38h06a4308_0 1.8 MB
pyopenssl-20.0.1 | pyhd3eb1b0_1 49 KB
readline-8.1 | h27cfd23_0 362 KB
requests-2.25.1 | pyhd3eb1b0_0 52 KB
setuptools-52.0.0 | py38h06a4308_0 714 KB
tqdm-4.56.0 | pyhd3eb1b0_0 80 KB
urllib3-1.26.3 | pyhd3eb1b0_0 105 KB
wheel-0.36.2 | pyhd3eb1b0_0 33 KB
------------------------------------------------------------
Total: 19.8 MB
The following NEW packages will be INSTALLED:
_openmp_mutex pkgs/main/linux-64::_openmp_mutex-4.5-1_gnu
libgomp pkgs/main/linux-64::libgomp-9.3.0-h9cbead1_17
The following packages will be UPDATED:
ca-certificates 2020.10.14-0 --> 2021.1.19-h06a4308_0
certifi pkgs/main/noarch::certifi-2020.6.20-p~ --> pkgs/main/linux-64::certifi-2020.12.5-py38h06a4308_0
cffi 1.14.3-py38h261ae71_2 --> 1.14.4-py38h261ae71_0
chardet 3.0.4-py38h06a4308_1003 --> 4.0.0-py38h06a4308_1003
cryptography 3.2.1-py38h3c74f83_1 --> 3.3.1-py38h3c74f83_0
ld_impl_linux-64 2.33.1-h53a641e_7 --> 2.35.1-h2b15070_1
libgcc-ng 9.1.0-hdf63c60_0 --> 9.3.0-h9cbead1_17
libstdcxx-ng 9.1.0-hdf63c60_0 --> 9.3.0-h2ae2ef3_17
openssl 1.1.1h-h7b6447c_0 --> 1.1.1i-h27cfd23_0
pip 20.2.4-py38h06a4308_0 --> 20.3.3-py38h06a4308_0
pyopenssl 19.1.0-pyhd3eb1b0_1 --> 20.0.1-pyhd3eb1b0_1
readline 8.0-h7b6447c_0 --> 8.1-h27cfd23_0
requests 2.24.0-py_0 --> 2.25.1-pyhd3eb1b0_0
setuptools 50.3.1-py38h06a4308_1 --> 52.0.0-py38h06a4308_0
tqdm 4.51.0-pyhd3eb1b0_0 --> 4.56.0-pyhd3eb1b0_0
urllib3 1.25.11-py_0 --> 1.26.3-pyhd3eb1b0_0
wheel 0.35.1-pyhd3eb1b0_0 --> 0.36.2-pyhd3eb1b0_0
The following packages will be DOWNGRADED:
idna 2.10-py_0 --> 2.10-pyhd3eb1b0_0
Downloading and Extracting Packages
tqdm-4.56.0 | 80 KB | #################################################################################################################################################################### | 100%
libgomp-9.3.0 | 377 KB | #################################################################################################################################################################### | 100%
pyopenssl-20.0.1 | 49 KB | #################################################################################################################################################################### | 100%
chardet-4.0.0 | 194 KB | #################################################################################################################################################################### | 100%
cryptography-3.3.1 | 566 KB | #################################################################################################################################################################### | 100%
cffi-1.14.4 | 226 KB | #################################################################################################################################################################### | 100%
libgcc-ng-9.3.0 | 7.8 MB | #################################################################################################################################################################### | 100%
ld_impl_linux-64-2.3 | 627 KB | #################################################################################################################################################################### | 100%
certifi-2020.12.5 | 141 KB | #################################################################################################################################################################### | 100%
requests-2.25.1 | 52 KB | #################################################################################################################################################################### | 100%
ca-certificates-2021 | 121 KB | #################################################################################################################################################################### | 100%
_openmp_mutex-4.5 | 22 KB | #################################################################################################################################################################### | 100%
readline-8.1 | 362 KB | #################################################################################################################################################################### | 100%
openssl-1.1.1i | 2.5 MB | #################################################################################################################################################################### | 100%
pip-20.3.3 | 1.8 MB | #################################################################################################################################################################### | 100%
urllib3-1.26.3 | 105 KB | #################################################################################################################################################################### | 100%
libstdcxx-ng-9.3.0 | 4.0 MB | #################################################################################################################################################################### | 100%
idna-2.10 | 52 KB | #################################################################################################################################################################### | 100%
wheel-0.36.2 | 33 KB | #################################################################################################################################################################### | 100%
setuptools-52.0.0 | 714 KB | #################################################################################################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Step 4: Installing conda channels to make tools available Different tools are packaged in what conda calls channels. We need to add some channels to make the bioinformatics and genomics tools available for installation:
# Install some conda channels
# A channel is where conda looks for packages
$ conda config --add channels defaults
$ conda config --add channels bioconda
$ conda config --add channels conda-forgeAttention
The order of adding channels is important. Make sure you use the shown order of commands.
Update System
Firstly we need to update the system through yum update command as shown below.
$ sudo yum update
Install Perl Package Once System is fully updated, you can install perl package through yum install perl command as shown below.
$ sudo yum install perl
Check
$ perl -v
Should get this info
This is perl 5, version 16, subversion 3 (v5.16.3) built for x86_64-linux-thread-multi
(with 44 registered patches, see perl -V for more detail)
Copyright 1987-2012, Larry Wall
Perl may be copied only under the terms of either the Artistic License or the
GNU General Public License, which may be found in the Perl 5 source kit.
Complete documentation for Perl, including FAQ lists, should be found on
this system using "man perl" or "perldoc perl". If you have access to the
Internet, point your browser at http://www.perl.org/, the Perl Home Page.
Install java
$ sudo yum install java-1.8.0-openjdk
Check
$ java -version
Should see this info
openjdk version "1.8.0_282"
OpenJDK Runtime Environment (build 1.8.0_282-b08)
OpenJDK 64-Bit Server VM (build 25.282-b08, mixed mode)
The easy way to install canu is to download the hicanu binary
$ wget https://github.com/marbl/canu/releases/download/v2.1.1/canu-2.1.1.Linux-amd64.tar.xz
Install from binary distribution
tar -xJf canu-2.1.1.Linux-amd64.tar.xz
Done! canu is well installed and available here
cd canu-2.1.1/bin
Check
./canu
Should get this
usage: canu [-version] [-citation] \
[-haplotype | -correct | -trim | -assemble | -trim-assemble] \
[-s <assembly-specifications-file>] \
-p <assembly-prefix> \
-d <assembly-directory> \
genomeSize=<number>[g|m|k] \
[other-options] \
[-haplotype{NAME} illumina.fastq.gz] \
[-corrected] \
[-trimmed] \
[-pacbio |
-nanopore |
-pacbio-hifi] file1 file2 ...
example: canu -d run1 -p godzilla genomeSize=1g -nanopore-raw reads/*.fasta.gz
To restrict canu to only a specific stage, use:
-haplotype - generate haplotype-specific reads
-correct - generate corrected reads
-trim - generate trimmed reads
-assemble - generate an assembly
-trim-assemble - generate trimmed reads and then assemble them
The assembly is computed in the -d <assembly-directory>, with output files named
using the -p <assembly-prefix>. This directory is created if needed. It is not
possible to run multiple assemblies in the same directory.
The genome size should be your best guess of the haploid genome size of what is being
assembled. It is used primarily to estimate coverage in reads, NOT as the desired
assembly size. Fractional values are allowed: '4.7m' equals '4700k' equals '4700000'
Some common options:
useGrid=string
- Run under grid control (true), locally (false), or set up for grid control
but don't submit any jobs (remote)
rawErrorRate=fraction-error
- The allowed difference in an overlap between two raw uncorrected reads. For lower
quality reads, use a higher number. The defaults are 0.300 for PacBio reads and
0.500 for Nanopore reads.
correctedErrorRate=fraction-error
- The allowed difference in an overlap between two corrected reads. Assemblies of
low coverage or data with biological differences will benefit from a slight increase
in this. Defaults are 0.045 for PacBio reads and 0.144 for Nanopore reads.
gridOptions=string
- Pass string to the command used to submit jobs to the grid. Can be used to set
maximum run time limits. Should NOT be used to set memory limits; Canu will do
that for you.
minReadLength=number
- Ignore reads shorter than 'number' bases long. Default: 1000.
minOverlapLength=number
- Ignore read-to-read overlaps shorter than 'number' bases long. Default: 500.
A full list of options can be printed with '-options'. All options can be supplied in
an optional sepc file with the -s option.
For TrioCanu, haplotypes are specified with the -haplotype{NAME} option, with any
number of haplotype-specific Illumina read files after. The {NAME} of each haplotype
is free text (but only letters and numbers, please). For example:
-haplotypeNANNY nanny/*gz
-haplotypeBILLY billy1.fasta.gz billy2.fasta.gz
Reads can be either FASTA or FASTQ format, uncompressed, or compressed with gz, bz2 or xz.
Reads are specified by the technology they were generated with, and any processing performed.
[processing]
-corrected
-trimmed
[technology]
-pacbio <files>
-nanopore <files>
-pacbio-hifi <files>
Complete documentation at http://canu.readthedocs.org/en/latest/
First install python3
sudo yum install python3-devel
clone the repository and compile
sudo git clone https://github.com/fenderglass/Flye
cd Flye
sudo make
Check
./flye -h
Should see:
usage: flye (--pacbio-raw | --pacbio-corr | --pacbio-hifi | --nano-raw |
--nano-corr | --subassemblies) file1 [file_2 ...]
--out-dir PATH
[--genome-size SIZE] [--threads int] [--iterations int]
[--meta] [--plasmids] [--trestle] [--polish-target]
[--keep-haplotypes] [--debug] [--version] [--help]
[--resume] [--resume-from] [--stop-after]
[--hifi-error] [--min-overlap SIZE]
Assembly of long reads with repeat graphs
optional arguments:
-h, --help show this help message and exit
--pacbio-raw path [path ...]
PacBio raw reads
--pacbio-corr path [path ...]
PacBio corrected reads
--pacbio-hifi path [path ...]
PacBio HiFi reads
--nano-raw path [path ...]
ONT raw reads
--nano-corr path [path ...]
ONT corrected reads
--subassemblies path [path ...]
high-quality contigs input
-g size, --genome-size size
estimated genome size (for example, 5m or 2.6g)
-o path, --out-dir path
Output directory
-t int, --threads int
number of parallel threads [1]
-i int, --iterations int
number of polishing iterations [1]
-m int, --min-overlap int
minimum overlap between reads [auto]
--asm-coverage int reduced coverage for initial disjointig assembly [not
set]
--hifi-error float expected HiFi reads error rate (e.g. 0.01 or 0.001)
[0.01]
--plasmids rescue short unassembled plasmids
--meta metagenome / uneven coverage mode
--keep-haplotypes do not collapse alternative haplotypes
--trestle enable Trestle [disabled]
--polish-target path run polisher on the target sequence
--resume resume from the last completed stage
--resume-from stage_name
resume from a custom stage
--stop-after stage_name
stop after the specified stage completed
--debug enable debug output
-v, --version show program's version number and exit
Input reads can be in FASTA or FASTQ format, uncompressed
or compressed with gz. Currently, PacBio (raw, corrected, HiFi)
and ONT reads (raw, corrected) are supported. Expected error rates are
<30% for raw, <3% for corrected, and <1% for HiFi. Note that Flye
was primarily developed to run on raw reads. Additionally, the
--subassemblies option performs a consensus assembly of multiple
sets of high-quality contigs. You may specify multiple
files with reads (separated by spaces). Mixing different read
types is not yet supported. The --meta option enables the mode
for metagenome/uneven coverage assembly.
Genome size estimate is no longer a required option. You
need to provide an estimate if using --asm-coverage option.
To reduce memory consumption for large genome assemblies,
you can use a subset of the longest reads for initial disjointig
assembly by specifying --asm-coverage and --genome-size options. Typically,
40x coverage is enough to produce good disjointigs.
You can run Flye polisher as a standalone tool using
--polish-target option.
Fine! Flye is installed.
Just do:
$ sudo git clone https://github.com/chhylp123/hifiasm
$ cd hifiasm && make
# download latest conda installer
$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
Now lets install conda:
# run the installer
$ bash Miniconda3-latest-Linux-x86_64.sh
Accept the license
Do you accept the license terms? [yes|no]
Press Yes
After you accepted the license agreement conda will be installed. At the end of the installation you will encounter the following:
Preparing transaction: done
Executing transaction: done
installation finished.
Do you wish the installer to initialize Miniconda3
by running conda init? [yes|no]
Should see the last info
no change /home/kplee/miniconda3/condabin/conda
no change /home/kplee/miniconda3/bin/conda
no change /home/kplee/miniconda3/bin/conda-env
no change /home/kplee/miniconda3/bin/activate
no change /home/kplee/miniconda3/bin/deactivate
no change /home/kplee/miniconda3/etc/profile.d/conda.sh
no change /home/kplee/miniconda3/etc/fish/conf.d/conda.fish
no change /home/kplee/miniconda3/shell/condabin/Conda.psm1
no change /home/kplee/miniconda3/shell/condabin/conda-hook.ps1
no change /home/kplee/miniconda3/lib/python3.8/site-packages/xontrib/conda.xsh
no change /home/kplee/miniconda3/etc/profile.d/conda.csh
modified /home/kplee/.bashrc
==> For changes to take effect, close and re-open your current shell. <==
If you'd prefer that conda's base environment not be activated on startup,
set the auto_activate_base parameter to false:
conda config --set auto_activate_base false
Thank you for installing Miniconda3!
close and open the terminal
After closing and re-opening the shell/terminal, we should be able to use the conda command:
$ conda update --yes conda
Installing conda channels to make tools available
# Install some conda channels
# A channel is where conda looks for packages
$ conda config --add channels defaults
$ conda config --add channels bioconda
$ conda config --add channels conda-forge
Upgrade the gcc
$ yum -y install centos-release-scl
$ yum -y install devtoolset-7-gcc devtoolset-7-gcc-c++ devtoolset-7-binutils
$ scl enable devtoolset-7 bash
Check
gcc -vget this:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/opt/rh/devtoolset-7/root/usr/libexec/gcc/x86_64-redhat-linux/7/lto-wrapper
Target: x86_64-redhat-linux
Configured with: ../configure --enable-bootstrap --enable-languages=c,c++,fortran,lto --prefix=/opt/rh/devtoolset-7/root/usr --mandir=/opt/rh/devtoolset-7/root/usr/share/man --infodir=/opt/rh/devtoolset-7/root/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-shared --enable-threads=posix --enable-checking=release --enable-multilib --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-gcc-major-version-only --enable-plugin --with-linker-hash-style=gnu --enable-initfini-array --with-default-libstdcxx-abi=gcc4-compatible --with-isl=/builddir/build/BUILD/gcc-7.3.1-20180303/obj-x86_64-redhat-linux/isl-install --enable-libmpx --enable-gnu-indirect-function --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 7.3.1 20180303 (Red Hat 7.3.1-5) (GCC)
Download and install via conda
git clone https://github.com/cschin/Peregrine.git
cd Peregrine
bash install_with_conda.shNote:
I modified the sh file by replacing . ~/miniconda3/bin/activate by . ~/anaconda3/bin/activate
conda create -n ipa
conda activate ipa
conda install pbipaRun on data
/usr/bin/time -o out.ram.txt -v ipa local --nthreads 16 --njobs 2 -i ~/datafile/001.i.bat.pacbio.hifi.reads/S_unknown.ccs.merged.fasta &> log &Step 1: Uninstall old versions Older versions of Docker were called docker or docker-engine. If these are installed, uninstall them, along with associated dependencies.
$ sudo yum remove docker \
docker-client \
docker-client-latest \
docker-common \
docker-latest \
docker-latest-logrotate \
docker-logrotate \
docker-engine
Log info
Loaded plugins: fastestmirror
No Match for argument: docker
No Match for argument: docker-client
No Match for argument: docker-client-latest
No Match for argument: docker-common
No Match for argument: docker-latest
No Match for argument: docker-latest-logrotate
No Match for argument: docker-logrotate
No Match for argument: docker-engine
No Packages marked for removal
Step 2: Install using the repository
Before you install Docker Engine for the first time on a new host machine, you need to set up the Docker repository. Afterward, you can install and update Docker from the repository.
Step 2.1: Install dependencies
The next step is to download the dependencies required for installing Docker.
Type in the following command:
sudo yum install -y yum-utils device-mapper-persistent-data lvm2Log info:
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
* base: mirror.kakao.com
* extras: mirror.kakao.com
* updates: mirror.kakao.com
base | 3.6 kB 00:00:00
extras | 2.9 kB 00:00:00
updates | 2.9 kB 00:00:00
Package device-mapper-persistent-data-0.8.5-3.el7_9.2.x86_64 already installed and latest version
Package 7:lvm2-2.02.187-6.el7_9.3.x86_64 already installed and latest version
Resolving Dependencies
--> Running transaction check
---> Package yum-utils.noarch 0:1.1.31-54.el7_8 will be installed
--> Processing Dependency: python-kitchen for package: yum-utils-1.1.31-54.el7_8.noarch
--> Processing Dependency: libxml2-python for package: yum-utils-1.1.31-54.el7_8.noarch
--> Running transaction check
---> Package libxml2-python.x86_64 0:2.9.1-6.el7.5 will be installed
---> Package python-kitchen.noarch 0:1.1.1-5.el7 will be installed
--> Processing Dependency: python-chardet for package: python-kitchen-1.1.1-5.el7.noarch
--> Running transaction check
---> Package python-chardet.noarch 0:2.2.1-3.el7 will be installed
--> Finished Dependency Resolution
Dependencies Resolved
===============================================================================================================================================================================================================
Package Arch Version Repository Size
===============================================================================================================================================================================================================
Installing:
yum-utils noarch 1.1.31-54.el7_8 base 122 k
Installing for dependencies:
libxml2-python x86_64 2.9.1-6.el7.5 base 247 k
python-chardet noarch 2.2.1-3.el7 base 227 k
python-kitchen noarch 1.1.1-5.el7 base 267 k
Transaction Summary
===============================================================================================================================================================================================================
Install 1 Package (+3 Dependent packages)
Total download size: 863 k
Installed size: 4.3 M
Downloading packages:
(1/4): libxml2-python-2.9.1-6.el7.5.x86_64.rpm | 247 kB 00:00:00
(2/4): python-chardet-2.2.1-3.el7.noarch.rpm | 227 kB 00:00:00
(3/4): yum-utils-1.1.31-54.el7_8.noarch.rpm | 122 kB 00:00:00
(4/4): python-kitchen-1.1.1-5.el7.noarch.rpm | 267 kB 00:00:00
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Total 1.7 MB/s | 863 kB 00:00:00
Running transaction check
Running transaction test
Transaction test succeeded
Running transaction
Installing : python-chardet-2.2.1-3.el7.noarch 1/4
Installing : python-kitchen-1.1.1-5.el7.noarch 2/4
Installing : libxml2-python-2.9.1-6.el7.5.x86_64 3/4
Installing : yum-utils-1.1.31-54.el7_8.noarch 4/4
Verifying : libxml2-python-2.9.1-6.el7.5.x86_64 1/4
Verifying : python-kitchen-1.1.1-5.el7.noarch 2/4
Verifying : yum-utils-1.1.31-54.el7_8.noarch 3/4
Verifying : python-chardet-2.2.1-3.el7.noarch 4/4
Installed:
yum-utils.noarch 0:1.1.31-54.el7_8
Dependency Installed:
libxml2-python.x86_64 0:2.9.1-6.el7.5 python-chardet.noarch 0:2.2.1-3.el7 python-kitchen.noarch 0:1.1.1-5.el7
Complete!
The –y switch indicates to the yum installer to answer “yes” to any prompts that may come up. The yum-utils switch adds the yum-config-manager. Docker uses a device mapper storage driver, and the device-mapper-persistent-data and lvm2 packages are required for it to run correctly.
Step 2.2: Add the Docker Repository to CentOS
$ sudo yum-config-manager \
--add-repo \
https://download.docker.com/linux/centos/docker-ce.repo
Log info
Loaded plugins: fastestmirror
adding repo from: https://download.docker.com/linux/centos/docker-ce.repo
grabbing file https://download.docker.com/linux/centos/docker-ce.repo to /etc/yum.repos.d/docker-ce.repo
repo saved to /etc/yum.repos.d/docker-ce.repo
Step 3: Install the latest version of Docker Engine and containerd
$ sudo yum install docker-ce docker-ce-cli containerd.io
Log info
Resolving Dependencies
--> Running transaction check
---> Package containerd.io.x86_64 0:1.4.3-3.1.el7 will be installed
--> Processing Dependency: container-selinux >= 2:2.74 for package: containerd.io-1.4.3-3.1.el7.x86_64
--> Processing Dependency: libseccomp for package: containerd.io-1.4.3-3.1.el7.x86_64
---> Package docker-ce.x86_64 3:20.10.3-3.el7 will be installed
--> Processing Dependency: docker-ce-rootless-extras for package: 3:docker-ce-20.10.3-3.el7.x86_64
---> Package docker-ce-cli.x86_64 1:20.10.3-3.el7 will be installed
--> Running transaction check
---> Package container-selinux.noarch 2:2.119.2-1.911c772.el7_8 will be installed
---> Package docker-ce-rootless-extras.x86_64 0:20.10.3-3.el7 will be installed
--> Processing Dependency: fuse-overlayfs >= 0.7 for package: docker-ce-rootless-extras-20.10.3-3.el7.x86_64
--> Processing Dependency: slirp4netns >= 0.4 for package: docker-ce-rootless-extras-20.10.3-3.el7.x86_64
---> Package libseccomp.x86_64 0:2.3.1-4.el7 will be installed
--> Running transaction check
---> Package fuse-overlayfs.x86_64 0:0.7.2-6.el7_8 will be installed
--> Processing Dependency: libfuse3.so.3(FUSE_3.2)(64bit) for package: fuse-overlayfs-0.7.2-6.el7_8.x86_64
--> Processing Dependency: libfuse3.so.3(FUSE_3.0)(64bit) for package: fuse-overlayfs-0.7.2-6.el7_8.x86_64
--> Processing Dependency: libfuse3.so.3()(64bit) for package: fuse-overlayfs-0.7.2-6.el7_8.x86_64
---> Package slirp4netns.x86_64 0:0.4.3-4.el7_8 will be installed
--> Running transaction check
---> Package fuse3-libs.x86_64 0:3.6.1-4.el7 will be installed
--> Finished Dependency Resolution
Dependencies Resolved
===============================================================================================================================================================================================================
Package Arch Version Repository Size
===============================================================================================================================================================================================================
Installing:
containerd.io x86_64 1.4.3-3.1.el7 docker-ce-stable 33 M
docker-ce x86_64 3:20.10.3-3.el7 docker-ce-stable 27 M
docker-ce-cli x86_64 1:20.10.3-3.el7 docker-ce-stable 33 M
Installing for dependencies:
container-selinux noarch 2:2.119.2-1.911c772.el7_8 extras 40 k
docker-ce-rootless-extras x86_64 20.10.3-3.el7 docker-ce-stable 9.0 M
fuse-overlayfs x86_64 0.7.2-6.el7_8 extras 54 k
fuse3-libs x86_64 3.6.1-4.el7 extras 82 k
libseccomp x86_64 2.3.1-4.el7 base 56 k
slirp4netns x86_64 0.4.3-4.el7_8 extras 81 k
Transaction Summary
===============================================================================================================================================================================================================
Install 3 Packages (+6 Dependent packages)
Total download size: 102 M
Installed size: 423 M
Type y to allow the operation to complete.
log info
Downloading packages:
(1/9): container-selinux-2.119.2-1.911c772.el7_8.noarch.rpm | 40 kB 00:00:00
warning: /var/cache/yum/x86_64/7/docker-ce-stable/packages/containerd.io-1.4.3-3.1.el7.x86_64.rpm: Header V4 RSA/SHA512 Signature, key ID 621e9f35: NOKEY ] 20 MB/s | 18 MB 00:00:04 ETA
Public key for containerd.io-1.4.3-3.1.el7.x86_64.rpm is not installed
(2/9): containerd.io-1.4.3-3.1.el7.x86_64.rpm | 33 MB 00:00:01
(3/9): docker-ce-cli-20.10.3-3.el7.x86_64.rpm | 33 MB 00:00:00
(4/9): docker-ce-20.10.3-3.el7.x86_64.rpm | 27 MB 00:00:02
(5/9): fuse-overlayfs-0.7.2-6.el7_8.x86_64.rpm | 54 kB 00:00:00
(6/9): libseccomp-2.3.1-4.el7.x86_64.rpm | 56 kB 00:00:00
(7/9): docker-ce-rootless-extras-20.10.3-3.el7.x86_64.rpm | 9.0 MB 00:00:00
(8/9): slirp4netns-0.4.3-4.el7_8.x86_64.rpm | 81 kB 00:00:00
(9/9): fuse3-libs-3.6.1-4.el7.x86_64.rpm | 82 kB 00:00:00
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Total 39 MB/s | 102 MB 00:00:02
Retrieving key from https://download.docker.com/linux/centos/gpg
Importing GPG key 0x621E9F35:
Userid : "Docker Release (CE rpm) <docker@docker.com>"
Fingerprint: 060a 61c5 1b55 8a7f 742b 77aa c52f eb6b 621e 9f35
From : https://download.docker.com/linux/centos/gpg
Is this ok [y/N]:
Type y to allow the operation to complete.
Log info
Downloading packages:
(1/9): container-selinux-2.119.2-1.911c772.el7_8.noarch.rpm | 40 kB 00:00:00
warning: /var/cache/yum/x86_64/7/docker-ce-stable/packages/containerd.io-1.4.3-3.1.el7.x86_64.rpm: Header V4 RSA/SHA512 Signature, key ID 621e9f35: NOKEY ] 20 MB/s | 18 MB 00:00:04 ETA
Public key for containerd.io-1.4.3-3.1.el7.x86_64.rpm is not installed
(2/9): containerd.io-1.4.3-3.1.el7.x86_64.rpm | 33 MB 00:00:01
(3/9): docker-ce-cli-20.10.3-3.el7.x86_64.rpm | 33 MB 00:00:00
(4/9): docker-ce-20.10.3-3.el7.x86_64.rpm | 27 MB 00:00:02
(5/9): fuse-overlayfs-0.7.2-6.el7_8.x86_64.rpm | 54 kB 00:00:00
(6/9): libseccomp-2.3.1-4.el7.x86_64.rpm | 56 kB 00:00:00
(7/9): docker-ce-rootless-extras-20.10.3-3.el7.x86_64.rpm | 9.0 MB 00:00:00
(8/9): slirp4netns-0.4.3-4.el7_8.x86_64.rpm | 81 kB 00:00:00
(9/9): fuse3-libs-3.6.1-4.el7.x86_64.rpm | 82 kB 00:00:00
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Total 39 MB/s | 102 MB 00:00:02
Retrieving key from https://download.docker.com/linux/centos/gpg
Importing GPG key 0x621E9F35:
Userid : "Docker Release (CE rpm) <docker@docker.com>"
Fingerprint: 060a 61c5 1b55 8a7f 742b 77aa c52f eb6b 621e 9f35
From : https://download.docker.com/linux/centos/gpg
Is this ok [y/N]: y
Running transaction check
Running transaction test
Transaction test succeeded
Running transaction
Installing : libseccomp-2.3.1-4.el7.x86_64 1/9
Installing : 2:container-selinux-2.119.2-1.911c772.el7_8.noarch 2/9
Installing : containerd.io-1.4.3-3.1.el7.x86_64 3/9
Installing : slirp4netns-0.4.3-4.el7_8.x86_64 4/9
Installing : 1:docker-ce-cli-20.10.3-3.el7.x86_64 5/9
Installing : fuse3-libs-3.6.1-4.el7.x86_64 6/9
Installing : fuse-overlayfs-0.7.2-6.el7_8.x86_64 7/9
Installing : 3:docker-ce-20.10.3-3.el7.x86_64 8/9
Installing : docker-ce-rootless-extras-20.10.3-3.el7.x86_64 9/9
Verifying : fuse3-libs-3.6.1-4.el7.x86_64 1/9
Verifying : 3:docker-ce-20.10.3-3.el7.x86_64 2/9
Verifying : fuse-overlayfs-0.7.2-6.el7_8.x86_64 3/9
Verifying : slirp4netns-0.4.3-4.el7_8.x86_64 4/9
Verifying : 2:container-selinux-2.119.2-1.911c772.el7_8.noarch 5/9
Verifying : libseccomp-2.3.1-4.el7.x86_64 6/9
Verifying : containerd.io-1.4.3-3.1.el7.x86_64 7/9
Verifying : docker-ce-rootless-extras-20.10.3-3.el7.x86_64 8/9
Verifying : 1:docker-ce-cli-20.10.3-3.el7.x86_64 9/9
Installed:
containerd.io.x86_64 0:1.4.3-3.1.el7 docker-ce.x86_64 3:20.10.3-3.el7 docker-ce-cli.x86_64 1:20.10.3-3.el7
Dependency Installed:
container-selinux.noarch 2:2.119.2-1.911c772.el7_8 docker-ce-rootless-extras.x86_64 0:20.10.3-3.el7 fuse-overlayfs.x86_64 0:0.7.2-6.el7_8 fuse3-libs.x86_64 0:3.6.1-4.el7 libseccomp.x86_64 0:2.3.1-4.el7
slirp4netns.x86_64 0:0.4.3-4.el7_8
Complete!
Step 3: Start Docker
Although you have installed Docker on CentOS, the service is still not running.
To start the service, enable it to run at startup. Run the following commands in the order listed below.
Start Docker:
$ sudo systemctl start dockerEnable Docker:
$ sudo systemctl enable dockerLog info
Created symlink from /etc/systemd/system/multi-user.target.wants/docker.service to /usr/lib/systemd/system/docker.service.
Verify that Docker Engine is installed correctly by running the hello-world image.
$ sudo docker run hello-world
Log info
Unable to find image 'hello-world:latest' locally
latest: Pulling from library/hello-world
0e03bdcc26d7: Pull complete
Digest: sha256:95ddb6c31407e84e91a986b004aee40975cb0bda14b5949f6faac5d2deadb4b9
Status: Downloaded newer image for hello-world:latest
Hello from Docker!
This message shows that your installation appears to be working correctly.
To generate this message, Docker took the following steps:
1. The Docker client contacted the Docker daemon.
2. The Docker daemon pulled the "hello-world" image from the Docker Hub.
(amd64)
3. The Docker daemon created a new container from that image which runs the
executable that produces the output you are currently reading.
4. The Docker daemon streamed that output to the Docker client, which sent it
to your terminal.
To try something more ambitious, you can run an Ubuntu container with:
$ docker run -it ubuntu bash
Share images, automate workflows, and more with a free Docker ID:
https://hub.docker.com/
For more examples and ideas, visit:
https://docs.docker.com/get-started/
$ sudo docker pull cschin/peregrine:latestLog info
latest: Pulling from cschin/peregrine
68ced04f60ab: Pull complete
9c388eb6d33c: Pull complete
96cf53b3a9dd: Pull complete
a6375835cc11: Pull complete
a6123f81f236: Pull complete
c192c677363e: Pull complete
72feafb40a2a: Pull complete
f87048dde396: Pull complete
b705c81cb779: Pull complete
479a525deff5: Pull complete
a50bb7798bdb: Pull complete
7a9fe8f5c810: Pull complete
b76d2d9f7e01: Pull complete
1fd67a3594ad: Pull complete
a58845b42830: Pull complete
2cbfcd7ac990: Pull complete
d7894c8c1c54: Pull complete
defb7009fa0e: Pull complete
21feb2a2fb0a: Pull complete
Digest: sha256:4f8fbc85c65d57ab0aad0fa430484aebba6271483edba2edf7f77e468aeaeed5
Status: Downloaded newer image for cschin/peregrine:latest
docker.io/cschin/peregrine:latest
prepare the input file
find /home/kplee/datafile/001.i.bat.pacbio.hifi.reads/ -name "S_unknown.ccs.merged.fasta" | sort > seqdata.lst
docker run -it -v //home/kplee/analysis/01.peregrine_assembly_sweetpotato_pacbio_hifi_data://home/kplee/analysis/01.peregrine_assembly_sweetpotato_pacbio_hifi_data \ cschin/peregrine:latest asm
/home/kplee/analysis/01.peregrine_assembly_sweetpotato_pacbio_hifi_data/seqdata.lst \
--with-consensus --shimmer-r 3 --best_n_ovlp 8 \
/usr/bin/time -o out.txt -v sudo docker run -it -v /home/kplee/analysis/01.peregrine_assembly_sweetpotato_pacbio_hifi_data:/wd
--user
/home/kplee/analysis/01.peregrine_assembly_sweetpotato_pacbio_hifi_data/seqdata.lst 32 32 32 32 32 32 32 32 32 --with-consensus --with-alt --shimmer-r 3
--best n ovlp 8 --output /home/kplee/analysis/01.peregrine_assembly_sweetpotato_pacbio_hifi_data/
Install ggc compiler version 9.3 using conda
$ conda install -c conda-forge gcc_linux-64Log info
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /home/kplee/program/miniconda3
added / updated specs:
- gcc_linux-64
The following packages will be downloaded:
package | build
---------------------------|-----------------
binutils_impl_linux-64-2.35.1| hd53bc6c_1 9.5 MB
binutils_linux-64-2.35 | hc3fd857_29 22 KB conda-forge
ca-certificates-2020.12.5 | ha878542_0 137 KB conda-forge
certifi-2020.12.5 | py38h578d9bd_1 143 KB conda-forge
conda-4.9.2 | py38h578d9bd_0 3.0 MB conda-forge
gcc_impl_linux-64-9.3.0 | h70c0ae5_18 43.1 MB conda-forge
gcc_linux-64-9.3.0 | h7247604_29 23 KB conda-forge
kernel-headers_linux-64-2.6.32| h77966d4_13 707 KB conda-forge
libgcc-devel_linux-64-9.3.0| h7864c58_18 4.0 MB conda-forge
openssl-1.1.1i | h7f98852_0 2.1 MB conda-forge
python_abi-3.8 | 1_cp38 4 KB conda-forge
sysroot_linux-64-2.12 | h77966d4_13 30.2 MB conda-forge
------------------------------------------------------------
Total: 93.0 MB
The following NEW packages will be INSTALLED:
binutils_impl_lin~ pkgs/main/linux-64::binutils_impl_linux-64-2.35.1-hd53bc6c_1
binutils_linux-64 conda-forge/linux-64::binutils_linux-64-2.35-hc3fd857_29
gcc_impl_linux-64 conda-forge/linux-64::gcc_impl_linux-64-9.3.0-h70c0ae5_18
gcc_linux-64 conda-forge/linux-64::gcc_linux-64-9.3.0-h7247604_29
kernel-headers_li~ conda-forge/noarch::kernel-headers_linux-64-2.6.32-h77966d4_13
libgcc-devel_linu~ conda-forge/linux-64::libgcc-devel_linux-64-9.3.0-h7864c58_18
python_abi conda-forge/linux-64::python_abi-3.8-1_cp38
sysroot_linux-64 conda-forge/noarch::sysroot_linux-64-2.12-h77966d4_13
The following packages will be UPDATED:
certifi pkgs/main::certifi-2020.12.5-py38h06a~ --> conda-forge::certifi-2020.12.5-py38h578d9bd_1
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates pkgs/main::ca-certificates-2021.1.19-~ --> conda-forge::ca-certificates-2020.12.5-ha878542_0
conda pkgs/main::conda-4.9.2-py38h06a4308_0 --> conda-forge::conda-4.9.2-py38h578d9bd_0
openssl pkgs/main::openssl-1.1.1i-h27cfd23_0 --> conda-forge::openssl-1.1.1i-h7f98852_0
Proceed ([y]/n)?
Press y
Log info
Downloading and Extracting Packages
ca-certificates-2020 | 137 KB | #################################################################################################################################################################### | 100%
binutils_linux-64-2. | 22 KB | #################################################################################################################################################################### | 100%
python_abi-3.8 | 4 KB | #################################################################################################################################################################### | 100%
certifi-2020.12.5 | 143 KB | #################################################################################################################################################################### | 100%
binutils_impl_linux- | 9.5 MB | #################################################################################################################################################################### | 100%
gcc_impl_linux-64-9. | 43.1 MB | #################################################################################################################################################################### | 100%
openssl-1.1.1i | 2.1 MB | #################################################################################################################################################################### | 100%
libgcc-devel_linux-6 | 4.0 MB | #################################################################################################################################################################### | 100%
conda-4.9.2 | 3.0 MB | #################################################################################################################################################################### | 100%
kernel-headers_linux | 707 KB | #################################################################################################################################################################### | 100%
gcc_linux-64-9.3.0 | 23 KB | #################################################################################################################################################################### | 100%
sysroot_linux-64-2.1 | 30.2 MB | #################################################################################################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
On new Centos
First install gcc
sudo yum group install "Development Tools"
Check
gcc --version
Got this
[yedomon@localhost]$ gcc --version
gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Now trying to install PAML tool
$ wget http://abacus.gene.ucl.ac.uk/software/paml4.9j.tgz
$ tar xf paml4.9j.tgz
$ cd paml4.9j
$ rm bin/*.exe
$ cd src
$ make -f Makefile
$ ls -lF
$ mv baseml basemlg codeml pamp evolver yn00 mcmctree chi2 ../bin
sudo yum install python3-pip.noarch
sudo pip3 install gbseqextractor
gbseqextractor --help
info
usage: gbseqextractor [-h] -f <STR> -prefix <STR> [-seqPrefix <STR>]
[-types {CDS,rRNA,tRNA,wholeseq,gene} [{CDS,rRNA,tRNA,wholeseq,gene} ...]]
[-cds_translation] [-gi] [-p] [-t] [-s] [-l] [-rv] [-F]
Extract any CDS or rNRA or tRNA DNA sequences of genes from Genbank file.
Seqid will be the value of '/gene=' or '/product=', if they both were not
present, the gene will not be output!
version 20201128:
Now we can handle compounlocation (feature location with "join")!
We can also output the translation for each CDS (retrived from '/translation=')
Please cite:
Guanliang Meng, Yiyuan Li, Chentao Yang, Shanlin Liu,
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation
and visualization, Nucleic Acids Research, https://doi.org/10.1093/nar/gkz173
optional arguments:
-h, --help show this help message and exit
-f <STR> Genbank file
-prefix <STR> prefix of output file. required.
-seqPrefix <STR> prefix of each seq id. default: None
-types {CDS,rRNA,tRNA,wholeseq,gene} [{CDS,rRNA,tRNA,wholeseq,gene} ...]
what kind of genes you want to extract? wholeseq for
whole fasta seq. WARNING: Each sequence in the result
files corresponds to ONE feature in the GenBank file,
I will NOT combine multiple CDS of the same gene into
ONE! [CDS]
-cds_translation Also output translated CDS (required -types CDS). The
translations are retrived directly from the
'/translation=' key word. [False]
-gi use gi number as sequence ID instead of accession
number when " gi number is present. (default:
accession number)
-p output the position information on the ID line.
Warning: the position on ID line is 0 left-most!
[False]
-t output the taxonomy lineage on ID line [False]
-s output the species name on the ID line [False]
-l output the seq length on the ID line [False]
-rv reverse and complement the sequences if the gene is on
minus strand. Always True!
-F only output full length genes,i.e., exclude the genes
with '>' or '<' in their location [False]
Server settings code
