Fixed bugs:

1. When using mitoz visualize --depth_file, there is no depth track in the resulting image (https://github.com/linzhi2013/MitoZ/issues/183)
2. https://github.com/linzhi2013/MitoZ/issues/185
3. shell problem and misuse of Mac OS cmsearch for Linux platform: https://github.com/linzhi2013/MitoZ/issues/187
4. fixed some bugs, fastq data sampling, file path problems.

New features

1. added tiara support to quickly identify mt contigs.

Fixed bugs:

1. Fixed the dependency problem of 'mitoz-tools': html5lib
2. Fixed the sub-sampling bug (it was 10 times than expected) (--data_size_for_mt_assembly <float1>,<float2>)
3. Fixed the bug on https://github.com/linzhi2013/MitoZ/issues/154 and https://github.com/linzhi2013/MitoZ/issues/24#issuecomment-572884734.
4. https://github.com/linzhi2013/MitoZ/issues/177
5. https://github.com/linzhi2013/MitoZ/issues/176 (new --tmp_dir option; beware that the directory must already exist!)

New features:

1. Should now also run on Mac OS (M1 and Intel chips); but the assembler SPAdes won't work on Mac OS due to https://github.com/ablab/spades/issues/873 and lack of proper version for Mac OS. However, you can download it from https://cab.spbu.ru/files/release3.15.4/SPAdes-3.15.4-Darwin.tar.gz and put it into the mitozEnv environment (or PATH variable). The assembler mitoassembler also does not work on Mac OS yet. NB: it could be very tricky to install the Circos problem on Mac OS; you might want to install Circos by following http://circos.ca/tutorials/lessons/configuration/perl_and_modules/.

2. Added a few tools to the 'mitoz-tools' command, see https://github.com/linzhi2013/MitoZ/wiki/Overview%3A-The-%27mitoz-tools%27-command.

3. Users can now use their own sqn template file (--template_sbt): https://github.com/linzhi2013/MitoZ/issues/153

mac OSX

$ circos --modules
missing            Math::Bezier
ok   1.999818 Math::BigFloat
missing            Math::Round
missing            Math::VecStat
ok    1.03_01 Memoize
ok       1.94 POSIX
missing            Params::Validate
ok       1.69 Pod::Usage
ok       2.05 Readonly
ok 2017060201 Regexp::Common
ok       2.87 SVG
missing            Set::IntSpan
missing            Statistics::Basic

$ cpan install Encode::Locale
$ cpanm Math::Bezier Math::Round Math::VecStat Set::IntSpan Statistics::Basic Params::Validate Module::Implementation IO::String

Fixed bugs:

1. Fixed the dependency problem of 'mitoz-tools': html5lib
2. Fixed the sub-sampling bug (it was 10 times than expected)
3. Fixed the bug on https://github.com/linzhi2013/MitoZ/issues/154 and https://github.com/linzhi2013/MitoZ/issues/24#issuecomment-572884734.

New features:

1. Should now also run on Mac OS (M1 and Intel chips); but the assembler SPAdes won't work on Mac OS due to https://github.com/ablab/spades/issues/873 and lack of proper version for Mac OS. However, you can download it from https://cab.spbu.ru/files/release3.15.4/SPAdes-3.15.4-Darwin.tar.gz and put it into the mitozEnv environment (or PATH variable). The assembler mitoassembler also does not work on Mac OS yet. NB: it could be very tricky to install the Circos problem on Mac OS; you might want to install Circos by following http://circos.ca/tutorials/lessons/configuration/perl_and_modules/.

2. Added a few tools to the 'mitoz-tools' command, see https://github.com/linzhi2013/MitoZ/wiki/Overview%3A-The-%27mitoz-tools%27-command.

3. Users can now use their own sqn template file ('--template_sbt'): https://github.com/linzhi2013/MitoZ/issues/153

# mac OSX
$ circos --modules
missing            Math::Bezier
ok   1.999818 Math::BigFloat
missing            Math::Round
missing            Math::VecStat
ok    1.03_01 Memoize
ok       1.94 POSIX
missing            Params::Validate
ok       1.69 Pod::Usage
ok       2.05 Readonly
ok 2017060201 Regexp::Common
ok       2.87 SVG
missing            Set::IntSpan
missing            Statistics::Basic

$ cpan install Encode::Locale
$ cpanm Math::Bezier Math::Round Math::VecStat Set::IntSpan Statistics::Basic Params::Validate Module::Implementation IO::String

Change log:

1. added a few tools to the 'mitoz-tools' command (https://github.com/linzhi2013/MitoZ/wiki/Overview%3A-The-%27mitoz-tools%27-command)
2. Fixed the dependency problem of 'mitoz-tools': html5lib
3. fixed the sub-sampling bug (it was 10 times than expected)
4. Should now also run on Mac OS (Not sure if the binaries complied on M1 chip work on Intel chips)
5. Users can now use their own sqn template file ('--template_sbt'): https://github.com/linzhi2013/MitoZ/issues/153

Fixed three bugs:

• https://github.com/linzhi2013/MitoZ/issues/30
• https://github.com/linzhi2013/MitoZ/issues/149
• https://github.com/linzhi2013/MitoZ/issues/150

The update is recommended!

Also, the mitozEnv.yml file has been updated (https://github.com/linzhi2013/MitoZ/issues/152)

1. optimize the abundance calculation workflow in the 'findmitoscaf' function.
2. add spades and megahit for mitogenome assembly
3. If mitoassemble/spades/megahit have finished previous runs, we will just skip them to save time.
4. fix a potential bug: a genus could belong to non-Metazoa

For installation and usage, please refer to https://github.com/linzhi2013/MitoZ/wiki/Installation. and https://github.com/linzhi2013/MitoZ/wiki/New-Features.

Installation

$ conda install mamba -n base -c conda-forge  # "mamba" is much much faster than the "conda" command!
$ mamba create -n mitozEnv -c bioconda mitoz=3.2
$ source activate mitozEnv   # or use "mamba" or "conda" instead of "source" the command here.

$ circos --modules # check if all Perl modules required by circos are installed. Some modules could still be missing (don't know why conda did not fix them automatically). Similar problems can be seen at https://github.com/bioconda/bioconda-recipes/issues/9830

# Now we are ready to go:
$ mitoz # all subcommands are within this command now!

$ mitoz-tools # some useful tools for mitochondrial genome analysis

If the above installation method does not work for you, you can try

$ conda install mamba -n base -c conda-forge  # "mamba" is much much faster than the "conda" command!
$ mamba env create -n mitozEnv  -f mitozEnv.yaml
$ conda activate mitozEnv
$ pip install ./mitoz-3.2.tar.gz
# or 
$ tar -zxvf mitoz-3.2.tar.gz
$ cd mitoz-3.2
$ python3 setup.py install

Changelog

1. Fixed a bug in 'filter_taxonomy_by_CDS_annotation.py', which did not parse the genetic code to the command correctly (always parsed 5 for all input genetic codes).

2. '--requiring_taxa' becomes a necessary option, in case the users set '--clade Chordata' but forget to set this option (because its default was 'Arthropoda').

3. Now the 'overlapping' information is copied to the resulting folder automatically.

4. The circularity information now is parsed to the annotation module correctly.

5. The length of sequence ids now is checked before running annotation.

6. Seems that the problem which in some cases circos not drawing SVG/PNG files is fixed.

7. For the dependency package 'ete3', now we change it to v3.1.2, this should fix the NCBITaxa() problem when creating or updating the database.

8. The circos' problem of missing Perl modules should be fixed now if you install MitoZ via bioconda channel, please raise an issue if the problem is still there.

Don't forget to have a look at https://github.com/linzhi2013/MitoZ/wiki.

Add the seqkit program to subsample clean data for mitochondrial assembly, so the users don't have to do it by themselves.

You can install MitoZ via

$ conda install mamba -n base -c conda-forge  # "mamba" is much much faster than the "conda" command!
$ mamba create -n mitozEnv -c bioconda mitoz=3.1
$ source activate mitozEnv   # or use "mamba" or "conda" instead of "source" the command here.

$ circos --modules # check if all Perl modules required by circos are installed. Some modules could still be missing (don't know why conda did not fix them automatically). Similar problems can be seen at https://github.com/bioconda/bioconda-recipes/issues/9830

# For me, the Perl modules "GD" and "GD::Polyline" were missing (although conda said they have been installed already when I ran 'conda install perl-gd'), I fixed them by running following three commands:
$ mamba install -c conda-forge pkg-config
$ mamba install -c anaconda gcc_linux-64
$ cpanm install GD
# I will try to fix the circos' problem in bioconda's MitoZ recipe file, but for the moment, please use the above solution, or try the "mitozEnv.yaml" solution below.
# You can use the ”cpanm“ command to install other missing Perl modules if necessary. 

# Now we are ready to go:
$ mitoz # all subcommands are within this command now!

$ mitoz-tools # some useful tools for mitochondrial genome analysis

If the above installation method does not work for you, you can try

$ conda install mamba -n base -c conda-forge  # "mamba" is much much faster than the "conda" command!
$ mamba env create -n mitozEnv  -f mitozEnv.yaml
$ conda activate mitozEnv
$ pip install ./mitoz-3.1.tar.gz
# or 
$ tar -zxvf mitoz-3.1.tar.gz
$ cd mitoz-3.1
$ python3 setup.py install

MitoZ 3.0 is coming.

Now MitoZ uses the Fastp program for raw data filtering, which is faster. Users are also allowed to specify multiple kmers directly for assembly via mitoz all or mitoz assemble commands (which could help some samples), you can also define your own profile directory path.

Now you can install MitoZ via

$ conda install mamba -n base -c conda-forge  # "mamba" is much much faster than the "conda" command!
$ mamba create -n mitozEnv -c bioconda mitoz=3.0
$ source activate mitozEnv   # or use "mamba" or "conda" instead of "source" the command here.

$ circos --modules # check if all Perl modules required by circos are installed. Some modules could still be missing (don't know why conda did not fix them automatically). Similar problems can be seen at https://github.com/bioconda/bioconda-recipes/issues/9830

# For me, the Perl modules "GD" and "GD::Polyline" were missing (although conda said they have been installed already when I ran 'conda install perl-gd'), I fixed them by running following three commands:
$ mamba install -c conda-forge pkg-config
$ mamba install -c anaconda gcc_linux-64
$ cpanm install GD
# I will try to fix the circos' problem in bioconda's MitoZ recipe file, but for the moment, please use the above solution, or try the "mitozEnv.yaml" solution below.
# You can use the ”cpanm“ command to install other missing Perl modules if necessary. 

# Now we are ready to go:
$ mitoz # all subcommands are within this command now!

$ mitoz-tools # some useful tools for mitochondrial genome analysis

I do not have enough time to update the documentation yet, but you can start to play with the mtioz and mitoz-tools commands now.

More features are coming.

If the above installation method does not work for you, you can try

$ conda install mamba -n base -c conda-forge  # "mamba" is much much faster than the "conda" command!
$ mamba env create -n mitozEnv  -f mitozEnv.yaml
$ conda activate mitozEnv
$ pip install ./mitoz-3.0.tar.gz
# or 
$ tar -zxvf mitoz-3.0.tar.gz
$ cd mitoz-3.0
$ python3 setup.py install

For the moment, MitoZ runs on Linux only. Mac OS platform is not fully supported yet, maybe later we can fix this.

If there are bugs, you can try the older version 2.3, and raise issues to report bugs, thanks!

Citations Specifically, when you use MitoZ for data analysis, you should cite both the MitoZ paper and the related software invoked by MitoZ.

• fastp # for the all or filter subcommand (MitoZ version >= 3.0)
• soapdenovo-trans # for the all or assemble subcommand
• hmmer # for the all or assemble or findmitoscaf subcommand
• blast # for the all or assemble or findmitoscaf or annotate subcommand
• genewise # for the all or assemble or findmitoscaf or annotate subcommand
• infernal # for the all or annotate subcommand
• MiTFi # for the all or annotate subcommand
• cricos # for the all or annotate or visualize subcommand
• bwa # for the all or annotate or visualize subcommand and you draw the sequencing coverage distribution track
• samtools # for the annotate or visualize subcommand and you draw the sequencing coverage distribution track

Please refer to the MitoZ paper for the reference details.

From now on, I will use Wiki (https://github.com/linzhi2013/MitoZ/wiki) to give more explanation on how to use MitoZ.

sources file for v2.3, v2.4-alpha.

To backup related files, and clean the master branch for future release.