segatalab / metaclock

A python package for assisting to reconstruct time-tree at the strain level using contemporary and ancient metagenomes.

MetaClock

MetaClock is an integrated framework for reconstructing time-resolved evolutionary history for microbial genomes using large-scale (meta)genomics data from ancient and contemporary samples.

Main features

• Automated reconstruction of whole-genome alignment from large-scale metagenomics data using multiple reference genomes
• Automated authentication for ancient DNA origin, damaged sites removal, SNV analysis etc.
• Rich utilities for manual curation to enhance the quality of phylogenetic and molecular dating analysis

Installation

Bioconda

You can install MetaClock in an isolated environment using conda as follows:

conda create -n mc -c bioconda metaclock

conda activate mc

Private conda channel

Temporarily, you can install MetaClock through a private conda channel. But this option will be replaced once bioconda channel is ready.

conda create -n metaclock -c khuang16 -c compbiocore -c kantorlab -c bioconda -c conda-forge metaclock

Due to the dependency bowtie2 is encountering tbb-related issue, after metaclock installation is completed please manually install tbb library as described below:

conda activate metaclock

conda install tbb=2020.2

Repository

You can clone the MetaClock repository from GitHub:

git clone https://github.com/SegataLab/metaclock.git

Dependencies:

Tutorials

• MetaClock User manual
• MetaClock Tutorials

Support

Please post your issues in our metaclock issues section

Citation

If you think our tool is helpful for your research please cite https://github.com/SegataLab/metaclock. Note: citation source will be updated soon when manuscript is published. Thank you for your patience!

metaclock's Issues

Error in gff3 parsing when tailoring using landscape option

Hello,
I am trying to use the metaclock_tailor landscape on my sampes, having already the gff3 file using the same command line

metaclock_tailor landscape results/results.fna -o landscape_opt_folder -s -nproc 10 -l 50 -mi 0.1 -fast_TempEst time_landscape.tsv -raxml -f CDS -gff3 landscape_opt_folder/GCA_001189515.2_ASM118951v2_genomic.fna.prokka/GCA_001189515.2_ASM118951v2_genomic.fna.gff

But I get the following error and I don't know how to solve it

2024-02-12 16:03:20,925 root INFO /mnt/nfs/home/minluke/archivio/Guattari/metaclock/landscape_ opt_folder exists: pass! 2024-02-12 16:03:20,926 root INFO The given annotation profile: landscape_opt_folder/GCA_001189515.2_ASM118 951v2_genomic.fna.prokka/GCA_001189515.2_ASM118951v2_genomic.fna.gff 2024-02-12 16:03:20,926 root INFO Start parsing gff3 file..... Traceback (most recent call last): File "/mnt/nfs/home/minluke/miniconda3/envs/metaclock/bin/metaclock_tailor", line 10, in <module> sys.exit(main()) File "/mnt/nfs/home/minluke/miniconda3/envs/metaclock/lib/python3.10/site-packages/metaclock/metaclock_t ailor.py", line 708, in main dict_lst_BigMatrix = Assessment_tab(wga_aln, args.gff3_annotation, args.number_of_processors) File "/mnt/nfs/home/minluke/miniconda3/envs/metaclock/lib/python3.10/site-packages/metaclock/metaclock_t ailor.py", line 511, in Assessment_tab gContent_db = parse_gff(wga_aln, gff3) File "/mnt/nfs/home/minluke/miniconda3/envs/metaclock/lib/python3.10/site-packages/metaclock/metaclock_t ailor.py", line 280, in parse_gff cds_product = I.attributes['product'] KeyError: 'product'

Can you please help me solve it?
thank you