Add rules for Diamond (blastp) and Prodigal

[zoey-rw]

Four new rules proposed, with no new software dependencies.

1. run_prodigal - predicts ORFs on contigs rather than assembled genomes (perhaps could be renamed to contig_prodigal to avoid confusion)
2. run_blastp - takes contig ORFs as input, uses the Diamond Blastp Snakemake wrapper: https://github.com/snakemake/snakemake-wrappers/tree/0.80.1/bio/diamond/blastp
3. binning - calls the outputs from concoct, metabat, and maxbin
4. binEvaluation - calls the outputs from binRefine and binReassembly

The parsing rules for binning and binEvaluation may be iffy - I tested on a login node, rather than as a cluster job.

[franciscozorrilla]

Thanks @zoey-rw, looks awesome! I will do some small tests and then merge into the main branch 💎

[paristzou]

After reading the article entitled "The National Ecological Observatory Network’s soil metagenomes: assembly and basic analysis [version 2; peer review: 2 approved with reservations]" (https://f1000research.com/articles/10-299/v2), I hope it can be added soon to benefit more. Thank you so much.

[franciscozorrilla]

Hi @paristzou, thanks for your interest in the development of metaGEM. Just FYI, these changes have now been merged into the master branch, so you should be able to see the new rules in the Snakefile.

[paristzou]

That's great. It makes life much easier.

[paristzou]

Is it possible to find a link to have the fastq.gz files for tutorial in https://github.com/franciscozorrilla/unseenbio_metaGEM , please ? Thank you.

[franciscozorrilla]

Hi @paristzou, unfortunately that metagenomic data is personal/private and I do not have consent to share it, as it was generated using the unseen bio metagenome sequencing service. Just to clarify, these particular samples were NOT used in the metaGEM publication/data analysis.

You can find more info about the 5 datasets we used in the metaGEM publication here.

Additionally, you may find useful the toy dataset that we generated by subsampling 3 paired end reads from the gut microbiome dataset.

[paristzou]

conda env list #

base * /newdisk2/anaconda3 snakemake /newdisk2/anaconda3/envs/snakemake /newdisk2/metaGEM/envs/metagem /newdisk2/metaGEM/envs/metawrap /newdisk2/metaGEM/envs/prokkaroary

source activate metagem Could not find conda environment: metagem You can list all discoverable environments with conda info --envs.

seems that metagem environment cannot be employed

[franciscozorrilla]

I believe that providing the full path to the env directory should do the trick, e.g.

source activate /newdisk2/metaGEM/envs/metagem

See also the conda documentation for a good reference on handling environments and such. Since this is unrelated to the PR topic, kindly open a new issue if you have further trouble with setup.