Commit 00c2cc68 authored by MARTIN Pierre's avatar MARTIN Pierre
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Update usage.md

parent 436673a1
......@@ -268,9 +268,11 @@ No parameters.
* `--diamond_bank "PATH/bank.dmnd"`: path to diamond bank used to align protein sequence of genes. This bank must be previously built with [diamond makedb](https://github.com/bbuchfink/diamond/wiki). Default `""`.
**WARNING 10:** You need to use a NCBI reference to have functional links in the output file _Quantifications_and_functional_annotations.tsv_ of `06_func_annot` step
#### **`06_func_annot` step:**
**WARNING 10:** `06_func_annot` step depends on `01_clean_qc`, `02_assembly`, `03_filtering` (if you use it), `04_structural_annot` and `05_alignment` steps. You need to use mandatory files of these six steps to run `06_func_annot`. See [II. Input files](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/usage.md#ii-input-files) and WARNINGS from 1 to 9.
**WARNING 11:** `06_func_annot` step depends on `01_clean_qc`, `02_assembly`, `03_filtering` (if you use it), `04_structural_annot` and `05_alignment` steps. You need to use mandatory files of these six steps to run `06_func_annot`. See [II. Input files](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/usage.md#ii-input-files) and WARNINGS from 1 to 9.
* `--percentage_identity [number]`: corresponds to cd-hit-est -c option to indicate sequence percentage identity for clustering genes. Default: `0.95` corresponding to 95% of sequence identity. Use: `number` must be between 0 and 1, and use `.` when you want to use a float.
......@@ -278,11 +280,11 @@ No parameters.
* `--eggnog_mapper_db_dir "PATH/database_directory/"`: indicates path to eggNOG-mapper database if you have already dowloaded it. If you run the `06_func_annot` step in different metagenomics projects, downloading the eggNOG-mapper database only once before running metagWGS avoids you to multiply the storage of this database and thus keep free disk space. See **WARNING 6**.
**WARNING 11**: you need to use `--eggnogmapper_db` or `--eggnog_mapper_db_dir`. If it is not the case, an error message will occur.
**WARNING 12:** you need to use `--eggnogmapper_db` or `--eggnog_mapper_db_dir`. If it is not the case, an error message will occur.
#### **`07_taxo_affi` step:**
**WARNING 12:** `07_taxo_affi` step depends on `01_clean_qc`, `02_assembly`, `03_filtering` (if you use it), `04_structural_annot` and `05_alignment` steps. You need to use mandatory files of these six steps to run `07_taxo_affi`. See [II. Input files](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/usage.md#ii-input-files) and WARNINGS from 1 to 9.
**WARNING 13:** `07_taxo_affi` step depends on `01_clean_qc`, `02_assembly`, `03_filtering` (if you use it), `04_structural_annot` and `05_alignment` steps. You need to use mandatory files of these six steps to run `07_taxo_affi`. See [II. Input files](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/usage.md#ii-input-files) and WARNINGS from 1 to 9.
* `--accession2taxid "FTP_PATH_TO_prot.accession2taxid.gz"`: indicates the FTP adress of the NCBI file `prot.accession2taxid.gz`. Default: `"ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz"`.
......@@ -292,13 +294,13 @@ No parameters.
#### **`08_binning` step:**
**WARNING 13:** `08_binning` step depends on `01_clean_qc`, `02_assembly`, `03_filtering` (if you use it), `04_structural_annot` and `05_alignment` steps. You need to use mandatory files of these six steps to run `08_binning`. See [II. Input files](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/usage.md#ii-input-files) and WARNINGS from 1 to 9.
**WARNING 14:** `08_binning` step depends on `01_clean_qc`, `02_assembly`, `03_filtering` (if you use it), `04_structural_annot` and `05_alignment` steps. You need to use mandatory files of these six steps to run `08_binning`. See [II. Input files](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/usage.md#ii-input-files) and WARNINGS from 1 to 9.
* `--min_contig_size [cutoff_length]`: contig length cutoff to filter contigs before binning. Must be greater than `1500`. Default: `1500`.
* `--busco_reference "PATH/file_db"`: path to BUSCO database. Default: `"https://busco-archive.ezlab.org/v3/datasets/bacteria_odb9.tar.gz"`. **WARNING 14:** We use BUSCO v3 from the `metagWGS.sif` Singularity container. Be careful not to use the BUSCO reference of other BUSCO versions.
* `--busco_reference "PATH/file_db"`: path to BUSCO database. Default: `"https://busco-archive.ezlab.org/v3/datasets/bacteria_odb9.tar.gz"`. **WARNING 15:** We use BUSCO v3 from the `metagWGS.sif` Singularity container. Be careful not to use the BUSCO reference of other BUSCO versions.
* `--cat_db "PATH/CAT_prepare_20190108.tar.gz"`: path to CAT/BAT database. Default: `false`. **WARNING 15:** you need to download this database before running metagWGS `08_binning` step. Download it with: `wget tbb.bio.uu.nl/bastiaan/CAT_prepare/CAT_prepare_20210107.tar.gz`.
* `--cat_db "PATH/CAT_prepare_20190108.tar.gz"`: path to CAT/BAT database. Default: `false`. **WARNING 16:** you need to download this database before running metagWGS `08_binning` step. Download it with: `wget tbb.bio.uu.nl/bastiaan/CAT_prepare/CAT_prepare_20210107.tar.gz`.
#### Others parameters
......@@ -316,4 +318,4 @@ See the description of output files in [this part](https://forgemia.inra.fr/geno
> If you have an account into [genologin cluster](http://bioinfo.genotoul.fr/) and you would like to familiarise yourself with metagWGS, see the tutorial available into the [use case documentation page](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/use_case.md). It allows to analyze big test dataset with metagWGS.
**WARNING:** the test dataset into `metagwgs/test` directory used in [I. Basic Usage](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/usage.md#i-basic-usage) is a small test dataset which does not allow to test all steps (`08_binning` doesn't work with this dataset).
**WARNING 17:** the test dataset into `metagwgs/test` directory used in [I. Basic Usage](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/usage.md#i-basic-usage) is a small test dataset which does not allow to test all steps (`08_binning` doesn't work with this dataset).
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