Commit 3c0a9fb1 authored by Magali Monnoye's avatar Magali Monnoye
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fin analyses frogs femelle vs males

parent 23a5b62e
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......@@ -308,17 +308,20 @@ Je vais rectifier toutes les multis affiliations sur "affiliationExplorer"
* Lien pour accéder au module: [affiliationExplorer](https://shiny.migale.inrae.fr/app/affiliationexplorer)
Je refais un <strong class="tool">affiliations_stats</strong> sur le biom nettoyé des multis affiliations
```{bash}
#Affiliation stat pour comparer avant et après correction avec affiliationExplorer
qsub -cwd -V -N affiliations_stats_cleaned -o LOGS -e LOGS -b y "conda activate frogs-3.2.2 && affiliations_stat.py --input-biom cleaned_biom-2021-06-23.biom --output-file FROGSfm/affiliations_stats_cleaned.html --log-file FROGSfm/affiliations_stats_cleaned.log --multiple-tag blast_affiliations --tax-consensus-tag blast_taxonomy --identity-tag perc_identity --coverage-tag perc_query_coverage && conda deactivate"
qsub -cwd -V -N affiliations_stats_cleaned -o LOGS -e LOGS -b y "conda activate frogs-3.2.2 && affiliations_stat.py --input-biom cleaned_biom-2022-01-18.biom --output-file FROGSfm/affiliations_stats_cleaned.html --log-file FROGSfm/affiliations_stats_cleaned.log --multiple-tag blast_affiliations --tax-consensus-tag blast_taxonomy --identity-tag perc_identity --coverage-tag perc_query_coverage && conda deactivate"
Job 3635034
```
Message du termminal: "Your job 4200552 ("affiliations_stats_cleaned") has been submitted"
Lien vers le [rapport affiliations_stats_cleaned](FROGSfm/affiliations_stats_cleaned.html)
### Tree
......@@ -331,14 +334,40 @@ Je crée l'arbre phylogénique avec <strong class="tool">tree</strong>
conda activate frogs-3.2.2 && tree.py --help
#Creation arbre phylogenique
qsub -cwd -V -N tree -o LOGS -e LOGS -b y "conda activate frogs-3.2.2 && tree.py --input-sequences FROGSfm/filters.fasta --biom-file cleaned_biom-2021-06-23.biom --out-tree FROGSfm/tree.nhx --html FROGSfm/tree.html --log-file FROGSfm/tree.log && conda deactivate"
qsub -cwd -V -N tree -o LOGS -e LOGS -b y "conda activate frogs-3.2.2 && tree.py --input-sequences FROGSfm/filters.fasta --biom-file cleaned_biom-2022-01-18.biom --out-tree FROGSfm/tree.nhx --html FROGSfm/tree.html --log-file FROGSfm/tree.log && conda deactivate"
Job 3635036
```
Message du termminal: "Your job 4200553 ("tree") has been submitted"
Lien vers l'arbre [Tree](FROGSfm/tree.nwk)
```{bash}
#Commit du fichier data.tar.gz qui est un fichier lourd
git add data.tar.gz
git add FROGS*.biom
git add *.html
git add *affiliation.tsv
#Enusite faire les commits
git commit -m "fichiers tar"
#Puis faire les push
git push
#Si gitlab fatal: pack exceeds maximum allowed size
#Pour supprimer dernier commit:
git reset HEAD~
#Pour supprimer les fichiers venndiagram
rm -f VennDiagram*.log
#Pour supprimer de force un dossier et tout ce qu'il contient
rm -rf ...
```
## Metagenomic phyloseq analysis
### Import données
......
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