{"id":397,"date":"2020-11-02T20:30:39","date_gmt":"2020-11-02T19:30:39","guid":{"rendered":"https:\/\/itrop.ird.fr\/wordpress\/?page_id=397"},"modified":"2022-04-06T14:50:28","modified_gmt":"2022-04-06T12:50:28","slug":"frogs","status":"publish","type":"page","link":"https:\/\/bioinfo.ird.fr\/index.php\/tutorials-fr\/frogs\/","title":{"rendered":"Tutorials &#8211; Frogs"},"content":{"rendered":"<table class=\"table-contact\">\n<tr>\n<td><img decoding=\"async\" width=\"100%\" src=\"http:\/\/frogs.toulouse.inra.fr\/img\/frogs.png\" alt=\"\" \/>\n<\/td>\n<td>\n<h1> FROGs en Ligne de Commande<\/h1>\n<p>\nThis page describes how to launch FROGs in command line from IRD cluster. From fastq files to OTU and Phyloseq analysis.\n<\/td>\n<\/tr>\n<\/table>\n<p>We need, in this tutorial:<\/p>\n<ul>\n<li>a compressed directory with fastq files<\/li>\n<li>a database used for the taxonomic assignation<\/li>\n<\/ul>\n<h3>Author(s)<\/h3>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Authors<\/th>\n<th style=\"text-align: left;\">Julie ORJUELA<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\">Research Unit<\/td>\n<td style=\"text-align: left;\">UMR IPME-DIADE-BOREA<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Institut<\/td>\n<td style=\"text-align: left;\">IRD<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h3>Keywords<\/h3>\n<p>flash, swarm, blastn, silva, vsearch, metabarcoding, 16S, 18S, ITS<\/p>\n<h3>Files format<\/h3>\n<p>fastq, OTU tables<\/p>\n<h3>Date<\/h3>\n<p>22\/03\/2019<\/p>\n<h2>Lancer FROGs en Ligne de Commande<\/h2>\n<p>On cr\u00e9e un dossier. Profitez pour le faire dans le \/scratch d'un noeud si vous \u00eates au cluster IRD. <\/p>\n<p><code>mkdir \/scratch\/TEST-FROGS\/<\/code><\/p>\n<h3>1. Pr\u00e9paration de fastq<\/h3>\n<p>Tous les fichiers fastq.gz (R1 et R2) seront mis dans un dossier qu'il faudra apres compresser en .tar.gz<br \/>\nPour compresser le fichier il faut:<\/p>\n<ul>\n<li>\n<p>se deplacer dans le dossier des fastq.gz<br \/>\n<code>cd dataset_path\/<\/code><\/p>\n<\/li>\n<li>\n<p>Compresser<br \/>\n<code>tar zcvf dataset_path * <\/code><\/p>\n<\/li>\n<li>\n<p>V\u00e9rifier que le dossier compress\u00e9 a tous les fichiers et qu'il n'y a pas de sous-dossier: Pour observer les fichiers sans le d\u00e9compresser utilise <code>tar -tf dataset_path.tar.gz<\/code>. Vous devez avoir la liste des fichiers fastq.gz sans sous-dossier.<\/p>\n<\/li>\n<\/ul>\n<p>Exemple :<\/p>\n<pre><code>\nsplA_01_R1.fastq.gz\nsplA_01_R2.fastq.gz\nsplA_02_R1.fastq.gz\nsplA_02_R2.fastq.gz\nsplA_03_R1.fastq.gz\nsplA_03_R2.fastq.gz\n<\/code><\/pre>\n<p>Documentation compression : <a href=\"https:\/\/openclassrooms.com\/fr\/courses\/43538-reprenez-le-controle-a-laide-de-linux\/41346-archiver-et-compresser\">https:\/\/openclassrooms.com\/fr\/courses\/43538-reprenez-le-controle-a-laide-de-linux\/41346-archiver-et-compresser<\/a><\/p>\n<p>extraire : <code>tar zxvf<\/code><\/p>\n<p>create:   <code>tar zcvf<\/code><\/p>\n<p>examiner: <code>tar -tf<\/code><\/p>\n<ul>\n<li>vous obtenez un fichier dataset_path.tar.gz que vous pouvez deplacer dans <code>\/scratch\/TEST-FROGS\/<\/code><\/li>\n<\/ul>\n<p><code>scp nas3:\/your_projet_path\/test_dataset.tar.gz \/scratch\/TEST-FROGS\/ <\/code>.<\/p>\n<h3>2. Pr\u00e9paration d'un fichier tabul\u00e9 &quot;sample_metadata.tsv&quot; qui R utilise<\/h3>\n<p>exemple 1 :<\/p>\n<pre><code>\n    Color   ID\nsplA_01 red rep1\nsplA_02 blue    rep2\nsplA_03 green   rep1<\/code><\/pre>\n<p>exemple2:<\/p>\n<pre><code>\nSample  Cell    Origin  Repetition  Color\n17MET040    Cell1   SolNu   R1  red\n17MET041    Cell1   SolNu   R2  red\n17MET042    Cell1   SolNu   R3  red\n17MET037    Cell1   Spergul R1  green\n17MET038    Cell1   Spergul R2  green\n17MET039    Cell1   Spergul R3  green\n17MET052    Cell2   Atriplex    R1  gray\n17MET035    Cell2   Atriplex    R2  gray\n17MET036    Cell2   Atriplex    R3  gray\n17MET049    Cell2   SolNu   R1  pink\n17MET050    Cell2   SolNu   R2  pink\n17MET051    Cell2   SolNu   R3  pink\n17MET046    Cell4   SolNu   R1  blue\n17MET047    Cell4   SolNu   R2  blue\n17MET048    Cell4   SolNu   R3  blue\n17MET043    Cell4   Viperine    R1  orange\n17MET044    Cell4   Viperine    R2  orange\n17MET045    Cell4   Viperine    R3  orange\n<\/code><\/pre>\n<h3>3. Connaitre le path de la base de donn\u00e9es pour les etapes d'assignation taxonomique<\/h3>\n<p>sur le cluster IRD :<\/p>\n<p><code>\/usr\/local\/frogs_databases-2.01\/silva_123_16S\/silva_123_16S.fasta<\/code><\/p>\n<h3>4. Visualiser\/modifier le script avant de le lancer :<\/h3>\n<p>Download <a href=\"https:\/\/southgreenplatform.github.io\/trainings\/files\/run_frogs_pipelinev2.sh\">run_frogs_pipeline.sh<\/a><\/p>\n<p>Ouvrir run_frogs_pipeline.sh dans un editeur.<\/p>\n<p>Vous pouvez modifier les lignes 3 et 4 du script pour ajouter le chemin vers les fichiers sample_metadata et la base de donn\u00e9es pour l'assignation taxonomique<\/p>\n<p><code>samplefile=&quot;\/scratch\/TEST-FROGS\/sample_metadata.tsv&quot;<\/code><\/p>\n<p><code>db=&quot;\/usr\/local\/frogs_databases-2.01\/silva_123_16S\/silva_123_16S.fasta&quot; <\/code><\/p>\n<p>+Le reste on ne touche pas sauf si vous savez ce que vous faites.+<\/p>\n<h3>5. Lancer le script run_frogs_pipeline.sh<\/h3>\n<p>Pour lancer le script place vous dans l'endroit ou vous voulez avoir les r\u00e9sultats :<code>cd \/scratch\/TEST-FROGS\/<\/code><\/p>\n<p>Attention: les amorces doivent etre ecrit en 5'-3' <\/p>\n<p><code>qsub -q bioinfo.q -N frogsCL -b yes -V -cwd -pe ompi 4 &#039;bash run_frogs_pipeline.sh 380 460 GGCGVACGGGTGAGTAA GTGCCAGCNGCNGCGG 250 250 420 OUTPUT \/scratch\/TEST-FROGS\/dataset_path.tar.gz&#039;<\/code><\/p>\n<p>les paramettres : <\/p>\n<pre><code>1&lt;minAmpliconSize&gt;\n2&lt;maxAmpliconSize&gt;\n3&lt;fivePrimPrimer&gt;\n4&lt;threePrimPrimer&gt;\n5&lt;R1size&gt;\n6&lt;R2size&gt;\n7&lt;expectedAmpliconSize&gt;\n8&lt;out_dir&gt;\n9&lt;datasetTarGz&gt;\n<\/code><\/pre>\n<p>Si tout se passe bien vous verrez \u00e7a:<\/p>\n<pre><code>380\n460\nGGCGVACGGGTGAGTAA\nGTGCCAGCNGCNGCGG\n250\n250\n420\nOUTPUT\n\/home\/orjuela\/TEST-FROGS\/fromGitExemple\/test_dataset.tar.gz\nStep preprocess ven. sept. 21 11:49:56 CEST 2018\nStep clustering ven. sept. 21 11:52:29 CEST 2018\nStep remove_chimera ven. sept. 21 11:52:44 CEST 2018\nStep filters ven. sept. 21 11:54:30 CEST 2018\nStep affiliation_OTU ven. sept. 21 11:54:33 CEST 2018 ...<\/code><\/pre>\n<p>Votre dossier OUTPUT doit rassembler \u00e0 \u00e7a<\/p>\n<pre><code>\norjuela@MPLCLTLP0157:~\/Documents\/tools\/FROGS\/test\/OUT$ ll\ntotal 91524\ndrwxr-xr-x 2 orjuela orjuela    53248 juin  15 15:23 .\/\ndrwxr-xr-x 4 orjuela orjuela     4096 juil. 12 14:40 ..\/\n-rw-r--r-- 1 orjuela orjuela 39183498 juin  15 15:12 01-prepro.fasta\n-rw-r--r-- 1 orjuela orjuela    34922 juin  15 15:12 01-prepro.html\n-rw-r--r-- 1 orjuela orjuela    19178 juin  15 15:12 01-prepro.log\n-rw-r--r-- 1 orjuela orjuela  4668203 juin  15 15:12 01-prepro.tsv\n-rw-r--r-- 1 orjuela orjuela  4941307 juin  15 15:13 02-clustering.biom\n-rw-r--r-- 1 orjuela orjuela  4325539 juin  15 15:13 02-clustering_compo.tsv\n-rw-r--r-- 1 orjuela orjuela 17010668 juin  15 15:13 02-clustering.fasta\n-rw-r--r-- 1 orjuela orjuela     3278 juin  15 15:13 02-clustering.log\n-rw-r--r-- 1 orjuela orjuela  1610390 juin  15 15:14 03-chimera.biom\n-rw-r--r-- 1 orjuela orjuela  5455138 juin  15 15:14 03-chimera.fasta\n-rw-r--r-- 1 orjuela orjuela    13943 juin  15 15:14 03-chimera.html\n-rw-r--r-- 1 orjuela orjuela    81978 juin  15 15:14 03-chimera.log\n-rw-r--r-- 1 orjuela orjuela   989852 juin  15 15:14 04-affiliation.biom\n-rw-r--r-- 1 orjuela orjuela    15831 juin  15 15:14 04-affiliation.html\n-rw-r--r-- 1 orjuela orjuela     1824 juin  15 15:14 04-affiliation.log\n-rw-r--r-- 1 orjuela orjuela   224506 juin  15 15:14 04-filters.biom\n-rw-r--r-- 1 orjuela orjuela   307008 juin  15 15:14 04-filters.excluded\n-rw-r--r-- 1 orjuela orjuela   661810 juin  15 15:14 04-filters.fasta\n-rw-r--r-- 1 orjuela orjuela   130418 juin  15 15:14 04-filters.html\n-rw-r--r-- 1 orjuela orjuela     1478 juin  15 15:14 04-filters.log\n-rw-r--r-- 1 orjuela orjuela   187007 juin  15 15:14 05-clustersStat.html\n-rw-r--r-- 1 orjuela orjuela      933 juin  15 15:14 05-clustersStat.log\n-rw-r--r-- 1 orjuela orjuela   248668 juin  15 15:14 06-affiliationsStat.html\n-rw-r--r-- 1 orjuela orjuela     1170 juin  15 15:14 06-affiliationsStat.log\n-rw-r--r-- 1 orjuela orjuela     1120 juin  15 15:14 07-biom2tsv.log\n-rw-r--r-- 1 orjuela orjuela    23252 juin  15 15:14 07-biom2tsv.multi\n-rw-r--r-- 1 orjuela orjuela  1138093 juin  15 15:14 07-biom2tsv.tsv\n-rw-r--r-- 1 orjuela orjuela   154897 juin  15 15:14 08-affiliation_multihit.tsv\n-rw-r--r-- 1 orjuela orjuela   844425 juin  15 15:14 08-affiliation_std.biom\n-rw-r--r-- 1 orjuela orjuela      338 juin  15 15:14 08-biom2stdbiom.log\n-rw-r--r-- 1 orjuela orjuela  1124530 juin  15 15:14 09-tsv2biom.biom\n-rw-r--r-- 1 orjuela orjuela   641114 juin  15 15:14 09-tsv2biom.fasta\n-rw-r--r-- 1 orjuela orjuela      882 juin  15 15:14 09-tsv2biom.log\n-rw-r--r-- 1 orjuela orjuela   182059 juin  15 15:17 10a-tree.html\n-rw-r--r-- 1 orjuela orjuela     1346 juin  15 15:17 10a-tree.log\n-rw-r--r-- 1 orjuela orjuela    64971 juin  15 15:17 10a-tree.nwk\n-rw-r--r-- 1 orjuela orjuela   180238 juin  15 15:18 10b-tree.html\n-rw-r--r-- 1 orjuela orjuela     1082 juin  15 15:18 10b-tree.log\n-rw-r--r-- 1 orjuela orjuela    67318 juin  15 15:18 10b-tree.nwk\n-rw-r--r-- 1 orjuela orjuela  1267549 juin  15 15:18 11-phylo_import.html\n-rw-r--r-- 1 orjuela orjuela     1295 juin  15 15:18 11-phylo_import.log\n-rw-r--r-- 1 orjuela orjuela    69734 juin  15 15:18 11-phylo_import.Rdata\n-rw-r--r-- 1 orjuela orjuela  4033991 juin  15 15:19 12-phylo_composition.html\n-rw-r--r-- 1 orjuela orjuela     1027 juin  15 15:19 12-phylo_composition.log\n-rw-r--r-- 1 orjuela orjuela  1214435 juin  15 15:22 13-phylo_alpha_div.html\n-rw-r--r-- 1 orjuela orjuela     1077 juin  15 15:22 13-phylo_alpha_div.log\n-rw-r--r-- 1 orjuela orjuela      223 juin  15 15:19 13-phylo_alpha_div.tsv\n-rw-r--r-- 1 orjuela orjuela   789726 juin  15 15:22 14-phylo_beta_div.html\n-rw-r--r-- 1 orjuela orjuela     1010 juin  15 15:22 14-phylo_beta_div.log\n-rw-r--r-- 1 orjuela orjuela      971 juin  15 15:23 16-phylo_clustering.log\n-rw-r--r-- 1 orjuela orjuela   865732 juin  15 15:23 16-phylo_clutering.html\n-rw-r--r-- 1 orjuela orjuela   748887 juin  15 15:23 17-phylo_manova.html\n-rw-r--r-- 1 orjuela orjuela      951 juin  15 15:23 17-phylo_manova.log\n-rw-r--r-- 1 orjuela orjuela       67 juin  15 15:22 Jaccard_binary.tsv\n-rw-r--r-- 1 orjuela orjuela       67 juin  15 15:22 Unifrac.tsv\n<\/code><\/pre>\n<p>Rapatrier les dossier OUTPUT dans votre projet puis dans votre machine local et visualiser les html.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>FROGs en Ligne de Commande This page describes how to launch FROGs in command line from IRD cluster. From fastq&hellip; <br \/> <a class=\"read-more\" href=\"https:\/\/bioinfo.ird.fr\/index.php\/tutorials-fr\/frogs\/\">Lire la suite<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":1325,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"inline_featured_image":false,"footnotes":""},"class_list":["post-397","page","type-page","status-publish","hentry"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.2 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Tutorials - Frogs - itrop<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/bioinfo.ird.fr\/index.php\/tutorials-fr\/frogs\/\" \/>\n<meta property=\"og:locale\" content=\"fr_FR\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Tutorials - Frogs - itrop\" \/>\n<meta property=\"og:description\" content=\"FROGs en Ligne de Commande This page describes how to launch FROGs in command line from IRD cluster. 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