From 792b90b3d57a6137d49254ff29686e55dfaccecb Mon Sep 17 00:00:00 2001
From: root <root@EB10PA4.newcefe.newage.fr>
Date: Fri, 6 Dec 2019 15:36:48 +0100
Subject: [PATCH] update input
---
.../species_abundance_per_sample/sample01-01-ranks.txt | 2 +-
.../species_abundance_per_sample/sample02-01-ranks.txt | 2 +-
.../species_abundance_per_sample/sample03-01-ranks.txt | 2 +-
.../species_abundance_per_sample/sample04-01-ranks.txt | 2 +-
.../species_abundance_per_sample/sample05-01-ranks.txt | 2 +-
.../species_abundance_per_sample/sample06-01-ranks.txt | 2 +-
.../species_abundance_per_sample/sample07-01-ranks.txt | 2 +-
.../species_abundance_per_sample/sample09-01-ranks.txt | 2 +-
.../species_abundance_per_sample/sample10-01-ranks.txt | 2 +-
.../species_abundance_per_sample/sample12-01-ranks.txt | 2 +-
.../species_abundance_per_sample/sample13-01-ranks.txt | 2 +-
.../species_abundance_per_sample/sample15-01-ranks.txt | 2 +-
.../species_abundance_per_sample/sample16-01-ranks.txt | 2 +-
.../species_abundance_per_sample/sample17-01-ranks.txt | 2 +-
.../species_abundance_per_sample/sample19-01-ranks.txt | 2 +-
.../species_abundance_per_sample/sample20-01-ranks.txt | 2 +-
.../species_abundance_per_sample/sample21-01-ranks.txt | 2 +-
.../species_abundance_per_sample/sample22-01-ranks.txt | 2 +-
.../species_abundance_per_sample/sample24-01-ranks.txt | 2 +-
.../species_abundance_per_sample/sample26-01-ranks.txt | 2 +-
.../species_abundance_per_sample/sample27-01-ranks.txt | 2 +-
.../species_abundance_per_sample/sample28-01-ranks.txt | 2 +-
.../species_abundance_per_sample/sample29-01-ranks.txt | 2 +-
optimal_pipeline/optimal_pipeline.sh | 4 ++--
24 files changed, 25 insertions(+), 25 deletions(-)
diff --git a/00_Input_data/species_abundance_per_sample/sample01-01-ranks.txt b/00_Input_data/species_abundance_per_sample/sample01-01-ranks.txt
index d170156..f67e0d8 100644
--- a/00_Input_data/species_abundance_per_sample/sample01-01-ranks.txt
+++ b/00_Input_data/species_abundance_per_sample/sample01-01-ranks.txt
@@ -1,4 +1,4 @@
-# rank seq_id rel_abund_perc
+rank seq_id rel_abund_perc
1 Pseudaspius_leptocephalus 50.0001907352276
2 Denticeps_clupeoides 25.0000953676138
3 Howella_brodiei 12.5000476838069
diff --git a/00_Input_data/species_abundance_per_sample/sample02-01-ranks.txt b/00_Input_data/species_abundance_per_sample/sample02-01-ranks.txt
index a30ab02..28ed452 100644
--- a/00_Input_data/species_abundance_per_sample/sample02-01-ranks.txt
+++ b/00_Input_data/species_abundance_per_sample/sample02-01-ranks.txt
@@ -1,4 +1,4 @@
-# rank seq_id rel_abund_perc
+rank seq_id rel_abund_perc
1 Geotria_australis 36.6867764555976
2 Odontamblyopus_rebecca 30.5723137163313
3 Tinca_tinca 10.1907712367771
diff --git a/00_Input_data/species_abundance_per_sample/sample03-01-ranks.txt b/00_Input_data/species_abundance_per_sample/sample03-01-ranks.txt
index 9fc1eba..ccd93d8 100644
--- a/00_Input_data/species_abundance_per_sample/sample03-01-ranks.txt
+++ b/00_Input_data/species_abundance_per_sample/sample03-01-ranks.txt
@@ -1,4 +1,4 @@
-# rank seq_id rel_abund_perc
+rank seq_id rel_abund_perc
1 Callionymus_enneactis 24.00066181096
2 Pareuchiloglanis_macrotrema 19.0664295207627
3 Petrochromis_trewavasae 18.875744540755
diff --git a/00_Input_data/species_abundance_per_sample/sample04-01-ranks.txt b/00_Input_data/species_abundance_per_sample/sample04-01-ranks.txt
index 6d46869..adfec49 100644
--- a/00_Input_data/species_abundance_per_sample/sample04-01-ranks.txt
+++ b/00_Input_data/species_abundance_per_sample/sample04-01-ranks.txt
@@ -1,4 +1,4 @@
-# rank seq_id rel_abund_perc
+rank seq_id rel_abund_perc
1 Tridentiger_obscurus 18.8640822805659
2 Odonus_niger 9.00059893827002
3 Colomesus_psittacus 8.33433156425003
diff --git a/00_Input_data/species_abundance_per_sample/sample05-01-ranks.txt b/00_Input_data/species_abundance_per_sample/sample05-01-ranks.txt
index 3a5ce49..b0aa63d 100644
--- a/00_Input_data/species_abundance_per_sample/sample05-01-ranks.txt
+++ b/00_Input_data/species_abundance_per_sample/sample05-01-ranks.txt
@@ -1,4 +1,4 @@
-# rank seq_id rel_abund_perc
+rank seq_id rel_abund_perc
1 Oreinus_molesworthi 31.0593653606212
2 Ichthyomyzon_gagei 17.0884287003418
3 Lepidocephalichthys_guntea 11.5555038302311
diff --git a/00_Input_data/species_abundance_per_sample/sample06-01-ranks.txt b/00_Input_data/species_abundance_per_sample/sample06-01-ranks.txt
index aa2cc48..3a442b9 100644
--- a/00_Input_data/species_abundance_per_sample/sample06-01-ranks.txt
+++ b/00_Input_data/species_abundance_per_sample/sample06-01-ranks.txt
@@ -1,4 +1,4 @@
-# rank seq_id rel_abund_perc
+rank seq_id rel_abund_perc
1 Amphiprion_frenatus 14.1424426584443
2 Parajulis_poecilepterus 13.9249283784683
3 Andinoacara_pulcher 11.0965128387794
diff --git a/00_Input_data/species_abundance_per_sample/sample07-01-ranks.txt b/00_Input_data/species_abundance_per_sample/sample07-01-ranks.txt
index 250dd41..16ece65 100644
--- a/00_Input_data/species_abundance_per_sample/sample07-01-ranks.txt
+++ b/00_Input_data/species_abundance_per_sample/sample07-01-ranks.txt
@@ -1,4 +1,4 @@
-# rank seq_id rel_abund_perc
+rank seq_id rel_abund_perc
1 Aperioptus_gracilentus 40.099983000802
2 Schizopygopsis_malacanthus 17.7275940503546
3 Pagellus_erythrinus 12.4746090302495
diff --git a/00_Input_data/species_abundance_per_sample/sample09-01-ranks.txt b/00_Input_data/species_abundance_per_sample/sample09-01-ranks.txt
index bd69403..4657dae 100644
--- a/00_Input_data/species_abundance_per_sample/sample09-01-ranks.txt
+++ b/00_Input_data/species_abundance_per_sample/sample09-01-ranks.txt
@@ -1,4 +1,4 @@
-# rank seq_id rel_abund_perc
+rank seq_id rel_abund_perc
1 Mesonoemacheilus_triangularis 3.3339666603334
2 Plagiognathops_microlepis 3.3339666603334
3 Melichthys_vidua 3.3339666603334
diff --git a/00_Input_data/species_abundance_per_sample/sample10-01-ranks.txt b/00_Input_data/species_abundance_per_sample/sample10-01-ranks.txt
index 960583e..d5137e7 100644
--- a/00_Input_data/species_abundance_per_sample/sample10-01-ranks.txt
+++ b/00_Input_data/species_abundance_per_sample/sample10-01-ranks.txt
@@ -1,4 +1,4 @@
-# rank seq_id rel_abund_perc
+rank seq_id rel_abund_perc
1 Sander_vitreus 23.0837004495383
2 Anguilla_luzonensis 17.7566926596449
3 Peltorhamphus_novaezeelandiae 13.6589943497268
diff --git a/00_Input_data/species_abundance_per_sample/sample12-01-ranks.txt b/00_Input_data/species_abundance_per_sample/sample12-01-ranks.txt
index c45b9a1..6ebf340 100644
--- a/00_Input_data/species_abundance_per_sample/sample12-01-ranks.txt
+++ b/00_Input_data/species_abundance_per_sample/sample12-01-ranks.txt
@@ -1,4 +1,4 @@
-# rank seq_id rel_abund_perc
+rank seq_id rel_abund_perc
1 Jinshaia_abbreviata 28.5759645594285
2 Parexocoetus_brachypterus 20.4114032595918
3 Pristis_pectinata 14.5795737597084
diff --git a/00_Input_data/species_abundance_per_sample/sample13-01-ranks.txt b/00_Input_data/species_abundance_per_sample/sample13-01-ranks.txt
index 1d6596c..59c8579 100644
--- a/00_Input_data/species_abundance_per_sample/sample13-01-ranks.txt
+++ b/00_Input_data/species_abundance_per_sample/sample13-01-ranks.txt
@@ -1,4 +1,4 @@
-# rank seq_id rel_abund_perc
+rank seq_id rel_abund_perc
1 Lycengraulis_grossidens 9.84160384319683
2 Salvelinus_namaycush 8.94691258517894
3 Pimelodus_pictus 8.13355689516267
diff --git a/00_Input_data/species_abundance_per_sample/sample15-01-ranks.txt b/00_Input_data/species_abundance_per_sample/sample15-01-ranks.txt
index 195e03d..c708d39 100644
--- a/00_Input_data/species_abundance_per_sample/sample15-01-ranks.txt
+++ b/00_Input_data/species_abundance_per_sample/sample15-01-ranks.txt
@@ -1,4 +1,4 @@
-# rank seq_id rel_abund_perc
+rank seq_id rel_abund_perc
1 Pungtungia_herzi 33.3353135620001
2 Carcharhinus_brevipinna 22.2235423713334
3 Scomberomorus_concolor 14.8156949108889
diff --git a/00_Input_data/species_abundance_per_sample/sample16-01-ranks.txt b/00_Input_data/species_abundance_per_sample/sample16-01-ranks.txt
index 937a757..5f11807 100644
--- a/00_Input_data/species_abundance_per_sample/sample16-01-ranks.txt
+++ b/00_Input_data/species_abundance_per_sample/sample16-01-ranks.txt
@@ -1,4 +1,4 @@
-# rank seq_id rel_abund_perc
+rank seq_id rel_abund_perc
1 Sciaenops_ocellatus 28.5730814611429
2 Scarus_schlegeli 20.4093439008164
3 Electrona_carlsbergi 14.5781027905831
diff --git a/00_Input_data/species_abundance_per_sample/sample17-01-ranks.txt b/00_Input_data/species_abundance_per_sample/sample17-01-ranks.txt
index b6dbd15..826269d 100644
--- a/00_Input_data/species_abundance_per_sample/sample17-01-ranks.txt
+++ b/00_Input_data/species_abundance_per_sample/sample17-01-ranks.txt
@@ -1,4 +1,4 @@
-# rank seq_id rel_abund_perc
+rank seq_id rel_abund_perc
1 Platytroctes_apus 16.6949311494992
2 Koreocobitis_rotundicaudata 13.9124426195826
3 Johnius_carouna 11.5937021896522
diff --git a/00_Input_data/species_abundance_per_sample/sample19-01-ranks.txt b/00_Input_data/species_abundance_per_sample/sample19-01-ranks.txt
index 9f8b7c8..5f0f0f9 100644
--- a/00_Input_data/species_abundance_per_sample/sample19-01-ranks.txt
+++ b/00_Input_data/species_abundance_per_sample/sample19-01-ranks.txt
@@ -1,4 +1,4 @@
-# rank seq_id rel_abund_perc
+rank seq_id rel_abund_perc
1 Conger_myriaster 9.643568023
2 Abudefduf_vaigiensis 8.766880021
3 Lates_niloticus 7.969890928
diff --git a/00_Input_data/species_abundance_per_sample/sample20-01-ranks.txt b/00_Input_data/species_abundance_per_sample/sample20-01-ranks.txt
index 607dbce..657e220 100644
--- a/00_Input_data/species_abundance_per_sample/sample20-01-ranks.txt
+++ b/00_Input_data/species_abundance_per_sample/sample20-01-ranks.txt
@@ -1,4 +1,4 @@
-# rank seq_id rel_abund_perc
+rank seq_id rel_abund_perc
1 Gymnodiptychus_dybowskii 16.7683890289939
2 Beryx_mollis 13.9736575291616
3 Oxygymnocypris_stewartii 11.6447146093013
diff --git a/00_Input_data/species_abundance_per_sample/sample21-01-ranks.txt b/00_Input_data/species_abundance_per_sample/sample21-01-ranks.txt
index 206cf55..0f4676a 100644
--- a/00_Input_data/species_abundance_per_sample/sample21-01-ranks.txt
+++ b/00_Input_data/species_abundance_per_sample/sample21-01-ranks.txt
@@ -1,4 +1,4 @@
-# rank seq_id rel_abund_perc
+rank seq_id rel_abund_perc
1 Schizothorax_richardsonii 35.0641470607013
2 Poecilia_latipinna 21.9150919104383
3 Variola_louti 13.6969324402739
diff --git a/00_Input_data/species_abundance_per_sample/sample22-01-ranks.txt b/00_Input_data/species_abundance_per_sample/sample22-01-ranks.txt
index 54a20ee..0c6e6b2 100644
--- a/00_Input_data/species_abundance_per_sample/sample22-01-ranks.txt
+++ b/00_Input_data/species_abundance_per_sample/sample22-01-ranks.txt
@@ -1,4 +1,4 @@
-# rank seq_id rel_abund_perc
+rank seq_id rel_abund_perc
1 Labeo_senegalensis 38.7811272838781
2 Devario_laoensis 22.8124278122812
3 Schismatogobius_ampluvinculus 13.4190751813419
diff --git a/00_Input_data/species_abundance_per_sample/sample24-01-ranks.txt b/00_Input_data/species_abundance_per_sample/sample24-01-ranks.txt
index 554c9ca..a0b658d 100644
--- a/00_Input_data/species_abundance_per_sample/sample24-01-ranks.txt
+++ b/00_Input_data/species_abundance_per_sample/sample24-01-ranks.txt
@@ -3,7 +3,7 @@ rank seq_id rel_abund_perc
2 Salvelinus_albus 21.7447943419355
3 Hypophthalmichthys_nobilis 14.3105695460114
4 Isurus_oxyrinchus 9.54037969534848
-5 Himantura_granulata 6.36025313023232
+5 Urogymnus_granulatus 6.36025313023232
6 Pampus_chinensis 4.24016875382029
7 Neolissochilus_stracheyi 2.82677916921352
8 Anguilla_bicolor 1.88451944614235
diff --git a/00_Input_data/species_abundance_per_sample/sample26-01-ranks.txt b/00_Input_data/species_abundance_per_sample/sample26-01-ranks.txt
index c519269..27724be 100644
--- a/00_Input_data/species_abundance_per_sample/sample26-01-ranks.txt
+++ b/00_Input_data/species_abundance_per_sample/sample26-01-ranks.txt
@@ -1,4 +1,4 @@
-# rank seq_id rel_abund_perc
+rank seq_id rel_abund_perc
1 Acanthaphritis_unoorum 23.2381704890705
2 Conocara_macropterum 21.125609539155
3 Pseudanthias_dispar 12.4268291395029
diff --git a/00_Input_data/species_abundance_per_sample/sample27-01-ranks.txt b/00_Input_data/species_abundance_per_sample/sample27-01-ranks.txt
index 38e2410..c5160ba 100644
--- a/00_Input_data/species_abundance_per_sample/sample27-01-ranks.txt
+++ b/00_Input_data/species_abundance_per_sample/sample27-01-ranks.txt
@@ -1,4 +1,4 @@
-# rank seq_id rel_abund_perc
+rank seq_id rel_abund_perc
1 Moxostoma_congestum 16.8680281993253
2 Conocara_murrayi 9.37112677462516
3 Hemiculterella_sauvagei 7.20855905771166
diff --git a/00_Input_data/species_abundance_per_sample/sample28-01-ranks.txt b/00_Input_data/species_abundance_per_sample/sample28-01-ranks.txt
index 3f0a26c..954a48f 100644
--- a/00_Input_data/species_abundance_per_sample/sample28-01-ranks.txt
+++ b/00_Input_data/species_abundance_per_sample/sample28-01-ranks.txt
@@ -1,4 +1,4 @@
-# rank seq_id rel_abund_perc
+rank seq_id rel_abund_perc
1 Dussumieria_elopsoides 16.6526237541057
2 Auxis_rochei 9.69944171486508
3 Triplophysa_dalaica 7.11650587996714
diff --git a/00_Input_data/species_abundance_per_sample/sample29-01-ranks.txt b/00_Input_data/species_abundance_per_sample/sample29-01-ranks.txt
index c7c44b2..00e772f 100644
--- a/00_Input_data/species_abundance_per_sample/sample29-01-ranks.txt
+++ b/00_Input_data/species_abundance_per_sample/sample29-01-ranks.txt
@@ -1,4 +1,4 @@
-# rank seq_id rel_abund_perc
+rank seq_id rel_abund_perc
1 Schistura_scaturigina 37.9594053507592
2 Carcharhinus_amblyrhynchoides 21.0885585304218
3 Thaumatichthys_pagidostomus 11.7158658502343
diff --git a/optimal_pipeline/optimal_pipeline.sh b/optimal_pipeline/optimal_pipeline.sh
index 029e7e7..2fc2ae5 100644
--- a/optimal_pipeline/optimal_pipeline.sh
+++ b/optimal_pipeline/optimal_pipeline.sh
@@ -54,8 +54,8 @@ fin_dir=`pwd`"/optimal_pipeline/Outputs/final"
###################################################################################################################
## path to 'tags.fasta'
-Tags_F=`pwd`"/02_demultiplex/Tags_F.fasta"
-Tags_R=`pwd`"/02_demultiplex/Tags_R.fasta"
+Tags_F=`pwd`"/optimal_pipeline/Tags_F.fasta"
+Tags_R=`pwd`"/optimal_pipeline/Tags_R.fasta"
## assign each sequence to a sample
$cutadapt --pair-adapters --pair-filter=both -g file:$Tags_F -G file:$Tags_R -y '; sample={name};' -e 0 -o $main_dir/R1.assigned.fastq -p $main_dir/R2.assigned.fastq --untrimmed-paired-output $main_dir/unassigned_R2.fastq --untrimmed-output $main_dir/unassigned_R1.fastq $R1_fastq $R2_fastq
--
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