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 d170156d1dec91a2bd676264ff2b5dbdb65bfb38..f67e0d8bc235e56b1bbc9bb8eb8287af8f4e1099 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 a30ab023b7f1bcd93a3d79f56d2e54fd4dc0fd44..28ed45292de67480abeda0f8972be7190f1b0b02 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 9fc1eba428f3f63aedb397c1da6dcf6e442e5f10..ccd93d8a46732dfc2ff51237d4c54d55b2da1905 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 6d46869dfaf9331cff7bb360098b00c16ba28ae9..adfec49ccc3c166b1b21976f9d6fbec4030b4a6d 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 3a5ce497a7b2c9afc765dafa30f40e77606143b9..b0aa63d58714c8d5505f55dd93967be7935f4859 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 aa2cc48e18667b5559b51b2eefaeb23a8d5c00b2..3a442b9ff76a12d63a95ecea43b6b190091cfda1 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 250dd415f76960e62c74cfb435b6b49af2884003..16ece650b39e80445c25ae8ef9abed77e96ea227 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 bd6940379cc152bd81fcbdce6415d8819d48399c..4657daef8cee677e26536653d26401c853df02df 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 960583e4930411592086b6510e4d8b05b862f80f..d5137e7406ee170b553cc88e6f24319f597d6195 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 c45b9a1209f43401f369461ef05833990cb4dd2b..6ebf34016ec2564ec76aab36f011387ef5e159f3 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 1d6596c97a39ebfe98467babc3fbe72a5f4982b4..59c857994ebc692835b0f82cb44b0754b1040bc7 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 195e03dc680a44e024d0e7a597945e20a5d910c2..c708d391ef45b741450b4d220c621ec82c390b76 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 937a757309df749dc48a380801c91964665ad575..5f11807ce2df0dfb5492ad9a1627aebbe1420d78 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 b6dbd15cb237b359a776e99a89b0933003f735fb..826269d1e22acbb2c327b511ee6a5093392673c6 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 9f8b7c892d27e3aaeaaaf62239c19b0156c6c2f2..5f0f0f9bb03080af2c68eb0065857a69011a5ea5 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 607dbce5b336fb01f8b11f472156fcc5d5b6adad..657e220503e462500a12307503a05e668c35aaef 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 206cf55ca21c85c38f0a158be04568180914dc66..0f4676a8d263fbe76afbf63197d4cb573bb7c493 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 54a20eeb6aea604617a9f02c74b460e718078b18..0c6e6b2b0c60191339c1dc5b352c57b4d966b8fc 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 554c9caf6ec71831b2a227c056d6a80aba34e2a5..a0b658de4fdb6d4f8d0f92cba53cd99e0e1dae62 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 c519269b0d1a4883117f0323ea198a4768a11ef6..27724be1eef248ffe337a5f607aafb7f7102a550 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 38e2410208ab55b07d6f4f5a89a9b9f1029e52c9..c5160bab523f97f3310b7c4b75c1009e9eea2c2c 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 3f0a26cb3827e4df9a50cb61d35b0104ac59a074..954a48f63c82bc3df8a04af5b24f062154df97a7 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 c7c44b2b31eee86024db8b6f24a1bce4b7e6a264..00e772f7b6a9eedd3374e14cce9bfc0ae55a636b 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 029e7e7baf91188382068c59eabb75e62462ac1d..2fc2ae50c3282a63d265830686507fcd1bdcc91e 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