Initial_data_dump BigOld

2f1279b7 · Simeon Rossmann · 22b26f91 · 2f1279b7 · 2f1279b7 · 2f1279b7
Commit 2f1279b7 authored 3 years ago by Simeon Rossmann
--- a/its2/mergers.txt
+++ b/its2/mergers.txt
--- a/its2/out.txt
+++ b/its2/out.txt
+"reads.in" "reads.out"
+"1-its2_S203_L001_R1_001.fastq.gz.trim.fastq.gz" 71344 16779
+"10-its2_S222_L001_R1_001.fastq.gz.trim.fastq.gz" 74196 18827
+"11-its2_S229_L001_R1_001.fastq.gz.trim.fastq.gz" 74777 12931
+"12-its2_S236_L001_R1_001.fastq.gz.trim.fastq.gz" 63049 9474
+"13-its2_S242_L001_R1_001.fastq.gz.trim.fastq.gz" 55444 6260
+"14-its2_S248_L001_R1_001.fastq.gz.trim.fastq.gz" 69735 8043
+"15-its2_S205_L001_R1_001.fastq.gz.trim.fastq.gz" 57198 3885
+"16-its2_S214_L001_R1_001.fastq.gz.trim.fastq.gz" 59013 8157
+"17-its2_S223_L001_R1_001.fastq.gz.trim.fastq.gz" 61411 7145
+"18-its2_S230_L001_R1_001.fastq.gz.trim.fastq.gz" 54728 8848
+"19-its2_S237_L001_R1_001.fastq.gz.trim.fastq.gz" 55093 9804
+"2-its2_S212_L001_R1_001.fastq.gz.trim.fastq.gz" 64257 13332
+"20-its2_S243_L001_R1_001.fastq.gz.trim.fastq.gz" 61047 8229
+"21-its2_S249_L001_R1_001.fastq.gz.trim.fastq.gz" 38999 3979
+"22-its2_S206_L001_R1_001.fastq.gz.trim.fastq.gz" 66325 11369
+"23-its2_S215_L001_R1_001.fastq.gz.trim.fastq.gz" 47593 5302
+"24-its2_S224_L001_R1_001.fastq.gz.trim.fastq.gz" 39861 3077
+"25-its2_S231_L001_R1_001.fastq.gz.trim.fastq.gz" 71081 8994
+"26-its2_S238_L001_R1_001.fastq.gz.trim.fastq.gz" 58781 8922
+"27-its2_S244_L001_R1_001.fastq.gz.trim.fastq.gz" 70765 8059
+"28-its2_S250_L001_R1_001.fastq.gz.trim.fastq.gz" 66554 10068
+"29-its2_S207_L001_R1_001.fastq.gz.trim.fastq.gz" 79984 12822
+"3-its2_S221_L001_R1_001.fastq.gz.trim.fastq.gz" 65957 12898
+"30-its2_S216_L001_R1_001.fastq.gz.trim.fastq.gz" 79124 12552
+"31-its2_S225_L001_R1_001.fastq.gz.trim.fastq.gz" 67150 14996
+"32-its2_S232_L001_R1_001.fastq.gz.trim.fastq.gz" 63058 10034
+"33-its2_S239_L001_R1_001.fastq.gz.trim.fastq.gz" 77900 11828
+"34-its2_S245_L001_R1_001.fastq.gz.trim.fastq.gz" 58528 9651
+"35-its2_S251_L001_R1_001.fastq.gz.trim.fastq.gz" 63014 11980
+"36-its2_S257_L001_R1_001.fastq.gz.trim.fastq.gz" 63694 11707
+"37-its2_S208_L001_R1_001.fastq.gz.trim.fastq.gz" 83119 10387
+"38-its2_S217_L001_R1_001.fastq.gz.trim.fastq.gz" 60832 7490
+"39-its2_S226_L001_R1_001.fastq.gz.trim.fastq.gz" 78882 11400
+"4-its2_S228_L001_R1_001.fastq.gz.trim.fastq.gz" 63846 12839
+"40-its2_S233_L001_R1_001.fastq.gz.trim.fastq.gz" 88074 13475
+"41-its2_S240_L001_R1_001.fastq.gz.trim.fastq.gz" 2 0
+"42-its2_S246_L001_R1_001.fastq.gz.trim.fastq.gz" 83709 8574
+"43-its2_S252_L001_R1_001.fastq.gz.trim.fastq.gz" 13 1
+"44-its2_S258_L001_R1_001.fastq.gz.trim.fastq.gz" 68792 7272
+"45-its2_S209_L001_R1_001.fastq.gz.trim.fastq.gz" 60615 4702
+"46-its2_S218_L001_R1_001.fastq.gz.trim.fastq.gz" 79895 11931
+"5-its2_S235_L001_R1_001.fastq.gz.trim.fastq.gz" 90925 19505
+"6-its2_S241_L001_R1_001.fastq.gz.trim.fastq.gz" 79014 22759
+"7-its2_S247_L001_R1_001.fastq.gz.trim.fastq.gz" 93317 30284
+"8-its2_S204_L001_R1_001.fastq.gz.trim.fastq.gz" 83004 20610
+"9-its2_S213_L001_R1_001.fastq.gz.trim.fastq.gz" 75900 18205
+"NegK1-its2_S210_L001_R1_001.fastq.gz.trim.fastq.gz" 5 2
+"NegK2-its2_S219_L001_R1_001.fastq.gz.trim.fastq.gz" 11 6
+"Posk1-its2_S211_L001_R1_001.fastq.gz.trim.fastq.gz" 94270 7652
+"Posk2-its2_S220_L001_R1_001.fastq.gz.trim.fastq.gz" 79931 6349
+"Posk3-its2_S227_L001_R1_001.fastq.gz.trim.fastq.gz" 64913 5301
+"Posk4-its2_S234_L001_R1_001.fastq.gz.trim.fastq.gz" 73357 5231
+"V1-its2_S253_L001_R1_001.fastq.gz.trim.fastq.gz" 18 3
+"V2-its2_S254_L001_R1_001.fastq.gz.trim.fastq.gz" 1 0
+"V3-its2_S255_L001_R1_001.fastq.gz.trim.fastq.gz" 29 11
--- a/its2/parameters_both31-01-22_1452.txt
+++ b/its2/parameters_both31-01-22_1452.txt
+"x"
+"Run on 31/01/22 14:52
+Path:  /home/simeon/Documents/Sunniva_felt21
+Samples:
+1-its2;10-its2;11-its2;12-its2;13-its2;14-its2;15-its2;16-its2;17-its2;18-its2;19-its2;2-its2;20-its2;21-its2;22-its2;23-its2;24-its2;25-its2;26-its2;27-its2;28-its2;29-its2;3-its2;30-its2;31-its2;32-its2;33-its2;34-its2;35-its2;36-its2;37-its2;38-its2;39-its2;4-its2;40-its2;41-its2;42-its2;43-its2;44-its2;45-its2;46-its2;5-its2;6-its2;7-its2;8-its2;9-its2;NegK1-its2;NegK2-its2;Posk1-its2;Posk2-its2;Posk3-its2;Posk4-its2;V1-its2;V2-its2;V3-its2
+Analysis type: both
+Database type: /home/simeon/Documents/tax_DBs/ITS1_databases/OomyceteDB/CoFiMiO3_OomycITS1_dada2_DB.fa
+dada2 Parameters
+maximum expected errors R1: 2
+maximum expected errors R2: 2
+minimum length:  100
+truncate at first instance of Qscore:  2
+truncation at length (0 = no trunc) 0,truncation at length (0 = no trunc) 0
+minimum overlap during merging:  30
+taxonomy bootstrap threshold:  80
+Collapse overlapping ASVs:  FALSE
+Minimum overlap if collapsing overlapping ASVs: 200
+Trimming 5' (R1, R2): 10,10"
--- a/its2/primers_after_cutadapt_15Samples_31-01-22_0857.txt
+++ b/its2/primers_after_cutadapt_15Samples_31-01-22_0857.txt
+"Sample" "Primer_Read" "Forward" "Complement" "Reverse" "RevComp"
+"1-its2_S203_L001_R1_001.fastq.gz.trim.fastq.gz 1-its2_S203_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"1-its2_S203_L001_R1_001.fastq.gz.trim.fastq.gz 1-its2_S203_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"1-its2_S203_L001_R1_001.fastq.gz.trim.fastq.gz 1-its2_S203_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
+"1-its2_S203_L001_R1_001.fastq.gz.trim.fastq.gz 1-its2_S203_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"10-its2_S222_L001_R1_001.fastq.gz.trim.fastq.gz 10-its2_S222_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"10-its2_S222_L001_R1_001.fastq.gz.trim.fastq.gz 10-its2_S222_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"10-its2_S222_L001_R1_001.fastq.gz.trim.fastq.gz 10-its2_S222_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
+"10-its2_S222_L001_R1_001.fastq.gz.trim.fastq.gz 10-its2_S222_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"11-its2_S229_L001_R1_001.fastq.gz.trim.fastq.gz 11-its2_S229_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"11-its2_S229_L001_R1_001.fastq.gz.trim.fastq.gz 11-its2_S229_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"11-its2_S229_L001_R1_001.fastq.gz.trim.fastq.gz 11-its2_S229_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
+"11-its2_S229_L001_R1_001.fastq.gz.trim.fastq.gz 11-its2_S229_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"12-its2_S236_L001_R1_001.fastq.gz.trim.fastq.gz 12-its2_S236_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"12-its2_S236_L001_R1_001.fastq.gz.trim.fastq.gz 12-its2_S236_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"12-its2_S236_L001_R1_001.fastq.gz.trim.fastq.gz 12-its2_S236_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
+"12-its2_S236_L001_R1_001.fastq.gz.trim.fastq.gz 12-its2_S236_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"13-its2_S242_L001_R1_001.fastq.gz.trim.fastq.gz 13-its2_S242_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"13-its2_S242_L001_R1_001.fastq.gz.trim.fastq.gz 13-its2_S242_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"13-its2_S242_L001_R1_001.fastq.gz.trim.fastq.gz 13-its2_S242_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
+"13-its2_S242_L001_R1_001.fastq.gz.trim.fastq.gz 13-its2_S242_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"14-its2_S248_L001_R1_001.fastq.gz.trim.fastq.gz 14-its2_S248_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"14-its2_S248_L001_R1_001.fastq.gz.trim.fastq.gz 14-its2_S248_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"14-its2_S248_L001_R1_001.fastq.gz.trim.fastq.gz 14-its2_S248_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
+"14-its2_S248_L001_R1_001.fastq.gz.trim.fastq.gz 14-its2_S248_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"15-its2_S205_L001_R1_001.fastq.gz.trim.fastq.gz 15-its2_S205_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"15-its2_S205_L001_R1_001.fastq.gz.trim.fastq.gz 15-its2_S205_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"15-its2_S205_L001_R1_001.fastq.gz.trim.fastq.gz 15-its2_S205_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
+"15-its2_S205_L001_R1_001.fastq.gz.trim.fastq.gz 15-its2_S205_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"16-its2_S214_L001_R1_001.fastq.gz.trim.fastq.gz 16-its2_S214_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"16-its2_S214_L001_R1_001.fastq.gz.trim.fastq.gz 16-its2_S214_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"16-its2_S214_L001_R1_001.fastq.gz.trim.fastq.gz 16-its2_S214_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
+"16-its2_S214_L001_R1_001.fastq.gz.trim.fastq.gz 16-its2_S214_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"17-its2_S223_L001_R1_001.fastq.gz.trim.fastq.gz 17-its2_S223_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"17-its2_S223_L001_R1_001.fastq.gz.trim.fastq.gz 17-its2_S223_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"17-its2_S223_L001_R1_001.fastq.gz.trim.fastq.gz 17-its2_S223_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
+"17-its2_S223_L001_R1_001.fastq.gz.trim.fastq.gz 17-its2_S223_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"18-its2_S230_L001_R1_001.fastq.gz.trim.fastq.gz 18-its2_S230_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"18-its2_S230_L001_R1_001.fastq.gz.trim.fastq.gz 18-its2_S230_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"18-its2_S230_L001_R1_001.fastq.gz.trim.fastq.gz 18-its2_S230_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
+"18-its2_S230_L001_R1_001.fastq.gz.trim.fastq.gz 18-its2_S230_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"19-its2_S237_L001_R1_001.fastq.gz.trim.fastq.gz 19-its2_S237_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"19-its2_S237_L001_R1_001.fastq.gz.trim.fastq.gz 19-its2_S237_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"19-its2_S237_L001_R1_001.fastq.gz.trim.fastq.gz 19-its2_S237_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
+"19-its2_S237_L001_R1_001.fastq.gz.trim.fastq.gz 19-its2_S237_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"2-its2_S212_L001_R1_001.fastq.gz.trim.fastq.gz 2-its2_S212_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"2-its2_S212_L001_R1_001.fastq.gz.trim.fastq.gz 2-its2_S212_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"2-its2_S212_L001_R1_001.fastq.gz.trim.fastq.gz 2-its2_S212_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
+"2-its2_S212_L001_R1_001.fastq.gz.trim.fastq.gz 2-its2_S212_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"20-its2_S243_L001_R1_001.fastq.gz.trim.fastq.gz 20-its2_S243_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"20-its2_S243_L001_R1_001.fastq.gz.trim.fastq.gz 20-its2_S243_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"20-its2_S243_L001_R1_001.fastq.gz.trim.fastq.gz 20-its2_S243_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
+"20-its2_S243_L001_R1_001.fastq.gz.trim.fastq.gz 20-its2_S243_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"21-its2_S249_L001_R1_001.fastq.gz.trim.fastq.gz 21-its2_S249_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"21-its2_S249_L001_R1_001.fastq.gz.trim.fastq.gz 21-its2_S249_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"21-its2_S249_L001_R1_001.fastq.gz.trim.fastq.gz 21-its2_S249_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
+"21-its2_S249_L001_R1_001.fastq.gz.trim.fastq.gz 21-its2_S249_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"22-its2_S206_L001_R1_001.fastq.gz.trim.fastq.gz 22-its2_S206_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"22-its2_S206_L001_R1_001.fastq.gz.trim.fastq.gz 22-its2_S206_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"22-its2_S206_L001_R1_001.fastq.gz.trim.fastq.gz 22-its2_S206_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
+"22-its2_S206_L001_R1_001.fastq.gz.trim.fastq.gz 22-its2_S206_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
--- a/its2/primers_before_cutadapt_15Samples_31-01-22_0850.txt
+++ b/its2/primers_before_cutadapt_15Samples_31-01-22_0850.txt
+"Sample" "Primer_Read" "Forward" "Complement" "Reverse" "RevComp"
+"1-its2_S203_L001_R1_001.fastq.gz 1-its2_S203_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"1-its2_S203_L001_R1_001.fastq.gz 1-its2_S203_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"1-its2_S203_L001_R1_001.fastq.gz 1-its2_S203_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 52879
+"1-its2_S203_L001_R1_001.fastq.gz 1-its2_S203_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"10-its2_S222_L001_R1_001.fastq.gz 10-its2_S222_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"10-its2_S222_L001_R1_001.fastq.gz 10-its2_S222_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"10-its2_S222_L001_R1_001.fastq.gz 10-its2_S222_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 30017
+"10-its2_S222_L001_R1_001.fastq.gz 10-its2_S222_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"11-its2_S229_L001_R1_001.fastq.gz 11-its2_S229_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"11-its2_S229_L001_R1_001.fastq.gz 11-its2_S229_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"11-its2_S229_L001_R1_001.fastq.gz 11-its2_S229_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 43709
+"11-its2_S229_L001_R1_001.fastq.gz 11-its2_S229_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"12-its2_S236_L001_R1_001.fastq.gz 12-its2_S236_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"12-its2_S236_L001_R1_001.fastq.gz 12-its2_S236_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"12-its2_S236_L001_R1_001.fastq.gz 12-its2_S236_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 39733
+"12-its2_S236_L001_R1_001.fastq.gz 12-its2_S236_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"13-its2_S242_L001_R1_001.fastq.gz 13-its2_S242_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"13-its2_S242_L001_R1_001.fastq.gz 13-its2_S242_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 1
+"13-its2_S242_L001_R1_001.fastq.gz 13-its2_S242_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 35068
+"13-its2_S242_L001_R1_001.fastq.gz 13-its2_S242_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"14-its2_S248_L001_R1_001.fastq.gz 14-its2_S248_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"14-its2_S248_L001_R1_001.fastq.gz 14-its2_S248_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"14-its2_S248_L001_R1_001.fastq.gz 14-its2_S248_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 48663
+"14-its2_S248_L001_R1_001.fastq.gz 14-its2_S248_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"15-its2_S205_L001_R1_001.fastq.gz 15-its2_S205_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"15-its2_S205_L001_R1_001.fastq.gz 15-its2_S205_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"15-its2_S205_L001_R1_001.fastq.gz 15-its2_S205_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 36096
+"15-its2_S205_L001_R1_001.fastq.gz 15-its2_S205_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"16-its2_S214_L001_R1_001.fastq.gz 16-its2_S214_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"16-its2_S214_L001_R1_001.fastq.gz 16-its2_S214_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"16-its2_S214_L001_R1_001.fastq.gz 16-its2_S214_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 34323
+"16-its2_S214_L001_R1_001.fastq.gz 16-its2_S214_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"17-its2_S223_L001_R1_001.fastq.gz 17-its2_S223_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"17-its2_S223_L001_R1_001.fastq.gz 17-its2_S223_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"17-its2_S223_L001_R1_001.fastq.gz 17-its2_S223_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 38722
+"17-its2_S223_L001_R1_001.fastq.gz 17-its2_S223_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"18-its2_S230_L001_R1_001.fastq.gz 18-its2_S230_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"18-its2_S230_L001_R1_001.fastq.gz 18-its2_S230_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"18-its2_S230_L001_R1_001.fastq.gz 18-its2_S230_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 32818
+"18-its2_S230_L001_R1_001.fastq.gz 18-its2_S230_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"19-its2_S237_L001_R1_001.fastq.gz 19-its2_S237_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"19-its2_S237_L001_R1_001.fastq.gz 19-its2_S237_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 1
+"19-its2_S237_L001_R1_001.fastq.gz 19-its2_S237_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 32042
+"19-its2_S237_L001_R1_001.fastq.gz 19-its2_S237_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"2-its2_S212_L001_R1_001.fastq.gz 2-its2_S212_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"2-its2_S212_L001_R1_001.fastq.gz 2-its2_S212_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"2-its2_S212_L001_R1_001.fastq.gz 2-its2_S212_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 42114
+"2-its2_S212_L001_R1_001.fastq.gz 2-its2_S212_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"20-its2_S243_L001_R1_001.fastq.gz 20-its2_S243_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"20-its2_S243_L001_R1_001.fastq.gz 20-its2_S243_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"20-its2_S243_L001_R1_001.fastq.gz 20-its2_S243_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 40318
+"20-its2_S243_L001_R1_001.fastq.gz 20-its2_S243_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"21-its2_S249_L001_R1_001.fastq.gz 21-its2_S249_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"21-its2_S249_L001_R1_001.fastq.gz 21-its2_S249_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"21-its2_S249_L001_R1_001.fastq.gz 21-its2_S249_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 22455
+"21-its2_S249_L001_R1_001.fastq.gz 21-its2_S249_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"22-its2_S206_L001_R1_001.fastq.gz 22-its2_S206_L001_R2_001.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"22-its2_S206_L001_R1_001.fastq.gz 22-its2_S206_L001_R2_001.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 6
+"22-its2_S206_L001_R1_001.fastq.gz 22-its2_S206_L001_R2_001.fastq.gz" "REV_primer_R1_Reads" 0 0 0 36666
+"22-its2_S206_L001_R1_001.fastq.gz 22-its2_S206_L001_R2_001.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
--- a/its2/qualityplots_fwd.pdf
+++ b/its2/qualityplots_fwd.pdf
--- a/its2/qualityplots_rev.pdf
+++ b/its2/qualityplots_rev.pdf
--- a/its2/seqtab.nochim.txt
+++ b/its2/seqtab.nochim.txt
--- a/its2/seqtab.rds
+++ b/its2/seqtab.rds
--- a/its2/seqtab_nochim.rds
+++ b/its2/seqtab_nochim.rds
--- a/its2/track.txt
+++ b/its2/track.txt
+"input" "filtered" "denoisedF" "denoisedR" "merged" "nonchim" "percent_retained"
+"1-its2" 71344 16779 16522 16293 14823 14323 20.0759699484189
+"10-its2" 74196 18827 18540 18388 13071 12517 16.8701816809531
+"11-its2" 74777 12931 12627 12228 9724 9248 12.3674391858459
+"12-its2" 63049 9474 9056 8758 6802 6450 10.2301384637346
+"13-its2" 55444 6260 5936 5682 4387 4356 7.85657600461727
+"14-its2" 69735 8043 7667 7396 6402 6071 8.70581487058149
+"15-its2" 57198 3885 3606 3351 2772 2677 4.68023357460051
+"16-its2" 59013 8157 7772 7262 5862 5599 9.48773998949384
+"17-its2" 61411 7145 6770 6325 5053 4926 8.02136425070427
+"18-its2" 54728 8848 8541 7990 6525 6341 11.5863908785265
+"19-its2" 55093 9804 9390 8979 7108 6953 12.6204781006661
+"2-its2" 64257 13332 13010 12777 11665 11320 17.6167577073315
+"20-its2" 61047 8229 7957 7553 5943 5766 9.44518158140449
+"21-its2" 38999 3979 3749 3529 2700 2700 6.9232544424216
+"22-its2" 66325 11369 10984 10530 8088 7908 11.9231059178289
+"23-its2" 47593 5302 5075 4861 3766 3766 7.91292837181939
+"24-its2" 39861 3077 2884 2681 2252 2204 5.52921401871503
+"25-its2" 71081 8994 8700 8415 6601 6371 8.96301402625174
+"26-its2" 58781 8922 8616 8336 6927 6846 11.6466205066263
+"27-its2" 70765 8059 7766 7508 6682 6682 9.44252102027839
+"28-its2" 66554 10068 9761 9524 8334 8214 12.3418577395799
+"29-its2" 79984 12822 12507 12281 10451 10098 12.625025005001
+"3-its2" 65957 12898 12557 12235 9954 9545 14.4715496459815
+"30-its2" 79124 12552 12187 11814 9833 9514 12.0241646023962
+"31-its2" 67150 14996 14712 14430 11464 10926 16.271034996277
+"32-its2" 63058 10034 9791 9510 7872 7764 12.3124742300739
+"33-its2" 77900 11828 11582 11254 8873 8772 11.2605905006418
+"34-its2" 58528 9651 9385 9140 7969 7936 13.5593220338983
+"35-its2" 63014 11980 11728 11315 9271 9138 14.501539340464
+"36-its2" 63694 11707 11387 11140 9022 8750 13.7375576977423
+"37-its2" 83119 10387 10067 9740 8038 7932 9.54294445313346
+"38-its2" 60832 7490 7254 6950 6177 6128 10.0736454497633
+"39-its2" 78882 11400 11171 10879 9525 9246 11.7213052407393
+"4-its2" 63846 12839 12580 12326 10081 9855 15.4355793628418
+"40-its2" 88074 13475 13210 12828 10012 9677 10.9873515452915
+"42-its2" 83709 8574 8271 8069 6878 6656 7.9513552903511
+"43-its2" 13 1 1 1 1 1 7.69230769230769
+"44-its2" 68792 7272 7034 6829 5063 5011 7.28427724153971
+"45-its2" 60615 4702 4542 4306 3547 3536 5.83353955291595
+"46-its2" 79895 11931 11606 11265 8706 8477 10.6101758558108
+"5-its2" 90925 19505 19299 19058 16932 16528 18.1776189166896
+"6-its2" 79014 22759 22482 22245 19805 18827 23.8274229883312
+"7-its2" 93317 30284 30044 30044 27128 25362 27.1783276359077
+"8-its2" 83004 20610 20457 20329 16305 14942 18.0015420943569
+"9-its2" 75900 18205 17876 17519 12059 11719 15.4400527009223
+"NegK1-its2" 5 2 2 2 0 0 0
+"NegK2-its2" 11 6 6 6 6 6 54.5454545454545
+"Posk1-its2" 94270 7652 7643 7594 6605 5838 6.19285032353877
+"Posk2-its2" 79931 6349 6337 6296 5530 4914 6.14780247963869
+"Posk3-its2" 64913 5301 5289 5249 4539 4023 6.19752591930738
+"Posk4-its2" 73357 5231 5231 5199 4452 3955 5.39144185285658
+"V1-its2" 18 3 2 2 0 0 0
+"V3-its2" 29 11 8 4 4 4 13.7931034482759
+"41-its2" 2 0 NA NA NA NA NA
+"V2-its2" 1 0 NA NA NA NA NA
--- a/oomy/ASVs_raw.fasta
+++ b/oomy/ASVs_raw.fasta
--- a/oomy/ASVs_withtax.fasta
+++ b/oomy/ASVs_withtax.fasta
--- a/oomy/R1_error_profile.pdf
+++ b/oomy/R1_error_profile.pdf
--- a/oomy/R2_error_profile.pdf
+++ b/oomy/R2_error_profile.pdf
--- a/oomy/blast_nt_ASVs.txt
+++ b/oomy/blast_nt_ASVs.txt
--- a/oomy/mergers.txt
+++ b/oomy/mergers.txt
--- a/oomy/out.txt
+++ b/oomy/out.txt
+"reads.in" "reads.out"
+"1-oomy_S259_L001_R1_001.fastq.gz.trim.fastq.gz" 85907 33183
+"10-oomy_S278_L001_R1_001.fastq.gz.trim.fastq.gz" 101128 19966
+"11-oomy_S285_L001_R1_001.fastq.gz.trim.fastq.gz" 67297 37629
+"12-oomy_S292_L001_R1_001.fastq.gz.trim.fastq.gz" 41557 25763
+"13-oomy_S298_L001_R1_001.fastq.gz.trim.fastq.gz" 71622 25880
+"14-oomy_S304_L001_R1_001.fastq.gz.trim.fastq.gz" 80721 26353
+"15-oomy_S261_L001_R1_001.fastq.gz.trim.fastq.gz" 51981 32877
+"16-oomy_S270_L001_R1_001.fastq.gz.trim.fastq.gz" 47519 27368
+"17-oomy_S279_L001_R1_001.fastq.gz.trim.fastq.gz" 81116 44131
+"18-oomy_S286_L001_R1_001.fastq.gz.trim.fastq.gz" 56157 34810
+"19-oomy_S293_L001_R1_001.fastq.gz.trim.fastq.gz" 94819 33513
+"2-oomy_S268_L001_R1_001.fastq.gz.trim.fastq.gz" 75965 28155
+"20-oomy_S299_L001_R1_001.fastq.gz.trim.fastq.gz" 63277 24810
+"21-oomy_S305_L001_R1_001.fastq.gz.trim.fastq.gz" 81131 33646
+"22-oomy_S262_L001_R1_001.fastq.gz.trim.fastq.gz" 55975 20754
+"23-oomy_S271_L001_R1_001.fastq.gz.trim.fastq.gz" 46133 25467
+"24-oomy_S280_L001_R1_001.fastq.gz.trim.fastq.gz" 82867 32811
+"25-oomy_S287_L001_R1_001.fastq.gz.trim.fastq.gz" 84489 57461
+"26-oomy_S294_L001_R1_001.fastq.gz.trim.fastq.gz" 66357 35202
+"27-oomy_S300_L001_R1_001.fastq.gz.trim.fastq.gz" 82768 53187
+"28-oomy_S306_L001_R1_001.fastq.gz.trim.fastq.gz" 67103 34424
+"29-oomy_S263_L001_R1_001.fastq.gz.trim.fastq.gz" 51308 31949
+"3-oomy_S277_L001_R1_001.fastq.gz.trim.fastq.gz" 99250 58776
+"30-oomy_S272_L001_R1_001.fastq.gz.trim.fastq.gz" 35575 16929
+"31-oomy_S281_L001_R1_001.fastq.gz.trim.fastq.gz" 76422 16439
+"32-oomy_S288_L001_R1_001.fastq.gz.trim.fastq.gz" 89821 64163
+"33-oomy_S295_L001_R1_001.fastq.gz.trim.fastq.gz" 78771 30934
+"34-oomy_S301_L001_R1_001.fastq.gz.trim.fastq.gz" 71857 38698
+"35-oomy_S307_L001_R1_001.fastq.gz.trim.fastq.gz" 82429 10860
+"36-oomy_S313_L001_R1_001.fastq.gz.trim.fastq.gz" 40987 29154
+"37-oomy_S264_L001_R1_001.fastq.gz.trim.fastq.gz" 34437 23004
+"38-oomy_S273_L001_R1_001.fastq.gz.trim.fastq.gz" 58719 39450
+"39-oomy_S282_L001_R1_001.fastq.gz.trim.fastq.gz" 53649 34477
+"4-oomy_S284_L001_R1_001.fastq.gz.trim.fastq.gz" 100345 33670
+"40-oomy_S289_L001_R1_001.fastq.gz.trim.fastq.gz" 46095 31773
+"41-oomy_S296_L001_R1_001.fastq.gz.trim.fastq.gz" 52064 33819
+"42-oomy_S302_L001_R1_001.fastq.gz.trim.fastq.gz" 39566 28288
+"43-oomy_S308_L001_R1_001.fastq.gz.trim.fastq.gz" 71681 47668
+"44-oomy_S314_L001_R1_001.fastq.gz.trim.fastq.gz" 48066 27333
+"45-oomy_S265_L001_R1_001.fastq.gz.trim.fastq.gz" 71570 45759
+"46-oomy_S274_L001_R1_001.fastq.gz.trim.fastq.gz" 78449 60139
+"5-oomy_S291_L001_R1_001.fastq.gz.trim.fastq.gz" 43587 32263
+"6-oomy_S297_L001_R1_001.fastq.gz.trim.fastq.gz" 55994 31126
+"7-oomy_S303_L001_R1_001.fastq.gz.trim.fastq.gz" 78524 46217
+"8-oomy_S260_L001_R1_001.fastq.gz.trim.fastq.gz" 40541 25494
+"9-oomy_S269_L001_R1_001.fastq.gz.trim.fastq.gz" 50587 4663
+"NegK2-oomy_S275_L001_R1_001.fastq.gz.trim.fastq.gz" 1 0
+"Posk1-oomy_S267_L001_R1_001.fastq.gz.trim.fastq.gz" 1e+05 69188
+"Posk2-oomy_S276_L001_R1_001.fastq.gz.trim.fastq.gz" 158687 117521
+"Posk3-oomy_S283_L001_R1_001.fastq.gz.trim.fastq.gz" 107300 75056
+"Posk4-oomy_S290_L001_R1_001.fastq.gz.trim.fastq.gz" 118546 84581
+"V3-oomy_S311_L001_R1_001.fastq.gz.trim.fastq.gz" 1 0
--- a/oomy/parameters_both26-01-22_0917.txt
+++ b/oomy/parameters_both26-01-22_0917.txt
+"x"
+"Run on 26/01/22 09:17
+Path:  /home/simeon/Documents/Sunniva_felt21
+Samples:
+1-oomy;10-oomy;11-oomy;12-oomy;13-oomy;14-oomy;15-oomy;16-oomy;17-oomy;18-oomy;19-oomy;2-oomy;20-oomy;21-oomy;22-oomy;23-oomy;24-oomy;25-oomy;26-oomy;27-oomy;28-oomy;29-oomy;3-oomy;30-oomy;31-oomy;32-oomy;33-oomy;34-oomy;35-oomy;36-oomy;37-oomy;38-oomy;39-oomy;4-oomy;40-oomy;41-oomy;42-oomy;43-oomy;44-oomy;45-oomy;46-oomy;5-oomy;6-oomy;7-oomy;8-oomy;9-oomy;NegK2-oomy;Posk1-oomy;Posk2-oomy;Posk3-oomy;Posk4-oomy;V3-oomy
+Analysis type: both
+Database type: /home/simeon/Documents/tax_DBs/ITS1_databases/OomyceteDB/CoFiMiO3_OomycITS1_dada2_DB.fa
+dada2 Parameters
+maximum expected errors R1: 2
+maximum expected errors R2: 2
+minimum length:  100
+truncate at first instance of Qscore:  2
+truncation at length (0 = no trunc) 0,truncation at length (0 = no trunc) 0
+minimum overlap during merging:  30
+taxonomy bootstrap threshold:  80
+Collapse overlapping ASVs:  FALSE
+Minimum overlap if collapsing overlapping ASVs: 200
+Trimming 5' (R1, R2): 10,10"
--- a/oomy/primers_after_cutadapt_15Samples_26-01-22_0916.txt
+++ b/oomy/primers_after_cutadapt_15Samples_26-01-22_0916.txt
+"Sample" "Primer_Read" "Forward" "Complement" "Reverse" "RevComp"
+"1-oomy_S259_L001_R1_001.fastq.gz.trim.fastq.gz 1-oomy_S259_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"1-oomy_S259_L001_R1_001.fastq.gz.trim.fastq.gz 1-oomy_S259_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"1-oomy_S259_L001_R1_001.fastq.gz.trim.fastq.gz 1-oomy_S259_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
+"1-oomy_S259_L001_R1_001.fastq.gz.trim.fastq.gz 1-oomy_S259_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"10-oomy_S278_L001_R1_001.fastq.gz.trim.fastq.gz 10-oomy_S278_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"10-oomy_S278_L001_R1_001.fastq.gz.trim.fastq.gz 10-oomy_S278_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"10-oomy_S278_L001_R1_001.fastq.gz.trim.fastq.gz 10-oomy_S278_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
+"10-oomy_S278_L001_R1_001.fastq.gz.trim.fastq.gz 10-oomy_S278_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R2_Reads" 0 0 0 0
+"11-oomy_S285_L001_R1_001.fastq.gz.trim.fastq.gz 11-oomy_S285_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R1_Reads" 0 0 0 0
+"11-oomy_S285_L001_R1_001.fastq.gz.trim.fastq.gz 11-oomy_S285_L001_R2_001.fastq.gz.trim.fastq.gz" "FWD_primer_R2_Reads" 0 0 0 0
+"11-oomy_S285_L001_R1_001.fastq.gz.trim.fastq.gz 11-oomy_S285_L001_R2_001.fastq.gz.trim.fastq.gz" "REV_primer_R1_Reads" 0 0 0 0
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