Starting /dee2/code/volunteer_pipeline.sh SRR5578508 current disk space = 1521995362304 free memory = 1387224884 SRR5578508 SRAfilesize 1db9ca64c6721b5b980e1a715d76c61b SRR5578508.sra SRR5578508.sra file validated SRR5578508 is paired end SRR5578508 is conventional basespace SRR5578508 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5578508_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.78125 34.0 34.0 34.0 33.0 34.0 2 33.4915 34.0 34.0 34.0 33.0 34.0 3 33.553 34.0 34.0 34.0 33.0 34.0 4 33.6055 34.0 34.0 34.0 33.0 34.0 5 33.64575 34.0 34.0 34.0 33.0 34.0 6 37.363 38.0 38.0 38.0 36.0 38.0 7 37.512 38.0 38.0 38.0 37.0 38.0 8 37.61275 38.0 38.0 38.0 38.0 38.0 9 37.65725 38.0 38.0 38.0 38.0 38.0 10-14 37.656099999999995 38.0 38.0 38.0 38.0 38.0 15-19 37.654199999999996 38.0 38.0 38.0 38.0 38.0 20-24 37.6276 38.0 38.0 38.0 38.0 38.0 25-29 37.5981 38.0 38.0 38.0 38.0 38.0 30-34 37.5612 38.0 38.0 38.0 38.0 38.0 35-39 37.51595 38.0 38.0 38.0 38.0 38.0 40-44 37.38885 38.0 38.0 38.0 38.0 38.0 45-49 37.366 38.0 38.0 38.0 38.0 38.0 50-54 37.3447 38.0 38.0 38.0 37.4 38.0 55-59 37.30735 38.0 38.0 38.0 37.0 38.0 60-64 37.268600000000006 38.0 38.0 38.0 37.0 38.0 65-69 37.195049999999995 38.0 38.0 38.0 37.0 38.0 70-74 37.1114 38.0 38.0 38.0 36.8 38.0 75-79 36.9105 38.0 38.0 38.0 36.4 38.0 80-84 36.85585 38.0 38.0 38.0 36.2 38.0 85-89 36.78145 38.0 38.0 38.0 36.0 38.0 90-94 36.66275 38.0 38.0 38.0 35.8 38.0 95-99 36.5906 38.0 38.0 38.0 35.2 38.0 100-104 36.439949999999996 38.0 38.0 38.0 35.0 38.0 105-109 36.339099999999995 38.0 38.0 38.0 34.8 38.0 110-114 36.226350000000004 38.0 38.0 38.0 34.0 38.0 115-119 36.07365 38.0 38.0 38.0 33.8 38.0 120-124 35.9602 38.0 38.0 38.0 33.8 38.0 125-129 35.7932 38.0 37.6 38.0 33.0 38.0 130-134 35.49504999999999 38.0 36.2 38.0 32.0 38.0 135-139 35.3128 38.0 36.0 38.0 31.2 38.0 140-144 34.82705 38.0 35.6 38.0 28.6 38.0 145-149 34.381150000000005 38.0 35.0 38.0 27.4 38.0 150-151 30.884875 36.5 29.5 38.0 12.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 2.0 7 2.0 8 2.0 9 2.0 10 1.0 11 1.0 12 5.0 13 1.0 14 1.0 15 6.0 16 5.0 17 3.0 18 12.0 19 18.0 20 4.0 21 2.0 22 6.0 23 8.0 24 7.0 25 11.0 26 7.0 27 14.0 28 16.0 29 16.0 30 28.0 31 30.0 32 27.0 33 55.0 34 78.0 35 177.0 36 523.0 37 2930.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.119096509240244 10.805954825462011 11.498973305954825 36.57597535934292 2 25.1 14.575 31.275 29.049999999999997 3 23.311655827913956 19.534767383691847 24.262131065532767 32.89144572286143 4 26.375 25.324999999999996 22.2 26.1 5 25.525 29.025000000000002 25.3 20.150000000000002 6 22.55 32.4 24.625 20.424999999999997 7 16.650000000000002 25.45 39.725 18.175 8 19.25 25.75 30.55 24.45 9 20.275000000000002 22.75 33.800000000000004 23.175 10-14 22.009999999999998 29.315 25.695 22.98 15-19 22.185 27.21 26.47 24.135 20-24 22.27 27.21 26.575 23.945 25-29 21.395 28.110000000000003 26.27 24.224999999999998 30-34 21.597159715971596 28.6028602860286 25.352535253525353 24.44744474447445 35-39 22.042204220422043 27.362736273627362 26.147614761476145 24.44744474447445 40-44 22.659531906381275 27.18043608721744 25.170034006801362 24.989997999599918 45-49 22.672267226722674 27.34773477347735 26.122612261226124 23.857385738573857 50-54 23.1 27.275 25.46 24.165 55-59 23.145 26.735 25.695 24.425 60-64 22.134999999999998 27.115000000000002 25.71 25.040000000000003 65-69 22.33 28.07 24.85 24.75 70-74 22.175 27.455000000000002 25.66 24.709999999999997 75-79 22.255 27.395000000000003 25.009999999999998 25.34 80-84 22.52 27.095000000000002 25.21 25.174999999999997 85-89 22.925 26.875 25.705 24.495 90-94 22.49 27.084999999999997 25.03 25.395 95-99 23.04 25.56 26.265 25.135 100-104 23.085 26.87 25.124999999999996 24.92 105-109 23.23 27.060000000000002 25.025 24.685000000000002 110-114 22.895 26.779999999999998 25.080000000000002 25.245 115-119 22.650000000000002 26.900000000000002 24.935 25.515 120-124 23.16310708748062 26.499274746161156 24.443555244335517 25.89406292202271 125-129 23.200080052033822 27.6529744333817 24.010606894481413 25.136338620103064 130-134 23.472604453340004 27.010257693269953 24.008006004503375 25.509131848886664 135-139 22.39559889972493 27.2768192048012 24.63115778944736 25.696424106026505 140-144 22.96114805740287 26.856342817140856 24.521226061303064 25.661283064153206 145-149 22.245 27.725 24.07 25.96 150-151 22.329246935201404 25.41906429822367 25.03127345509132 27.220415311483613 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 6.0 1 4.0 2 1.5 3 1.5 4 2.0 5 1.0 6 0.5 7 1.0 8 1.5 9 1.0 10 0.0 11 1.0 12 1.0 13 0.0 14 0.0 15 0.0 16 0.5 17 0.5 18 0.0 19 0.5 20 1.0 21 0.5 22 0.0 23 0.0 24 0.5 25 0.5 26 1.0 27 2.5 28 7.0 29 14.0 30 18.5 31 31.0 32 36.5 33 47.5 34 61.0 35 69.0 36 93.0 37 127.5 38 141.0 39 131.0 40 146.5 41 146.5 42 155.0 43 178.5 44 175.5 45 167.5 46 166.0 47 158.0 48 149.0 49 157.5 50 154.0 51 136.0 52 128.0 53 132.5 54 118.5 55 101.0 56 105.0 57 100.5 58 86.0 59 76.5 60 57.5 61 42.5 62 34.0 63 34.0 64 44.5 65 45.0 66 38.5 67 32.0 68 25.0 69 21.0 70 16.5 71 11.5 72 12.0 73 13.0 74 9.5 75 6.5 76 6.0 77 4.0 78 3.0 79 1.5 80 0.0 81 0.5 82 0.5 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 2.6 2 0.0 3 0.05 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.01 35-39 0.01 40-44 0.02 45-49 0.01 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.034999999999999996 125-129 0.065 130-134 0.075 135-139 0.025 140-144 0.005 145-149 0.0 150-151 0.075 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 92.25 #Duplication Level Percentage of deduplicated Percentage of total 1 95.96205962059621 88.52499999999999 2 2.7642276422764227 5.1 3 0.5420054200542005 1.5 4 0.21680216802168023 0.8 5 0.08130081300813008 0.375 6 0.10840108401084012 0.6 7 0.16260162601626016 1.05 8 0.02710027100271003 0.2 9 0.0 0.0 >10 0.13550135501355012 1.8499999999999999 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source GATCGGAAGAGCACACGTCTGAACTCCAGTCACACATCTATCTCGTATGC 23 0.575 TruSeq Adapter, Index 8 (97% over 37bp) GCCTTATGTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGA 17 0.42500000000000004 No Hit GCCTCACTTAGTTACAGTTTTATGGATAATTGGGATATTCTTTGGTATAG 13 0.325 No Hit CTTATGTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGAGT 11 0.27499999999999997 No Hit GGGGTTATGAGTAGGGATGAGCATAAACCAACAACTCTCAAAGAAGATGG 10 0.25 No Hit GGGCTATTGATATTTAACAAATATCCAGCAAAGGTTTTTCCAGGAGATGT 8 0.2 No Hit TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 7 0.17500000000000002 No Hit CCAGGAGATGTTGGAACTCTACCAATTGGAGCTTTCTTAGCTGTCTTAGC 7 0.17500000000000002 No Hit CCCATTTTTAGTTATAATGATGCCTTATGTGATAGATGCCTCTTTAAAAT 7 0.17500000000000002 No Hit GTGGCTATCTATCCCTACCAAGGCTTATATTGAAGTATAAACCAATGAGA 7 0.17500000000000002 No Hit GGGGATAATTGCGCGGTTTTGACTGCGGAAGGAAGCCAAGGCCCACCTAA 7 0.17500000000000002 No Hit GGAAGCTATACTATATAGGTGGCTATCTATCCCTACCAAGGCTTATATTG 7 0.17500000000000002 No Hit GATGCCTTATGTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTA 6 0.15 No Hit GCGTGGTAGAATTACTGGCACTCCAATGATTCCATATAACGGCCATAATG 6 0.15 No Hit GCTATCTATCCCTACCAAGGCTTATATTGAAGTATAAACCAATGAGAGAG 6 0.15 No Hit GTTTGGTTAAAGAACAGTCGCAGTTTTCCTCAAATCCCGCCACGAAACTA 6 0.15 No Hit GCAGTAGTTTATAAGGAATATATCCCATTTTTAGTTATAATGATGCCTTA 5 0.125 No Hit GAGCTTTCTTAGCTGTCTTAGCAGTAGTTTATAAGGAATATATCCCATTT 5 0.125 No Hit GGGGAACAGTCGCATGACGAGGCAGTTTCCAGAAACGTGTATCACATCTA 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0125 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.07500000000000001 0.0 0.0 0.0 0.0 76-77 0.1375 0.0 0.0 0.0 0.0 78-79 0.225 0.0 0.0 0.0 0.0 80-81 0.3625 0.0 0.0 0.0 0.0 82-83 0.3875 0.0 0.0 0.0 0.0 84-85 0.5125 0.0 0.0 0.0 0.0 86-87 0.6375 0.0 0.0 0.0 0.0 88-89 0.6875 0.0 0.0 0.0 0.0 90-91 0.8 0.0 0.0 0.0 0.0 92-93 0.9375 0.0 0.0 0.0 0.0 94-95 1.1625 0.0 0.0 0.0 0.0 96-97 1.4625 0.0 0.0 0.0 0.0 98-99 1.6749999999999998 0.0 0.0 0.0 0.0 100-101 1.9625000000000001 0.0 0.0 0.0 0.0 102-103 2.4375 0.0 0.0 0.0 0.0 104-105 2.8875 0.0 0.0 0.0 0.0 106-107 3.3625 0.0 0.0 0.0 0.0 108-109 4.1125 0.0 0.0 0.0 0.0 110-111 4.8125 0.0 0.0 0.0 0.0 112-113 5.575 0.0 0.0 0.0 0.0 114-115 6.487500000000001 0.0 0.0 0.0 0.0 116-117 7.1375 0.0 0.0 0.0 0.0 118-119 7.725 0.0 0.0 0.0 0.0 120-121 8.4 0.0 0.0 0.0 0.0 122-123 9.05 0.0 0.0 0.0 0.0 124-125 10.125 0.0 0.0 0.0 0.0 126-127 11.1875 0.0 0.0 0.0 0.0 128-129 12.125 0.0 0.0 0.0 0.0 130-131 12.8875 0.0 0.0 0.0 0.0 132-133 13.975 0.0 0.0 0.0 0.0 134-135 15.0625 0.0 0.0 0.0 0.0 136-137 16.15 0.0 0.0 0.0 0.0 138-139 17.0625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGCACAG 10 0.0068343505 144.975 7 TAGCTCA 10 0.0068343505 144.975 3 CTGCACA 10 0.0068343505 144.975 6 AACTCCA 40 0.0056251725 54.365623 145 >>END_MODULE SRR5578508 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5578508_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.00575 33.0 33.0 34.0 32.0 34.0 2 33.1355 34.0 33.0 34.0 33.0 34.0 3 33.10025 34.0 33.0 34.0 33.0 34.0 4 33.06825 34.0 33.0 34.0 33.0 34.0 5 33.128 34.0 33.0 34.0 33.0 34.0 6 37.23475 38.0 38.0 38.0 37.0 38.0 7 37.215 38.0 38.0 38.0 37.0 38.0 8 37.268 38.0 38.0 38.0 37.0 38.0 9 37.1955 38.0 38.0 38.0 37.0 38.0 10-14 37.226350000000004 38.0 38.0 38.0 37.6 38.0 15-19 37.1924 38.0 38.0 38.0 37.0 38.0 20-24 37.2059 38.0 38.0 38.0 37.0 38.0 25-29 37.254450000000006 38.0 38.0 38.0 38.0 38.0 30-34 37.218650000000004 38.0 38.0 38.0 37.6 38.0 35-39 37.20705 38.0 38.0 38.0 37.6 38.0 40-44 37.182050000000004 38.0 38.0 38.0 37.0 38.0 45-49 37.15794999999999 38.0 38.0 38.0 37.0 38.0 50-54 37.1226 38.0 38.0 38.0 37.0 38.0 55-59 37.1431 38.0 38.0 38.0 37.0 38.0 60-64 37.0556 38.0 38.0 38.0 37.0 38.0 65-69 36.9586 38.0 38.0 38.0 36.6 38.0 70-74 36.7028 38.0 38.0 38.0 36.0 38.0 75-79 36.65140000000001 38.0 38.0 38.0 36.0 38.0 80-84 36.6478 38.0 38.0 38.0 36.0 38.0 85-89 36.536249999999995 38.0 38.0 38.0 35.4 38.0 90-94 36.50715 38.0 38.0 38.0 35.0 38.0 95-99 36.3402 38.0 38.0 38.0 34.8 38.0 100-104 36.08454999999999 38.0 38.0 38.0 34.0 38.0 105-109 35.9392 38.0 38.0 38.0 33.8 38.0 110-114 35.758 38.0 38.0 38.0 32.8 38.0 115-119 35.4956 38.0 37.4 38.0 31.8 38.0 120-124 35.29344999999999 38.0 36.6 38.0 31.0 38.0 125-129 34.96835 38.0 36.0 38.0 29.6 38.0 130-134 34.61045 38.0 35.8 38.0 27.6 38.0 135-139 34.149 38.0 34.6 38.0 25.0 38.0 140-144 33.3217 38.0 33.0 38.0 20.2 38.0 145-149 31.8499 38.0 32.6 38.0 8.2 38.0 150-151 26.31975 33.0 16.5 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 12.0 3 2.0 4 0.0 5 3.0 6 1.0 7 1.0 8 0.0 9 2.0 10 1.0 11 3.0 12 2.0 13 3.0 14 6.0 15 4.0 16 6.0 17 24.0 18 6.0 19 3.0 20 6.0 21 10.0 22 13.0 23 7.0 24 12.0 25 10.0 26 13.0 27 17.0 28 29.0 29 18.0 30 41.0 31 54.0 32 62.0 33 81.0 34 153.0 35 231.0 36 638.0 37 2526.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.175 18.099999999999998 14.499999999999998 28.225 2 29.599999999999998 24.275 26.075 20.05 3 24.575 25.474999999999998 27.625 22.325 4 27.075 30.2 22.2 20.525 5 27.800000000000004 34.025 19.950000000000003 18.224999999999998 6 24.25 34.699999999999996 19.825 21.224999999999998 7 23.95 19.85 34.35 21.85 8 24.7 23.799999999999997 22.525000000000002 28.975 9 24.55 23.775 27.150000000000002 24.525 10-14 25.85 26.31 22.96 24.88 15-19 26.075 25.16 24.834999999999997 23.93 20-24 26.31 26.11 24.23 23.35 25-29 26.590000000000003 25.290000000000003 24.709999999999997 23.41 30-34 26.52 25.130000000000003 25.155 23.195 35-39 25.840000000000003 24.9 25.03 24.23 40-44 26.855 24.43 24.990000000000002 23.724999999999998 45-49 26.615 24.02 25.985000000000003 23.380000000000003 50-54 25.655 23.96 26.625 23.76 55-59 25.779999999999998 25.124999999999996 26.424999999999997 22.67 60-64 24.865000000000002 25.180000000000003 26.669999999999998 23.285 65-69 25.35 25.91 26.035000000000004 22.705000000000002 70-74 24.779999999999998 25.545 26.334999999999997 23.34 75-79 24.375 25.745 25.805 24.075 80-84 24.81 26.334999999999997 25.995 22.86 85-89 24.98 26.41 25.779999999999998 22.830000000000002 90-94 25.319999999999997 26.279999999999998 26.150000000000002 22.25 95-99 24.915000000000003 26.840000000000003 25.724999999999998 22.52 100-104 25.45 26.640000000000004 25.665 22.245 105-109 25.014999999999997 27.189999999999998 25.814999999999998 21.98 110-114 24.945 26.939999999999998 25.345000000000002 22.770000000000003 115-119 25.745 27.375 25.395 21.485000000000003 120-124 26.52 26.584999999999997 25.21 21.685 125-129 26.325 27.155 25.035 21.485000000000003 130-134 26.729999999999997 26.75 25.674999999999997 20.845 135-139 26.83 27.555000000000003 25.174999999999997 20.44 140-144 28.155 26.195 25.47 20.18 145-149 28.199999999999996 26.490000000000002 24.895 20.415 150-151 28.5875 26.0125 25.7375 19.662499999999998 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.5 7 0.5 8 0.0 9 0.0 10 0.5 11 0.5 12 0.0 13 0.5 14 0.5 15 0.0 16 0.5 17 0.5 18 0.0 19 0.5 20 0.5 21 0.5 22 0.5 23 0.0 24 0.0 25 0.5 26 1.0 27 1.5 28 3.0 29 8.0 30 10.0 31 13.0 32 21.5 33 25.5 34 32.5 35 44.5 36 52.0 37 76.0 38 111.0 39 131.0 40 153.0 41 147.5 42 130.5 43 150.0 44 163.5 45 166.5 46 173.0 47 181.5 48 168.5 49 151.0 50 156.0 51 155.5 52 151.5 53 148.0 54 139.5 55 135.5 56 127.5 57 108.0 58 97.0 59 81.0 60 58.0 61 56.0 62 58.5 63 53.0 64 47.5 65 42.0 66 39.0 67 39.5 68 37.5 69 29.0 70 23.0 71 22.0 72 17.5 73 14.0 74 11.5 75 7.0 76 7.0 77 6.0 78 4.5 79 2.5 80 1.5 81 1.5 82 0.5 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 90.0 #Duplication Level Percentage of deduplicated Percentage of total 1 95.58333333333333 86.02499999999999 2 2.555555555555556 4.6 3 1.0 2.7 4 0.16666666666666669 0.6 5 0.19444444444444445 0.8750000000000001 6 0.1111111111111111 0.6 7 0.027777777777777776 0.17500000000000002 8 0.05555555555555555 0.4 9 0.0 0.0 >10 0.3055555555555556 4.025 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 23 0.575 Illumina Single End PCR Primer 1 (100% over 50bp) GGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTC 18 0.44999999999999996 No Hit AATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGA 17 0.42500000000000004 No Hit CATTAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAAT 15 0.375 No Hit GCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCC 15 0.375 No Hit GAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCC 15 0.375 No Hit CCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATGGT 14 0.35000000000000003 No Hit CTTCAATATAAGCCTTGGTAGGGATAGATAGCCACCTATATAGTATAGCT 12 0.3 No Hit ATTAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATA 12 0.3 No Hit GGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTT 10 0.25 No Hit CCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATGG 10 0.25 No Hit GGGATAGATAGCCACCTATATAGTATAGCTTCCCATCTTCTTTGAGAGTT 8 0.2 No Hit GGGAGGTATCCCAATAGGAGGTTTCCTCCTATGGTTTTCAAAACAATCAC 8 0.2 No Hit TAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGT 7 0.17500000000000002 No Hit AAAGAATATCCCAATTATCCATAAAACTGTAACTAAGTGAGGCTCTCTCA 6 0.15 No Hit ATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAG 6 0.15 No Hit TAGGAATGGGAGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGATG 6 0.15 No Hit TAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGG 6 0.15 No Hit AAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTA 5 0.125 No Hit CTCTCTCATTGGTTTATACTTCAATATAAGCCTTGGTAGGGATAGATAGC 5 0.125 No Hit CTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATGGTT 5 0.125 No Hit AGAATATCCCAATTATCCATAAAACTGTAACTAAGTGAGGCTCTCTCATT 5 0.125 No Hit GCCCAAGCTGCTCACAGTATACGGGCGTCGGCATCCAGACCGTCGGCTGA 5 0.125 No Hit CAAAGAATATCCCAATTATCCATAAAACTGTAACTAAGTGAGGCTCTCTC 5 0.125 No Hit GGAGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGATGGTTTTTAC 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0125 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.07500000000000001 0.0 0.0 0.0 0.0 76-77 0.1375 0.0 0.0 0.0 0.0 78-79 0.225 0.0 0.0 0.0 0.0 80-81 0.3625 0.0 0.0 0.0 0.0 82-83 0.3875 0.0 0.0 0.0 0.0 84-85 0.5125 0.0 0.0 0.0 0.0 86-87 0.6875 0.0 0.0 0.0 0.0 88-89 0.7625 0.0 0.0 0.0 0.0 90-91 0.875 0.0 0.0 0.0 0.0 92-93 1.0125 0.0 0.0 0.0 0.0 94-95 1.25 0.0 0.0 0.0 0.0 96-97 1.5625 0.0 0.0 0.0 0.0 98-99 1.775 0.0 0.0 0.0 0.0 100-101 2.025 0.0 0.0 0.0 0.0 102-103 2.4875 0.0 0.0 0.0 0.0 104-105 2.8875 0.0 0.0 0.0 0.0 106-107 3.3875 0.0 0.0 0.0 0.0 108-109 4.125 0.0 0.0 0.0 0.0 110-111 4.875 0.0 0.0 0.0 0.0 112-113 5.625 0.0 0.0 0.0 0.0 114-115 6.5125 0.0 0.0 0.0 0.0 116-117 7.1875 0.0 0.0 0.0 0.0 118-119 7.85 0.0 0.0 0.0 0.0 120-121 8.575 0.0 0.0 0.0 0.0 122-123 9.275 0.0 0.0 0.0 0.0 124-125 10.3625 0.0 0.0 0.0 0.0 126-127 11.3875 0.0 0.0 0.0 0.0 128-129 12.3125 0.0 0.0 0.0 0.0 130-131 13.087499999999999 0.0 0.0 0.0 0.0 132-133 14.1375 0.0 0.0 0.0 0.0 134-135 15.149999999999999 0.0 0.0 0.0 0.0 136-137 16.237499999999997 0.0 0.0 0.0 0.0 138-139 17.125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGCTTCT 10 0.006830828 145.0 5 >>END_MODULE Read 781786 spots for SRR5578508.sra Written 781786 spots for SRR5578508.sra Read 781786 spots for SRR5578508.sra Written 781786 spots for SRR5578508.sra Read 781786 spots for SRR5578508.sra Written 781786 spots for SRR5578508.sra Read 781786 spots for SRR5578508.sra Written 781786 spots for SRR5578508.sra Read 781786 spots for SRR5578508.sra Written 781786 spots for SRR5578508.sra Read 781786 spots for SRR5578508.sra Written 781786 spots for SRR5578508.sra Read 781786 spots for SRR5578508.sra Written 781786 spots for SRR5578508.sra Read 781786 spots for SRR5578508.sra Written 781786 spots for SRR5578508.sra Read 781786 spots for SRR5578508.sra Written 781786 spots for SRR5578508.sra Read 781786 spots for SRR5578508.sra Written 781786 spots for SRR5578508.sra Read 781793 spots for SRR5578508.sra Written 781793 spots for SRR5578508.sra Read 781786 spots for SRR5578508.sra Written 781786 spots for SRR5578508.sra Read 781786 spots for SRR5578508.sra Written 781786 spots for SRR5578508.sra Read 781786 spots for SRR5578508.sra Written 781786 spots for SRR5578508.sra Read 781786 spots for SRR5578508.sra Written 781786 spots for SRR5578508.sra Read 781786 spots for SRR5578508.sra Written 781786 spots for SRR5578508.sra Read 781786 spots for SRR5578508.sra Written 781786 spots for SRR5578508.sra Read 781786 spots for SRR5578508.sra Written 781786 spots for SRR5578508.sra Read 781786 spots for SRR5578508.sra Written 781786 spots for SRR5578508.sra Read 781786 spots for SRR5578508.sra Written 781786 spots for SRR5578508.sra SRR ids: ['SRR5578508.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_gukteobf SRR5578508.sra spots: 15635727 blocks: [[1, 781786], [781787, 1563572], [1563573, 2345358], [2345359, 3127144], [3127145, 3908930], [3908931, 4690716], [4690717, 5472502], [5472503, 6254288], [6254289, 7036074], [7036075, 7817860], [7817861, 8599646], [8599647, 9381432], [9381433, 10163218], [10163219, 10945004], [10945005, 11726790], [11726791, 12508576], [12508577, 13290362], [13290363, 14072148], [14072149, 14853934], [14853935, 15635727]] SRR5578508 file size 5276734 SRR5578508 completed basic pipeline successfully skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -q 10 -k inf -t 20 -o SRR5578508 SRR5578508_1.fastq SRR5578508_2.fastq Input file: SRR5578508_1.fastq Paired file: SRR5578508_2.fastq trimmed: SRR5578508-trimmed-pair1.fastq, SRR5578508-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Mon Dec 9 21:23:02 2024 >> started Mon Dec 9 21:23:26 2024 >> done (24.615s) 15635727 read pairs processed; of these: 28666 ( 0.18%) short read pairs filtered out after trimming by size control 101662 ( 0.65%) empty read pairs filtered out after trimming by size control 15505399 (99.17%) read pairs available; of these: 8411523 (54.25%) trimmed read pairs available after processing 7093876 (45.75%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 10 0.00% 19 13 0.00% 20 9 0.00% 21 16 0.00% 22 21 0.00% 23 19 0.00% 24 22 0.00% 25 15 0.00% 26 31 0.00% 27 23 0.00% 28 29 0.00% 29 17 0.00% 30 31 0.00% 31 30 0.00% 32 38 0.00% 33 37 0.00% 34 45 0.00% 35 50 0.00% 36 59 0.00% 37 48 0.00% 38 37 0.00% 39 55 0.00% 40 65 0.00% 41 61 0.00% 42 78 0.00% 43 104 0.00% 44 97 0.00% 45 112 0.00% 46 133 0.00% 47 157 0.00% 48 175 0.00% 49 210 0.00% 50 208 0.00% 51 269 0.00% 52 257 0.00% 53 291 0.00% 54 285 0.00% 55 350 0.00% 56 391 0.00% 57 484 0.00% 58 540 0.00% 59 523 0.00% 60 596 0.00% 61 687 0.00% 62 839 0.01% 63 906 0.01% 64 1019 0.01% 65 1228 0.01% 66 1475 0.01% 67 1924 0.01% 68 2651 0.02% 69 6684 0.04% 70 6372 0.04% 71 3403 0.02% 72 3114 0.02% 73 3365 0.02% 74 3669 0.02% 75 3916 0.03% 76 4243 0.03% 77 4706 0.03% 78 5411 0.03% 79 5994 0.04% 80 6709 0.04% 81 7439 0.05% 82 8734 0.06% 83 10027 0.06% 84 12201 0.08% 85 14087 0.09% 86 15416 0.10% 87 17138 0.11% 88 18594 0.12% 89 19231 0.12% 90 20218 0.13% 91 21396 0.14% 92 22653 0.15% 93 24001 0.15% 94 25885 0.17% 95 27568 0.18% 96 28863 0.19% 97 30228 0.19% 98 31682 0.20% 99 33066 0.21% 100 35100 0.23% 101 36606 0.24% 102 38347 0.25% 103 40853 0.26% 104 43446 0.28% 105 45631 0.29% 106 47746 0.31% 107 49393 0.32% 108 50964 0.33% 109 51599 0.33% 110 52982 0.34% 111 55073 0.36% 112 58046 0.37% 113 61310 0.40% 114 65059 0.42% 115 67727 0.44% 116 68903 0.44% 117 68693 0.44% 118 68847 0.44% 119 69687 0.45% 120 72018 0.46% 121 72683 0.47% 122 74979 0.48% 123 77055 0.50% 124 79570 0.51% 125 81618 0.53% 126 84034 0.54% 127 85080 0.55% 128 84458 0.54% 129 87976 0.57% 130 86678 0.56% 131 88203 0.57% 132 90506 0.58% 133 93517 0.60% 134 96170 0.62% 135 96843 0.62% 136 99487 0.64% 137 100902 0.65% 138 104894 0.68% 139 107069 0.69% 140 110339 0.71% 141 111955 0.72% 142 120873 0.78% 143 125943 0.81% 144 134609 0.87% 145 149882 0.97% 146 172343 1.11% 147 209859 1.35% 148 292349 1.89% 149 567668 3.66% 150 3113168 20.08% 151 7093876 45.75% 15505399 reads passed initial QC criterion=sequence-density sequence-density=0.26 sequence-density-rank=1 fanout-score=21.96 fanout-score-rank=3 prefix-density=2.98 prefix-fanout=1.9 sequence=TTCGTTTTTTTTCTTG criterion=fanout-score sequence-density=0.01 sequence-density-rank=41 fanout-score=35.45 fanout-score-rank=1 prefix-density=0.28 prefix-fanout=1.7 sequence=TTTTTTTTCCAGAATTCAAGACGTTAACAGTTCTTGGCGCAAATAGCGCTGAATCGCTTCTTTAAAGGCTGCAGCGTCGTCCTCAAATTTCGCACTGACCATAATGTGATCCCTTCCGGCGGTCGGTATAAAATCAGGCAGTTTTTGATCACGTTTATTGTAAGCCGTCAGCATCGGGATATCATCTGCTTCAAGCTCCTCAAGCAGCCGAAGCACTGTTTTTTCATGTCCCGCATAATCCTCATTTGAAGAATCAATTAAATGCAGAATTAAATCCGCTTCTTTTACTTCCTCAAGCGTTGAGCGGAATGCAGCAATCAATGTCGTCGGAAGATCCTGAATAAATCCTACTGTATCTGAAAGAAGAACACTGTAGCCGCTTGGCAGGACCATTTTTCTGGTCATCGGGTCCAGCGTGGCAAACAGGAGGTCTTCTTCATAGCTGTCAGCACTCGTCAGGCGGTTGAACCATGTTGATTTCCCTGCGTTTGTATAGCCGACAAGCGCAATT criterion=sequence-density sequence-density=0.49 sequence-density-rank=1 fanout-score=4.70 fanout-score-rank=15 prefix-density=2.27 prefix-fanout=1.0 sequence=CAAGAAAAAAAACGAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=44 fanout-score=33.24 fanout-score-rank=1 prefix-density=0.06 prefix-fanout=2.9 sequence=TTCATCTCCTCTAACTTTGGAGAGGTAGGAATGGGAGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGATGGTTTTTACTATGTTGGGTATGCTGTTCGATTTCTTAAAGGACTGAATATTCGGTGGCAGTATGGGATTTCTAAAAATAATGTTAAGAATTTTTGCTGGTTTTTTGCGACGTTGGTGTTGTATTCTATAGCTCCATTATGGCCGTTATATGGAATCATTGGAGTGCCAGTAATTCTACCACGCCTTATATTTAAAGACAAAAAGAAGTGTCTAACAACAACATCCACACTACTACTCCTTGTCATATTTCTTCCTGAATTGCTGATTCTTATTGGATTTCTGATATTTCCTATTGTTATGGGCTATTACATCTCTAAGGAATTGGTGAAGTAAAATGGTGAAGCTTATGAATTTGTGGAGTGAGAGGATTAAAGATAGGGAAGTTGTTGAAGTT SRR5578508 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 09 21:25:17 Started mapping on | Dec 09 21:25:18 Finished on | Dec 09 21:42:54 Mapping speed, Million of reads per hour | 52.86 Number of input reads | 15505399 Average input read length | 286 UNIQUE READS: Uniquely mapped reads number | 10192912 Uniquely mapped reads % | 65.74% Average mapped length | 284.78 Number of splices: Total | 6302649 Number of splices: Annotated (sjdb) | 5870561 Number of splices: GT/AG | 6212704 Number of splices: GC/AG | 80015 Number of splices: AT/AC | 2802 Number of splices: Non-canonical | 7128 Mismatch rate per base, % | 0.09% Deletion rate per base | 0.01% Deletion average length | 1.47 Insertion rate per base | 0.00% Insertion average length | 1.12 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 262367 % of reads mapped to multiple loci | 1.69% Number of reads mapped to too many loci | 73806 % of reads mapped to too many loci | 0.48% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 29.66% % of reads unmapped: other | 2.43% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 5064639 5064639 5064639 N_multimapping 262367 262367 262367 N_noFeature 372660 9791504 487520 N_ambiguous 314675 1042 29221 UnstrandedReadsAssigned:9505577 PositiveStrandReadsAssigned:400366 NegativeStrandReadsAssigned:9676171 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=139 echo kmer=135 SRR5578508 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in paired-end mode [quant] will process pair 1: SRR5578508-trimmed-pair1.fastq SRR5578508-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 15,505,399 reads, 9,817,085 reads pseudoaligned [quant] estimated average fragment length: 196.956 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,083 rounds 52973 SRR5578508.ke.tsv 35125 SRR5578508.se.tsv 88098 total ==> SRR5578508.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 740.205 0 0 PNS24247 1044 848.044 2.07964 0.323832 PNS24249 1928 1732.04 34.1103 2.60062 PNS24246 1044 848.044 2.07964 0.323832 PNS24248 1044 848.044 2.07964 0.323832 PNS24244 1471 1275.04 195.651 20.2632 PNS24243 293 118.284 0 0 KQK14069 1603 1407.04 1853.07 173.914 KQK14071 474 282.629 18.383 8.58916 ==> SRR5578508.se.tsv <== BRADI_1g14170v3 1893 BRADI_1g53295v3 47 BRADI_1g59795v3 85 BRADI_1g07683v3 0 BRADI_1g00485v3 5 BRADI_1g20270v3 228 BRADI_1g74790v3 264 BRADI_1g09890v3 0 BRADI_1g77505v3 109 BRADI_1g48960v3 0 SRR5578508 completed mapping pipeline successfully