Starting /dee2/code/volunteer_pipeline.sh SRR7168895 current disk space = 3059273048064 free memory = 1405756688 SRR7168895 SRAfilesize 469ce2af52bbe4cee9af3c665f2ba4e2 SRR7168895.sra SRR7168895.sra file validated SRR7168895 is paired end SRR7168895 is conventional basespace SRR7168895 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7168895_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.10125 34.0 33.0 34.0 32.0 34.0 2 33.094 34.0 33.0 34.0 32.0 34.0 3 33.19425 34.0 33.0 34.0 32.0 34.0 4 33.272 34.0 33.0 34.0 33.0 34.0 5 33.3405 34.0 33.0 34.0 33.0 34.0 6 36.929 38.0 37.0 38.0 36.0 38.0 7 37.06325 38.0 38.0 38.0 36.0 38.0 8 37.28375 38.0 38.0 38.0 37.0 38.0 9 37.358 38.0 38.0 38.0 37.0 38.0 10-14 37.428850000000004 38.0 38.0 38.0 37.0 38.0 15-19 37.43495 38.0 38.0 38.0 37.0 38.0 20-24 37.40405 38.0 38.0 38.0 37.0 38.0 25-29 37.35825 38.0 38.0 38.0 37.0 38.0 30-34 37.4102 38.0 38.0 38.0 37.0 38.0 35-39 37.29795 38.0 38.0 38.0 37.0 38.0 40-44 36.8454 38.0 38.0 38.0 35.2 38.0 45-49 37.26375 38.0 38.0 38.0 37.0 38.0 50-54 37.19185 38.0 38.0 38.0 36.6 38.0 55-59 37.05505 38.0 38.0 38.0 36.0 38.0 60-64 36.91029999999999 38.0 38.0 38.0 35.6 38.0 65-69 36.4447 38.0 38.0 38.0 34.4 38.0 70-74 36.127050000000004 38.0 38.0 38.0 33.0 38.0 75-79 34.04365 38.0 37.2 38.0 19.2 38.0 80-84 34.00005 38.0 37.4 38.0 15.0 38.0 85-89 33.8373 38.0 37.0 38.0 15.0 38.0 90-94 33.70855 38.0 37.0 38.0 15.0 38.0 95-99 33.5857 38.0 36.8 38.0 15.0 38.0 100-104 33.350699999999996 38.0 36.2 38.0 14.6 38.0 105-109 32.9894 38.0 36.0 38.0 13.8 38.0 110-114 33.00595 38.0 35.6 38.0 13.8 38.0 115-119 32.6516 38.0 34.8 38.0 13.0 38.0 120-124 32.352199999999996 38.0 34.4 38.0 6.4 38.0 125-129 31.772699999999997 38.0 33.4 38.0 2.0 38.0 130-134 31.090749999999996 38.0 31.8 38.0 2.0 38.0 135-139 30.6295 38.0 31.0 38.0 2.0 38.0 140-144 29.94825 38.0 28.6 38.0 2.0 38.0 145-149 28.948500000000003 38.0 26.6 38.0 2.0 38.0 150-151 24.466 32.5 11.5 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 5 1.0 6 0.0 7 1.0 8 0.0 9 0.0 10 0.0 11 1.0 12 4.0 13 3.0 14 3.0 15 8.0 16 10.0 17 23.0 18 108.0 19 160.0 20 11.0 21 21.0 22 14.0 23 19.0 24 23.0 25 18.0 26 16.0 27 41.0 28 52.0 29 50.0 30 64.0 31 68.0 32 62.0 33 111.0 34 156.0 35 245.0 36 611.0 37 2096.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 33.012737197816485 14.63478034832337 13.25708344164284 39.095399012217314 2 22.75 22.8 30.65 23.799999999999997 3 19.35 25.0 28.175 27.474999999999998 4 21.5 25.650000000000002 23.175 29.675 5 27.525 29.875 21.175 21.425 6 28.975 31.574999999999996 23.150000000000002 16.3 7 17.424999999999997 29.299999999999997 37.375 15.9 8 17.075000000000003 33.75 26.674999999999997 22.5 9 22.45 27.375 28.475 21.7 10-14 20.79 31.46 23.06 24.69 15-19 19.975 27.29 27.165 25.569999999999997 20-24 19.945 30.28 26.545 23.23 25-29 19.075 28.02 26.784999999999997 26.119999999999997 30-34 18.285 28.815 27.33 25.569999999999997 35-39 22.21 29.965000000000003 24.285 23.54 40-44 17.45 28.67 29.035 24.845 45-49 21.055 27.98 28.799999999999997 22.165000000000003 50-54 21.32 24.94 26.515 27.224999999999998 55-59 18.785 24.84 32.165 24.21 60-64 21.240000000000002 26.275 29.299999999999997 23.185 65-69 18.224999999999998 35.655 24.959999999999997 21.16 70-74 18.695 36.325 23.799999999999997 21.18 75-79 18.515 33.06 24.955 23.47 80-84 19.925 30.17 26.795 23.11 85-89 19.139999999999997 30.404999999999998 26.655 23.799999999999997 90-94 20.495 29.28 26.22 24.005000000000003 95-99 19.994999999999997 30.764999999999997 25.445 23.794999999999998 100-104 20.215 30.385 25.735000000000003 23.665 105-109 20.064999999999998 28.634999999999998 27.1 24.2 110-114 20.26 29.48 26.275 23.985 115-119 20.555 28.12 27.43 23.895 120-124 20.86 28.249999999999996 26.555 24.335 125-129 20.985 30.495 25.495 23.025000000000002 130-134 20.835 31.365 24.875 22.925 135-139 20.8 30.11 25.4 23.69 140-144 20.535 29.385 25.35 24.73 145-149 21.145 29.94 25.074999999999996 23.84 150-151 21.6 29.799999999999997 24.55 24.05 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 1.0 1 0.5 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 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.5 20 0.5 21 0.5 22 2.0 23 2.0 24 1.0 25 2.0 26 3.5 27 4.0 28 7.0 29 9.0 30 18.0 31 28.0 32 31.0 33 38.0 34 49.5 35 74.0 36 90.5 37 106.5 38 151.0 39 175.5 40 194.5 41 233.5 42 258.0 43 273.5 44 275.0 45 251.0 46 231.0 47 237.5 48 240.0 49 220.5 50 182.5 51 140.0 52 107.5 53 92.5 54 70.0 55 44.0 56 33.5 57 31.0 58 28.5 59 16.5 60 12.5 61 11.5 62 6.5 63 3.5 64 2.5 65 1.0 66 0.0 67 1.0 68 2.5 69 1.5 70 0.0 71 0.0 72 0.5 73 0.5 74 0.5 75 0.5 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 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 3.8249999999999997 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 88.44999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 99.37817976257773 87.9 2 0.4239683436970039 0.75 3 0.05652911249293386 0.15 4 0.0 0.0 5 0.02826455624646693 0.125 6 0.0 0.0 7 0.0 0.0 8 0.02826455624646693 0.2 9 0.0 0.0 >10 0.02826455624646693 0.325 >50 0.0 0.0 >100 0.05652911249293386 10.549999999999999 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGCGAATCTCGTATGC 247 6.175 TruSeq Adapter, Index 10 (97% over 37bp) AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGCGAATCTCGTATG 175 4.375 TruSeq Adapter, Index 10 (97% over 37bp) NATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGCGAATCTCGTATGC 13 0.325 TruSeq Adapter, Index 1 (97% over 34bp) NGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGCGAATCTCGTATG 8 0.2 TruSeq Adapter, Index 10 (97% over 37bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGCGAATATCGTATGC 5 0.125 TruSeq Adapter, Index 10 (97% over 37bp) >>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 4.625 0.0 0.0 0.0 0.0 2 4.625 0.0 0.0 0.0 0.0 3 4.625 0.0 0.0 0.0 0.0 4 4.625 0.0 0.0 0.0 0.0 5 4.625 0.0 0.0 0.0 0.0 6 4.625 0.0 0.0 0.0 0.0 7 4.625 0.0 0.0 0.0 0.0 8 4.625 0.0 0.0 0.0 0.0 9 4.625 0.0 0.0 0.0 0.0 10-11 4.625 0.0 0.0 0.0 0.0 12-13 4.675 0.0 0.0 0.0 0.0 14-15 4.7 0.0 0.0 0.0 0.0 16-17 4.7 0.0 0.0 0.0 0.0 18-19 4.7 0.0 0.0 0.0 0.0 20-21 4.7 0.0 0.0 0.0 0.0 22-23 4.7 0.0 0.0 0.0 0.0 24-25 4.7 0.0 0.0 0.0 0.0 26-27 4.7 0.0 0.0 0.0 0.0 28-29 4.7 0.0 0.0 0.0 0.0 30-31 4.7 0.0 0.0 0.0 0.0 32-33 4.7 0.0 0.0 0.0 0.0 34-35 4.7 0.0 0.0 0.0 0.0 36-37 4.7 0.0 0.0 0.0 0.0 38-39 4.7 0.0 0.0 0.0 0.0 40-41 4.7125 0.0 0.0 0.0 0.0 42-43 4.725 0.0 0.0 0.0 0.0 44-45 4.725 0.0 0.0 0.0 0.0 46-47 4.725 0.0 0.0 0.0 0.0 48-49 4.725 0.0 0.0 0.0 0.0 50-51 4.725 0.0 0.0 0.0 0.0 52-53 4.7375 0.0 0.0 0.0 0.0 54-55 4.75 0.0 0.0 0.0 0.0 56-57 4.75 0.0 0.0 0.0 0.0 58-59 4.75 0.0 0.0 0.0 0.0 60-61 4.775 0.0 0.0 0.0 0.0 62-63 4.7875 0.0 0.0 0.0 0.0 64-65 4.8 0.0 0.0 0.0 0.0 66-67 4.825 0.0 0.0 0.0 0.0 68-69 4.85 0.0 0.0 0.0 0.0 70-71 4.9 0.0 0.0 0.0 0.0 72-73 4.9 0.0 0.0 0.0 0.0 74-75 4.9375 0.0 0.0 0.0 0.0 76-77 4.95 0.0 0.0 0.0 0.0 78-79 5.025 0.0 0.0 0.0 0.0 80-81 5.075 0.0 0.0 0.0 0.0 82-83 5.137499999999999 0.0 0.0 0.0 0.0 84-85 5.1875 0.0 0.0 0.0 0.0 86-87 5.275 0.0 0.0 0.0 0.0 88-89 5.375 0.0 0.0 0.0 0.0 90-91 5.525 0.0 0.0 0.0 0.0 92-93 5.6125 0.0 0.0 0.0 0.0 94-95 5.7375 0.0 0.0 0.0 0.0 96-97 5.925000000000001 0.0 0.0 0.0 0.0 98-99 6.075 0.0 0.0 0.0 0.0 100-101 6.3125 0.0 0.0 0.0 0.0 102-103 6.6125 0.0 0.0 0.0 0.0 104-105 6.9125 0.0 0.0 0.0 0.0 106-107 7.137499999999999 0.0 0.0 0.0 0.0 108-109 7.2875 0.0 0.0 0.0 0.0 110-111 7.55 0.0 0.0 0.0 0.0 112-113 7.775 0.0 0.0 0.0 0.0 114-115 8.0875 0.0 0.0 0.0 0.0 116-117 8.350000000000001 0.0 0.0 0.0 0.0 118-119 8.7375 0.0 0.0 0.0 0.0 120-121 9.25 0.0 0.0 0.0 0.0 122-123 9.6875 0.0 0.0 0.0 0.0 124-125 10.162500000000001 0.0 0.0 0.0 0.0 126-127 10.5625 0.0 0.0 0.0 0.0 128-129 11.125 0.0 0.0 0.0 0.0 130-131 11.3875 0.0 0.0 0.0 0.0 132-133 11.7875 0.0 0.0 0.0 0.0 134-135 12.337499999999999 0.0 0.0 0.0 0.0 136-137 12.712499999999999 0.0 0.0 0.0 0.0 138-139 13.2625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGATCGG 70 1.2084451E-5 53.104397 1 GATCGGA 85 4.449344E-5 42.639706 2 CGGAAGA 85 4.449344E-5 42.639706 5 TCGGAAG 90 6.235395E-5 40.270832 4 AGAGCAC 90 6.235395E-5 40.270832 9 ATCGGAA 90 6.235395E-5 40.270832 3 GGAAGAG 90 6.235395E-5 40.270832 6 AAGAGCA 95 8.577827E-5 38.151314 8 GAAGAGC 95 8.577827E-5 38.151314 7 GAGCACA 85 0.0024317855 34.111767 9 CAAGCGA 60 1.5079422E-8 24.162498 30-34 GCGAATC 50 2.1026408E-6 23.196001 35-39 CGAATCT 50 2.1026408E-6 23.196001 35-39 TATGCCG 65 3.5270205E-8 22.303846 45-49 TCTGCTT 65 3.5270205E-8 22.303846 55-59 ATGCCGT 65 3.5270205E-8 22.303846 45-49 GTCTTCT 65 3.5270205E-8 22.303846 50-54 CTGCTTG 65 3.5270205E-8 22.303846 55-59 TCGTATG 65 3.5270205E-8 22.303846 40-44 ACAAGCG 65 3.5270205E-8 22.303846 30-34 >>END_MODULE SRR7168895 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7168895_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 44 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.05725 33.0 33.0 34.0 31.0 34.0 2 32.365 33.0 33.0 34.0 31.0 34.0 3 32.21175 33.0 33.0 34.0 31.0 34.0 4 32.12975 33.0 33.0 34.0 31.0 34.0 5 32.078 33.0 33.0 34.0 31.0 34.0 6 36.47425 38.0 38.0 38.0 34.0 38.0 7 36.52025 38.0 38.0 38.0 35.0 38.0 8 36.679 38.0 38.0 38.0 36.0 38.0 9 36.57875 38.0 38.0 38.0 35.0 38.0 10-14 36.38935 38.0 38.0 38.0 34.8 38.0 15-19 36.203199999999995 38.0 38.0 38.0 34.2 38.0 20-24 36.370850000000004 38.0 38.0 38.0 34.8 38.0 25-29 36.23165 38.0 38.0 38.0 34.4 38.0 30-34 35.8052 38.0 38.0 38.0 32.0 38.0 35-39 35.5427 38.0 38.0 38.0 29.6 38.0 40-44 35.745349999999995 38.0 38.0 38.0 32.2 38.0 45-49 35.2406 38.0 37.4 38.0 28.0 38.0 50-54 35.2204 38.0 37.4 38.0 28.0 38.0 55-59 35.4034 38.0 37.8 38.0 29.6 38.0 60-64 35.8861 38.0 38.0 38.0 33.6 38.0 65-69 34.80435 38.0 37.6 38.0 25.4 38.0 70-74 32.132799999999996 38.0 36.4 38.0 2.0 38.0 75-79 31.93345 38.0 36.0 38.0 2.0 38.0 80-84 31.8 38.0 36.0 38.0 2.0 38.0 85-89 31.6151 38.0 35.0 38.0 2.0 38.0 90-94 31.62885 38.0 35.2 38.0 2.0 38.0 95-99 31.5853 38.0 35.4 38.0 2.0 38.0 100-104 31.48355 38.0 34.6 38.0 2.0 38.0 105-109 31.349249999999994 38.0 34.2 38.0 2.0 38.0 110-114 31.0767 38.0 33.8 38.0 2.0 38.0 115-119 30.8762 38.0 33.6 38.0 2.0 38.0 120-124 30.6053 38.0 32.6 38.0 2.0 38.0 125-129 30.40265 38.0 31.8 38.0 2.0 38.0 130-134 29.9243 38.0 30.0 38.0 2.0 38.0 135-139 29.3864 38.0 27.8 38.0 2.0 38.0 140-144 28.7046 38.0 24.4 38.0 2.0 38.0 145-149 27.40215 36.0 13.0 38.0 2.0 38.0 150-151 22.95075 31.0 2.0 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 36.0 3 10.0 4 5.0 5 10.0 6 6.0 7 9.0 8 8.0 9 7.0 10 10.0 11 15.0 12 23.0 13 37.0 14 30.0 15 55.0 16 109.0 17 184.0 18 25.0 19 9.0 20 15.0 21 6.0 22 7.0 23 18.0 24 19.0 25 19.0 26 20.0 27 19.0 28 37.0 29 30.0 30 49.0 31 42.0 32 96.0 33 114.0 34 142.0 35 229.0 36 596.0 37 1954.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 30.8 18.725 22.675 27.800000000000004 2 24.925 28.799999999999997 30.675 15.6 3 20.75 28.999999999999996 33.25 17.0 4 21.85 27.075 25.575 25.5 5 29.025000000000002 30.825000000000003 20.625 19.525000000000002 6 30.2 32.05 21.8 15.950000000000001 7 21.099999999999998 24.5 37.4 17.0 8 18.975 34.0 24.975 22.05 9 27.250000000000004 26.924999999999997 25.674999999999997 20.150000000000002 10-14 26.1 27.860000000000003 24.37 21.67 15-19 25.005 24.709999999999997 29.110000000000003 21.175 20-24 27.001350067503378 28.651432571628582 26.036301815090756 18.31091554577729 25-29 23.830000000000002 32.775 25.169999999999998 18.224999999999998 30-34 24.945 26.889999999999997 29.654999999999998 18.509999999999998 35-39 21.61 27.185 29.360000000000003 21.845 40-44 28.676433821691084 24.556227811390567 27.406370318515926 19.36096804840242 45-49 23.865 24.725 27.455000000000002 23.955000000000002 50-54 23.035 26.865 28.965000000000003 21.135 55-59 20.39 30.2 30.0 19.41 60-64 20.28 35.85 25.074999999999996 18.795 65-69 20.560000000000002 35.565000000000005 25.490000000000002 18.385 70-74 21.401070053502675 33.77168858442922 25.151257562878143 19.675983799189957 75-79 23.12615630781539 31.216560828041402 26.001300065003253 19.655982799139956 80-84 24.10120506025301 29.371468573428672 26.31631581579079 20.211010550527526 85-89 24.653628770069524 29.540339118691545 25.6489771419997 20.157054969239233 90-94 24.684936987397478 29.43088617723545 25.70514102820564 20.179035807161434 95-99 23.604441776710683 29.366746698679474 26.50560224089636 20.523209283713488 100-104 23.835958989747436 29.30232558139535 25.866466616654165 20.99524881220305 105-109 24.117411741174116 30.063006300630065 25.34253425342534 20.477047704770477 110-114 24.676169042260565 28.802200550137535 26.25156289072268 20.27006751687922 115-119 23.553533029954494 29.124368655298294 26.173926088913333 21.148172225833875 120-124 24.208631294694204 29.049357403610543 26.368955343301497 20.37305595839376 125-129 24.267426742674267 30.14801480148015 25.657565756575657 19.926992699269928 130-134 24.140863388524835 29.9434745635536 25.571507178230203 20.344154869691362 135-139 25.042512753826145 29.558867660298088 25.70271081324397 19.69590877263179 140-144 24.753713056958542 29.38940841126169 25.473821073160973 20.383057458618794 145-149 25.346336584146034 29.532383095773945 25.446361590397597 19.67491872968242 150-151 25.36884221055264 29.56989247311828 25.743935983995996 19.317329332333085 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.5 9 0.5 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.5 20 0.5 21 0.5 22 1.0 23 0.5 24 0.5 25 2.0 26 2.5 27 4.0 28 8.0 29 12.0 30 14.0 31 20.0 32 33.0 33 44.0 34 56.5 35 69.5 36 86.5 37 119.0 38 148.0 39 176.0 40 216.0 41 242.0 42 266.5 43 277.5 44 276.5 45 274.5 46 262.5 47 241.5 48 206.0 49 187.0 50 156.5 51 116.0 52 96.0 53 85.0 54 69.0 55 55.0 56 41.5 57 32.5 58 31.0 59 18.0 60 8.5 61 8.0 62 10.5 63 7.0 64 2.0 65 2.5 66 2.5 67 1.5 68 1.5 69 1.0 70 0.5 71 0.5 72 0.0 73 0.5 74 0.5 75 0.5 76 0.5 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 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 0.5 96 0.5 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 0.005 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.005 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.005 75-79 0.005 80-84 0.005 85-89 0.034999999999999996 90-94 0.02 95-99 0.04 100-104 0.025 105-109 0.01 110-114 0.025 115-119 0.015 120-124 0.015 125-129 0.01 130-134 0.045 135-139 0.03 140-144 0.015 145-149 0.025 150-151 0.025 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 89.875 #Duplication Level Percentage of deduplicated Percentage of total 1 99.221140472879 89.17500000000001 2 0.47287899860917937 0.8500000000000001 3 0.13908205841446453 0.375 4 0.055632823365785816 0.2 5 0.027816411682892908 0.125 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.027816411682892908 0.22499999999999998 >10 0.0 0.0 >50 0.0 0.0 >100 0.055632823365785816 9.049999999999999 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 203 5.075 Illumina Single End PCR Primer 1 (100% over 50bp) AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC 159 3.975 Illumina Single End PCR Primer 1 (100% over 50bp) GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGGAGATCTCGGTGGTCGCCG 9 0.22499999999999998 Illumina Single End PCR Primer 1 (98% over 50bp) AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAGCTCGGTGGTCGCC 5 0.125 Illumina Single End PCR Primer 1 (98% over 50bp) >>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 4.45 0.0 0.0 0.0 0.0 2 4.45 0.0 0.0 0.0 0.0 3 4.45 0.0 0.0 0.0 0.0 4 4.45 0.0 0.0 0.0 0.0 5 4.45 0.0 0.0 0.0 0.0 6 4.45 0.0 0.0 0.0 0.0 7 4.45 0.0 0.0 0.0 0.0 8 4.45 0.0 0.0 0.0 0.0 9 4.45 0.0 0.0 0.0 0.0 10-11 4.45 0.0 0.0 0.0 0.0 12-13 4.45 0.0 0.0 0.0 0.0 14-15 4.45 0.0 0.0 0.0 0.0 16-17 4.45 0.0 0.0 0.0 0.0 18-19 4.45 0.0 0.0 0.0 0.0 20-21 4.45 0.0 0.0 0.0 0.0 22-23 4.45 0.0 0.0 0.0 0.0 24-25 4.45 0.0 0.0 0.0 0.0 26-27 4.45 0.0 0.0 0.0 0.0 28-29 4.45 0.0 0.0 0.0 0.0 30-31 4.45 0.0 0.0 0.0 0.0 32-33 4.45 0.0 0.0 0.0 0.0 34-35 4.45 0.0 0.0 0.0 0.0 36-37 4.45 0.0 0.0 0.0 0.0 38-39 4.45 0.0 0.0 0.0 0.0 40-41 4.4625 0.0 0.0 0.0 0.0 42-43 4.475 0.0 0.0 0.0 0.0 44-45 4.475 0.0 0.0 0.0 0.0 46-47 4.475 0.0 0.0 0.0 0.0 48-49 4.475 0.0 0.0 0.0 0.0 50-51 4.475 0.0 0.0 0.0 0.0 52-53 4.475 0.0 0.0 0.0 0.0 54-55 4.475 0.0 0.0 0.0 0.0 56-57 4.475 0.0 0.0 0.0 0.0 58-59 4.475 0.0 0.0 0.0 0.0 60-61 4.475 0.0 0.0 0.0 0.0 62-63 4.475 0.0 0.0 0.0 0.0 64-65 4.475 0.0 0.0 0.0 0.0 66-67 4.5 0.0 0.0 0.0 0.0 68-69 4.525 0.0 0.0 0.0 0.0 70-71 4.575 0.0 0.0 0.0 0.0 72-73 4.575 0.0 0.0 0.0 0.0 74-75 4.6125 0.0 0.0 0.0 0.0 76-77 4.625 0.0 0.0 0.0 0.0 78-79 4.675000000000001 0.0 0.0 0.0 0.0 80-81 4.725 0.0 0.0 0.0 0.0 82-83 4.7875 0.0 0.0 0.0 0.0 84-85 4.8375 0.0 0.0 0.0 0.0 86-87 4.925 0.0 0.0 0.0 0.0 88-89 5.025 0.0 0.0 0.0 0.0 90-91 5.175000000000001 0.0 0.0 0.0 0.0 92-93 5.2625 0.0 0.0 0.0 0.0 94-95 5.3375 0.0 0.0 0.0 0.0 96-97 5.525 0.0 0.0 0.0 0.0 98-99 5.725 0.0 0.0 0.0 0.0 100-101 5.9625 0.0 0.0 0.0 0.0 102-103 6.25 0.0 0.0 0.0 0.0 104-105 6.475 0.0 0.0 0.0 0.0 106-107 6.6875 0.0 0.0 0.0 0.0 108-109 6.85 0.0 0.0 0.0 0.0 110-111 7.125 0.0 0.0 0.0 0.0 112-113 7.3625 0.0 0.0 0.0 0.0 114-115 7.7125 0.0 0.0 0.0 0.0 116-117 7.975 0.0 0.0 0.0 0.0 118-119 8.3875 0.0 0.0 0.0 0.0 120-121 8.9 0.0 0.0 0.0 0.0 122-123 9.3625 0.0 0.0 0.0 0.0 124-125 9.85 0.0 0.0 0.0 0.0 126-127 10.2 0.0 0.0 0.0 0.0 128-129 10.75 0.0 0.0 0.0 0.0 130-131 11.0625 0.0 0.0 0.0 0.0 132-133 11.4375 0.0 0.0 0.0 0.0 134-135 11.9875 0.0 0.0 0.0 0.0 136-137 12.3625 0.0 0.0 0.0 0.0 138-139 12.8875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGAGCGT 70 1.4094447E-5 51.785717 9 AAGAGCG 75 2.1205773E-5 48.333336 8 GAAGAGC 80 3.1063704E-5 45.3125 7 GGAAGAG 80 3.1063704E-5 45.3125 6 GAGCGTC 70 9.353284E-4 41.428574 9 CGGAAGA 75 0.0013135396 38.666668 4 AGATCGG 75 0.0013135396 38.666668 1 GATCGGA 80 0.0018040554 36.25 1 TCGGAAG 80 0.0018040554 36.25 3 ATCGGAA 80 0.0018040554 36.25 2 CCGTATC 30 4.189703E-5 29.000002 45-49 TCGCCGT 30 4.189703E-5 29.000002 45-49 GCCGTAT 30 4.189703E-5 29.000002 45-49 CGCCGTA 30 4.189703E-5 29.000002 45-49 ATCTCGG 35 3.5374105E-6 29.0 35-39 GTATCAT 25 4.977651E-4 29.0 50-54 TCTCGGT 35 3.5374105E-6 29.0 35-39 TATCATT 25 4.977651E-4 29.0 50-54 ATCATTA 35 3.5374105E-6 29.0 50-54 TGGTCGC 45 2.538036E-8 28.999998 40-44 >>END_MODULE Read 949977 spots for SRR7168895.sra Written 949977 spots for SRR7168895.sra Read 949977 spots for SRR7168895.sra Written 949977 spots for SRR7168895.sra Read 949977 spots for SRR7168895.sra Written 949977 spots for SRR7168895.sra Read 949977 spots for SRR7168895.sra Written 949977 spots for SRR7168895.sra Read 949977 spots for SRR7168895.sra Written 949977 spots for SRR7168895.sra Read 949977 spots for SRR7168895.sra Written 949977 spots for SRR7168895.sra Read 949977 spots for SRR7168895.sra Written 949977 spots for SRR7168895.sra Read 949977 spots for SRR7168895.sra Written 949977 spots for SRR7168895.sra Read 949977 spots for SRR7168895.sra Written 949977 spots for SRR7168895.sra Read 949977 spots for SRR7168895.sra Written 949977 spots for SRR7168895.sra Read 949977 spots for SRR7168895.sra Written 949977 spots for SRR7168895.sra Read 949977 spots for SRR7168895.sra Written 949977 spots for SRR7168895.sra Read 949977 spots for SRR7168895.sra Written 949977 spots for SRR7168895.sra Read 949977 spots for SRR7168895.sra Written 949977 spots for SRR7168895.sra Read 949977 spots for SRR7168895.sra Written 949977 spots for SRR7168895.sra Read 949977 spots for SRR7168895.sra Written 949977 spots for SRR7168895.sra Read 949977 spots for SRR7168895.sra Written 949977 spots for SRR7168895.sra Read 949977 spots for SRR7168895.sra Written 949977 spots for SRR7168895.sra Read 949986 spots for SRR7168895.sra Written 949986 spots for SRR7168895.sra Read 949977 spots for SRR7168895.sra Written 949977 spots for SRR7168895.sra SRR ids: ['SRR7168895.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_zgovh3pt SRR7168895.sra spots: 18999549 blocks: [[1, 949977], [949978, 1899954], [1899955, 2849931], [2849932, 3799908], [3799909, 4749885], [4749886, 5699862], [5699863, 6649839], [6649840, 7599816], [7599817, 8549793], [8549794, 9499770], [9499771, 10449747], [10449748, 11399724], [11399725, 12349701], [12349702, 13299678], [13299679, 14249655], [14249656, 15199632], [15199633, 16149609], [16149610, 17099586], [17099587, 18049563], [18049564, 18999549]] SRR7168895 file size 6416623 SRR7168895 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 SRR7168895 SRR7168895_1.fastq SRR7168895_2.fastq Input file: SRR7168895_1.fastq Paired file: SRR7168895_2.fastq trimmed: SRR7168895-trimmed-pair1.fastq, SRR7168895-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 Feb 10 10:32:57 2025 >> started Mon Feb 10 10:33:18 2025 >> done (21.116s) 18999549 read pairs processed; of these: 106676 ( 0.56%) short read pairs filtered out after trimming by size control 2261935 (11.91%) empty read pairs filtered out after trimming by size control 16630938 (87.53%) read pairs available; of these: 9600770 (57.73%) trimmed read pairs available after processing 7030168 (42.27%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 178 0.00% 19 134 0.00% 20 93 0.00% 21 267 0.00% 22 199 0.00% 23 242 0.00% 24 208 0.00% 25 160 0.00% 26 147 0.00% 27 128 0.00% 28 200 0.00% 29 3593 0.02% 30 401 0.00% 31 762 0.00% 32 394 0.00% 33 483 0.00% 34 687 0.00% 35 901 0.01% 36 251 0.00% 37 308 0.00% 38 448 0.00% 39 810 0.00% 40 1082 0.01% 41 1518 0.01% 42 528 0.00% 43 469 0.00% 44 629 0.00% 45 686 0.00% 46 882 0.01% 47 1048 0.01% 48 1182 0.01% 49 1252 0.01% 50 1342 0.01% 51 1759 0.01% 52 2191 0.01% 53 1768 0.01% 54 1816 0.01% 55 2980 0.02% 56 3267 0.02% 57 2536 0.02% 58 4414 0.03% 59 5737 0.03% 60 6286 0.04% 61 8574 0.05% 62 2795 0.02% 63 2099 0.01% 64 2326 0.01% 65 2946 0.02% 66 3226 0.02% 67 4936 0.03% 68 13532 0.08% 69 59840 0.36% 70 29830 0.18% 71 8581 0.05% 72 6558 0.04% 73 6074 0.04% 74 5923 0.04% 75 6254 0.04% 76 6413 0.04% 77 6743 0.04% 78 7266 0.04% 79 7578 0.05% 80 8686 0.05% 81 10320 0.06% 82 9694 0.06% 83 10645 0.06% 84 12665 0.08% 85 13752 0.08% 86 14336 0.09% 87 15079 0.09% 88 15611 0.09% 89 16218 0.10% 90 17498 0.11% 91 18251 0.11% 92 19996 0.12% 93 20175 0.12% 94 21120 0.13% 95 22451 0.13% 96 23611 0.14% 97 24333 0.15% 98 25076 0.15% 99 25778 0.16% 100 26737 0.16% 101 27511 0.17% 102 28892 0.17% 103 30097 0.18% 104 31257 0.19% 105 32796 0.20% 106 34079 0.20% 107 35145 0.21% 108 35966 0.22% 109 37443 0.23% 110 37474 0.23% 111 38581 0.23% 112 39941 0.24% 113 41005 0.25% 114 42480 0.26% 115 43869 0.26% 116 45354 0.27% 117 46878 0.28% 118 47587 0.29% 119 48696 0.29% 120 49903 0.30% 121 50967 0.31% 122 52973 0.32% 123 54059 0.33% 124 56368 0.34% 125 57909 0.35% 126 59969 0.36% 127 61854 0.37% 128 63730 0.38% 129 65513 0.39% 130 68162 0.41% 131 69905 0.42% 132 72990 0.44% 133 75585 0.45% 134 78829 0.47% 135 82575 0.50% 136 86796 0.52% 137 92217 0.55% 138 97135 0.58% 139 104533 0.63% 140 111091 0.67% 141 120475 0.72% 142 131689 0.79% 143 147074 0.88% 144 169835 1.02% 145 200464 1.21% 146 248938 1.50% 147 328704 1.98% 148 487531 2.93% 149 928780 5.58% 150 3981274 23.94% 151 7030168 42.27% 16630938 reads passed initial QC criterion=sequence-density sequence-density=0.30 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=20 prefix-density=0.31 prefix-fanout=2.0 sequence=TTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGGGTATGAATGTGTTCTCTG criterion=fanout-score sequence-density=0.11 sequence-density-rank=24 fanout-score=27.49 fanout-score-rank=1 prefix-density=0.30 prefix-fanout=10.2 sequence=CCATTCTTGAGTTCCTTCACCTTCAACTC criterion=sequence-density sequence-density=0.28 sequence-density-rank=1 fanout-score=2.08 fanout-score-rank=28 prefix-density=0.28 prefix-fanout=2.1 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.02 sequence-density-rank=31 fanout-score=45.48 fanout-score-rank=1 prefix-density=0.10 prefix-fanout=6.8 sequence=CAAGCAGAAGACGGCATACGAGATTCGCTTGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC SRR7168895 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 10 10:34:25 Started mapping on | Feb 10 10:34:26 Finished on | Feb 10 10:36:06 Mapping speed, Million of reads per hour | 598.71 Number of input reads | 16630938 Average input read length | 279 UNIQUE READS: Uniquely mapped reads number | 13607272 Uniquely mapped reads % | 81.82% Average mapped length | 282.61 Number of splices: Total | 13075756 Number of splices: Annotated (sjdb) | 12754887 Number of splices: GT/AG | 12825985 Number of splices: GC/AG | 199213 Number of splices: AT/AC | 7753 Number of splices: Non-canonical | 42805 Mismatch rate per base, % | 0.42% Deletion rate per base | 0.03% Deletion average length | 2.58 Insertion rate per base | 0.02% Insertion average length | 2.02 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 436011 % of reads mapped to multiple loci | 2.62% Number of reads mapped to too many loci | 144328 % of reads mapped to too many loci | 0.87% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 14.52% % of reads unmapped: other | 0.17% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2619603 2619603 2619603 N_multimapping 436011 436011 436011 N_noFeature 596735 13329541 769764 N_ambiguous 282000 4312 173557 UnstrandedReadsAssigned:12728537 PositiveStrandReadsAssigned:273419 NegativeStrandReadsAssigned:12663951 Dataset is classified negative stranded MeadianReadLen=143 20thPercentileLength=138 echo kmer=133 SRR7168895 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: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR7168895-trimmed-pair1.fastq SRR7168895-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 16,630,938 reads, 14,330,399 reads pseudoaligned [quant] estimated average fragment length: 221.341 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,054 rounds 52401 SRR7168895.ke.tsv 34699 SRR7168895.se.tsv 87100 total ==> SRR7168895.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1797.66 653 27.9801 Potri.005G024800.1.v4.1 1035 814.659 296 27.9872 Potri.004G059700.1.v4.1 961 740.691 16 1.6639 Potri.007G009000.2.v4.1 1416 1195.66 0 0 Potri.003G141000.2.v4.1 2943 2722.66 1092.79 30.9163 Potri.016G087400.1.v4.1 270 95.0396 717 581.109 Potri.015G069301.1.v4.1 564 348.424 0 0 Potri.010G195200.1.v4.1 1773 1552.66 55.8227 2.76935 Potri.012G127500.1.v4.1 977 756.68 113 11.5029 ==> SRR7168895.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 572 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 217 Potri.001G212900.v4.1 2 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 12 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 9 SRR7168895 completed mapping pipeline successfully