Starting /dee2/code/volunteer_pipeline.sh SRR7171119 current disk space = 3085143154688 free memory = 1581030316 SRR7171119 SRAfilesize 83a575e514d57a0f178e368cfa44e208 SRR7171119.sra SRR7171119.sra file validated SRR7171119 is paired end SRR7171119 is conventional basespace SRR7171119 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171119_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 43 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 20.94575 18.0 18.0 25.0 18.0 32.0 2 26.48125 27.0 25.0 29.0 18.0 31.0 3 27.27475 29.0 25.0 31.0 18.0 33.0 4 30.2905 31.0 29.0 33.0 27.0 33.0 5 31.1755 33.0 31.0 33.0 29.0 33.0 6 35.887 37.0 36.0 38.0 33.0 38.0 7 36.73075 38.0 37.0 38.0 35.0 38.0 8 36.912 38.0 38.0 38.0 35.0 38.0 9 36.1955 38.0 38.0 38.0 33.0 38.0 10-14 37.316950000000006 38.0 38.0 38.0 36.4 38.0 15-19 37.5359 38.0 38.0 38.0 37.6 38.0 20-24 37.553999999999995 38.0 38.0 38.0 38.0 38.0 25-29 37.5001 38.0 38.0 38.0 37.8 38.0 30-34 37.4487 38.0 38.0 38.0 37.6 38.0 35-39 37.3874 38.0 38.0 38.0 37.4 38.0 40-44 37.01955 38.0 38.0 38.0 36.0 38.0 45-49 36.90675 38.0 38.0 38.0 35.6 38.0 50-54 35.98975 38.0 36.4 38.0 30.4 38.0 55-59 36.97715 38.0 38.0 38.0 35.8 38.0 60-64 37.07325 38.0 38.0 38.0 36.0 38.0 65-69 36.95864999999999 38.0 38.0 38.0 36.0 38.0 70-74 36.84454999999999 38.0 38.0 38.0 36.0 38.0 75-79 35.04645000000001 38.0 38.0 38.0 30.2 38.0 80-84 33.9946 38.0 37.0 38.0 21.4 38.0 85-89 34.25085 38.0 37.6 38.0 24.8 38.0 90-94 34.222750000000005 38.0 37.8 38.0 24.2 38.0 95-99 34.1793 38.0 37.6 38.0 23.6 38.0 100-104 34.089 38.0 37.0 38.0 23.2 38.0 105-109 34.0655 38.0 37.2 38.0 21.8 38.0 110-114 33.6912 38.0 36.4 38.0 15.0 38.0 115-119 33.5263 38.0 36.0 38.0 15.0 38.0 120-124 33.32065 38.0 36.0 38.0 15.0 38.0 125-129 33.00845 38.0 35.0 38.0 13.4 38.0 130-134 31.937649999999998 38.0 32.4 38.0 13.0 38.0 135-139 32.35145 38.0 33.0 38.0 12.6 38.0 140-144 31.966300000000007 38.0 33.0 38.0 3.8 38.0 145-149 31.068049999999992 38.0 32.2 38.0 2.0 38.0 150-151 25.976125 33.0 16.5 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 1.0 7 1.0 8 0.0 9 1.0 10 2.0 11 4.0 12 4.0 13 6.0 14 8.0 15 10.0 16 8.0 17 19.0 18 99.0 19 135.0 20 13.0 21 10.0 22 8.0 23 9.0 24 4.0 25 14.0 26 13.0 27 20.0 28 28.0 29 36.0 30 29.0 31 42.0 32 87.0 33 89.0 34 150.0 35 298.0 36 984.0 37 1868.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.96905621454358 18.92728210417741 6.7560598246518815 34.34760185662712 2 17.4 20.775 42.225 19.6 3 13.950000000000001 21.2 36.625 28.225 4 17.7 28.875 25.224999999999998 28.199999999999996 5 25.21891418563923 32.624468351263445 24.168126094570926 17.988491368526393 6 22.15 33.074999999999996 25.900000000000002 18.875 7 12.45 28.975 42.75 15.825 8 14.575 28.575 33.775 23.075000000000003 9 19.975 22.25 33.15 24.625 10-14 19.759999999999998 29.854999999999997 25.729999999999997 24.654999999999998 15-19 19.18 28.794999999999998 27.655 24.37 20-24 18.965 30.330000000000002 27.794999999999998 22.91 25-29 19.12 28.475 27.860000000000003 24.545 30-34 19.134999999999998 29.185 27.48 24.2 35-39 21.42 28.525 26.595000000000002 23.46 40-44 19.595000000000002 30.425 27.250000000000004 22.73 45-49 20.18 28.455000000000002 28.044999999999998 23.32 50-54 21.105 27.05 27.315 24.529999999999998 55-59 18.525 26.415 30.275000000000002 24.785 60-64 19.314999999999998 26.575 30.464999999999996 23.645 65-69 19.794999999999998 32.1 26.240000000000002 21.865000000000002 70-74 18.43 33.87 25.81 21.89 75-79 19.2 32.975 25.605 22.220000000000002 80-84 19.225 30.97 26.85 22.955000000000002 85-89 19.895 31.31 25.945 22.85 90-94 19.97 30.345 26.405 23.28 95-99 20.5 28.970000000000002 27.339999999999996 23.189999999999998 100-104 20.555 29.110000000000003 26.87 23.465 105-109 20.5 29.195 27.089999999999996 23.215 110-114 21.435000000000002 29.69 26.32 22.555 115-119 20.44 31.025000000000002 25.995 22.54 120-124 20.09 30.599999999999998 25.88 23.43 125-129 21.15 30.959999999999997 25.069999999999997 22.82 130-134 20.630000000000003 30.54 25.419999999999998 23.41 135-139 20.82 30.11 25.465 23.605 140-144 21.435000000000002 30.25 25.25 23.064999999999998 145-149 20.849999999999998 30.264999999999997 25.259999999999998 23.625 150-151 21.366879459256477 29.991237952184253 24.62135436224809 24.02052822631118 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 5.0 1 5.0 2 3.5 3 2.0 4 2.0 5 1.5 6 2.0 7 2.0 8 1.0 9 1.0 10 0.5 11 0.5 12 0.5 13 0.5 14 1.5 15 1.0 16 0.0 17 0.0 18 0.5 19 2.0 20 2.5 21 4.5 22 4.5 23 4.0 24 5.5 25 6.0 26 8.5 27 12.5 28 13.0 29 18.0 30 26.0 31 33.5 32 45.5 33 65.0 34 77.0 35 90.0 36 108.0 37 129.0 38 163.0 39 192.5 40 203.0 41 211.0 42 230.5 43 255.5 44 251.0 45 228.5 46 220.0 47 204.5 48 185.5 49 162.5 50 144.0 51 132.5 52 113.0 53 92.0 54 85.5 55 70.5 56 45.5 57 38.5 58 27.0 59 16.0 60 17.5 61 14.0 62 7.5 63 2.5 64 1.5 65 0.5 66 0.0 67 0.5 68 1.0 69 0.5 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 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 3.05 2 0.0 3 0.0 4 0.0 5 0.075 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 0.13749999999999998 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 91.95 #Duplication Level Percentage of deduplicated Percentage of total 1 98.12398042414355 90.225 2 1.3866231647634584 2.55 3 0.19032082653616098 0.525 4 0.13594344752582926 0.5 5 0.02718868950516585 0.125 6 0.02718868950516585 0.15 7 0.02718868950516585 0.17500000000000002 8 0.0 0.0 9 0.02718868950516585 0.22499999999999998 >10 0.02718868950516585 0.6 >50 0.0 0.0 >100 0.02718868950516585 4.925 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGCGATAGATCTCGTAT 197 4.925 TruSeq Adapter, Index 1 (97% over 36bp) AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGCGATAGATCTCGTA 24 0.6 TruSeq Adapter, Index 1 (97% over 36bp) AATCGGAAGAGCACACGTCTGAACTCCAGTCACAGCGATAGATCTCGTAT 9 0.22499999999999998 TruSeq Adapter, Index 13 (97% over 35bp) GATCGGAAAAGCACACGTCTGAACTCCAGTCACAGCGATAGATCTCGTAT 7 0.17500000000000002 TruSeq Adapter, Index 13 (97% over 35bp) CGGAAGAGCACACGTCTGAACTCCAGTCACAGCGATAGATCTCGTATGCC 6 0.15 TruSeq Adapter, Index 1 (96% over 33bp) CTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAAC 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 0.675 0.0 0.0 0.0 0.0 2 0.7 0.0 0.0 0.0 0.0 3 0.7 0.0 0.0 0.0 0.0 4 0.7 0.0 0.0 0.0 0.0 5 0.7 0.0 0.0 0.0 0.0 6 0.7 0.0 0.0 0.0 0.0 7 0.7 0.0 0.0 0.0 0.0 8 0.7 0.0 0.0 0.0 0.0 9 0.7 0.0 0.0 0.0 0.0 10-11 0.7 0.0 0.0 0.0 0.0 12-13 0.7 0.0 0.0 0.0 0.0 14-15 0.7 0.0 0.0 0.0 0.0 16-17 0.7 0.0 0.0 0.0 0.0 18-19 0.7 0.0 0.0 0.0 0.0 20-21 0.7 0.0 0.0 0.0 0.0 22-23 0.7 0.0 0.0 0.0 0.0 24-25 0.7 0.0 0.0 0.0 0.0 26-27 0.7 0.0 0.0 0.0 0.0 28-29 0.7 0.0 0.0 0.0 0.0 30-31 0.7 0.0 0.0 0.0 0.0 32-33 0.7 0.0 0.0 0.0 0.0 34-35 0.7 0.0 0.0 0.0 0.0 36-37 0.7 0.0 0.0 0.0 0.0 38-39 0.7 0.0 0.0 0.0 0.0 40-41 0.7 0.0 0.0 0.0 0.0 42-43 0.7 0.0 0.0 0.0 0.0 44-45 0.7 0.0 0.0 0.0 0.0 46-47 0.7 0.0 0.0 0.0 0.0 48-49 0.725 0.0 0.0 0.0 0.0 50-51 0.725 0.0 0.0 0.0 0.0 52-53 0.725 0.0 0.0 0.0 0.0 54-55 0.7375 0.0 0.0 0.0 0.0 56-57 0.75 0.0 0.0 0.0 0.0 58-59 0.75 0.0 0.0 0.0 0.0 60-61 0.75 0.0 0.0 0.0 0.0 62-63 0.7875000000000001 0.0 0.0 0.0 0.0 64-65 0.825 0.0 0.0 0.0 0.0 66-67 0.825 0.0 0.0 0.0 0.0 68-69 0.85 0.0 0.0 0.0 0.0 70-71 0.9 0.0 0.0 0.0 0.0 72-73 0.9375 0.0 0.0 0.0 0.0 74-75 1.0 0.0 0.0 0.0 0.0 76-77 1.025 0.0 0.0 0.0 0.0 78-79 1.1625 0.0 0.0 0.0 0.0 80-81 1.3250000000000002 0.0 0.0 0.0 0.0 82-83 1.375 0.0 0.0 0.0 0.0 84-85 1.4375 0.0 0.0 0.0 0.0 86-87 1.6375 0.0 0.0 0.0 0.0 88-89 1.875 0.0 0.0 0.0 0.0 90-91 2.1125 0.0 0.0 0.0 0.0 92-93 2.4 0.0 0.0 0.0 0.0 94-95 2.6500000000000004 0.0 0.0 0.0 0.0 96-97 2.9375 0.0 0.0 0.0 0.0 98-99 3.2375 0.0 0.0 0.0 0.0 100-101 3.575 0.0 0.0 0.0 0.0 102-103 3.875 0.0 0.0 0.0 0.0 104-105 4.300000000000001 0.0 0.0 0.0 0.0 106-107 4.7875 0.0 0.0 0.0 0.0 108-109 5.2625 0.0 0.0 0.0 0.0 110-111 5.8125 0.0 0.0 0.0 0.0 112-113 6.3125 0.0 0.0 0.0 0.0 114-115 6.775 0.0 0.0 0.0 0.0 116-117 7.525 0.0 0.0 0.0 0.0 118-119 8.25 0.0 0.0 0.0 0.0 120-121 8.8625 0.0 0.0 0.0 0.0 122-123 9.55 0.0 0.0 0.0 0.0 124-125 9.95 0.0 0.0 0.0 0.0 126-127 10.4375 0.0 0.0 0.0 0.0 128-129 11.0875 0.0 0.0 0.0 0.0 130-131 11.7125 0.0 0.0 0.0 0.0 132-133 12.4625 0.0 0.0 0.0 0.0 134-135 13.2625 0.0 0.0 0.0 0.0 136-137 14.1 0.0 0.0 0.0 0.0 138-139 14.7125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGAGCCA 10 0.006836113 144.9625 7 ATAGAGC 10 0.006836113 144.9625 5 TAGAGCC 10 0.006836113 144.9625 6 GATCGGA 95 1.8189894E-12 71.34176 1 ATCGGAA 100 5.456968E-12 65.23313 2 GAAGAGC 90 1.8007995E-10 64.42778 6 GAGCACA 90 1.8007995E-10 64.42778 9 CGGAAGA 90 1.8007995E-10 64.42778 4 AGAGCAC 90 1.8007995E-10 64.42778 8 GGAAGAG 90 1.8007995E-10 64.42778 5 AAGAGCA 95 2.910383E-10 61.036842 7 TCGGAAG 95 2.910383E-10 61.036842 3 TCTGCTT 55 5.97538E-9 26.356817 55-59 GTCTTCT 55 5.97538E-9 26.356817 50-54 CGTCTTC 55 5.97538E-9 26.356817 50-54 TTCTGCT 60 1.5092155E-8 24.160418 55-59 CTGCTTG 60 1.5092155E-8 24.160418 55-59 CCGTCTT 50 2.1042179E-6 23.194 50-54 GCCGTCT 50 2.1042179E-6 23.194 50-54 TCTCGTA 65 3.5302946E-8 22.301924 40-44 >>END_MODULE SRR7171119 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171119_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 pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.332 33.0 33.0 34.0 31.0 34.0 2 30.94025 33.0 32.0 34.0 18.0 34.0 3 32.152 33.0 32.0 34.0 28.0 34.0 4 32.42225 33.0 33.0 34.0 32.0 34.0 5 32.6455 33.0 33.0 34.0 32.0 34.0 6 36.87225 38.0 38.0 38.0 36.0 38.0 7 36.9395 38.0 38.0 38.0 37.0 38.0 8 37.02 38.0 38.0 38.0 37.0 38.0 9 37.0045 38.0 38.0 38.0 37.0 38.0 10-14 36.868449999999996 38.0 38.0 38.0 36.2 38.0 15-19 36.83905 38.0 38.0 38.0 36.0 38.0 20-24 35.697500000000005 38.0 36.8 38.0 28.8 38.0 25-29 36.71169999999999 38.0 38.0 38.0 35.2 38.0 30-34 36.69304999999999 38.0 38.0 38.0 35.4 38.0 35-39 36.85045 38.0 38.0 38.0 36.0 38.0 40-44 36.8235 38.0 38.0 38.0 36.0 38.0 45-49 35.955349999999996 38.0 37.4 38.0 30.0 38.0 50-54 36.693749999999994 38.0 38.0 38.0 35.8 38.0 55-59 36.5145 38.0 38.0 38.0 34.4 38.0 60-64 35.6388 38.0 36.8 38.0 29.0 38.0 65-69 36.480399999999996 38.0 38.0 38.0 34.6 38.0 70-74 36.54135 38.0 38.0 38.0 35.0 38.0 75-79 36.43975 38.0 38.0 38.0 34.4 38.0 80-84 33.32935 38.0 35.0 38.0 19.8 38.0 85-89 33.98625 38.0 37.0 38.0 18.2 38.0 90-94 34.08835 38.0 37.2 38.0 20.2 38.0 95-99 33.96575 38.0 37.2 38.0 16.2 38.0 100-104 33.6978 38.0 36.6 38.0 15.0 38.0 105-109 32.62795 37.8 33.0 38.0 14.6 38.0 110-114 31.267150000000004 37.2 27.8 38.0 14.4 38.0 115-119 32.923 38.0 34.2 38.0 14.6 38.0 120-124 32.83095 38.0 34.0 38.0 13.4 38.0 125-129 32.55965 38.0 33.4 38.0 12.6 38.0 130-134 32.094849999999994 38.0 33.0 38.0 9.2 38.0 135-139 31.382799999999996 38.0 31.8 38.0 2.0 38.0 140-144 30.421000000000003 38.0 29.2 38.0 2.0 38.0 145-149 29.3452 37.4 27.6 38.0 2.0 38.0 150-151 23.535125 29.0 11.5 35.5 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 19.0 3 3.0 4 1.0 5 1.0 6 2.0 7 1.0 8 1.0 9 2.0 10 4.0 11 3.0 12 2.0 13 4.0 14 5.0 15 9.0 16 12.0 17 18.0 18 34.0 19 80.0 20 133.0 21 12.0 22 7.0 23 9.0 24 16.0 25 20.0 26 22.0 27 27.0 28 32.0 29 50.0 30 53.0 31 63.0 32 95.0 33 127.0 34 224.0 35 340.0 36 921.0 37 1648.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.175 25.55 7.3999999999999995 25.874999999999996 2 25.074999999999996 27.0 34.575 13.350000000000001 3 16.079019754938734 25.98149537384346 40.735183795948984 17.20430107526882 4 21.5 32.75 23.65 22.1 5 29.25 35.099999999999994 19.475 16.175 6 24.425 38.625 20.625 16.325 7 19.625 25.95 37.574999999999996 16.85 8 18.35 29.525000000000002 28.299999999999997 23.825 9 24.975 23.025000000000002 29.525000000000002 22.475 10-14 24.64 27.985 25.7 21.675 15-19 24.07 26.495 28.58 20.855 20-24 25.22 28.505000000000003 26.655 19.62 25-29 24.585 30.049999999999997 26.700000000000003 18.665000000000003 30-34 23.244999999999997 26.169999999999998 29.9 20.685000000000002 35-39 23.32 25.275 27.87 23.535 40-44 24.87 26.745 29.32 19.064999999999998 45-49 22.845 28.860000000000003 27.750000000000004 20.544999999999998 50-54 24.345 26.040000000000003 28.515 21.099999999999998 55-59 25.490000000000002 26.205000000000002 27.725 20.580000000000002 60-64 22.95 26.96 27.894999999999996 22.195 65-69 22.07 26.745 30.29 20.895 70-74 21.465 33.235 25.86 19.439999999999998 75-79 22.1 32.96 25.380000000000003 19.56 80-84 22.7 31.535000000000004 26.125 19.64 85-89 23.849999999999998 29.95 26.340000000000003 19.86 90-94 23.73 29.635 26.55 20.085 95-99 24.23 28.65 26.865 20.255000000000003 100-104 24.8 28.360000000000003 26.924999999999997 19.915 105-109 24.565 28.715000000000003 26.86 19.86 110-114 24.955 28.875 26.810000000000002 19.36 115-119 24.645 30.314999999999998 25.83 19.21 120-124 25.03 29.445 26.025 19.5 125-129 24.445 29.035 26.55 19.97 130-134 25.6 28.52 26.495 19.384999999999998 135-139 25.655 28.225 26.534999999999997 19.585 140-144 26.16 28.38 26.08 19.38 145-149 26.645000000000003 27.805000000000003 26.235000000000003 19.314999999999998 150-151 26.514772158237353 27.32849273910866 25.550826239359036 20.605908863294943 >>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 0.0 7 0.5 8 0.5 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 0.0 20 2.0 21 2.5 22 1.0 23 1.5 24 2.5 25 4.0 26 4.5 27 5.0 28 6.0 29 11.5 30 18.0 31 21.0 32 28.5 33 43.5 34 59.5 35 73.5 36 87.0 37 110.5 38 140.5 39 163.0 40 189.0 41 203.5 42 264.0 43 314.5 44 279.0 45 266.5 46 264.0 47 227.5 48 204.5 49 178.5 50 151.0 51 126.5 52 101.0 53 97.0 54 89.0 55 72.0 56 53.5 57 36.5 58 24.5 59 20.5 60 17.5 61 13.0 62 8.0 63 5.0 64 2.5 65 0.0 66 0.5 67 1.5 68 1.0 69 0.0 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.5 76 0.5 77 0.5 78 0.5 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 0.0 2 0.0 3 0.025 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 0.15 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 92.425 #Duplication Level Percentage of deduplicated Percentage of total 1 98.80984582093589 91.325 2 0.7573708412226129 1.4000000000000001 3 0.10819583446037327 0.3 4 0.08114687584527995 0.3 5 0.08114687584527995 0.375 6 0.0 0.0 7 0.0 0.0 8 0.027048958615093318 0.2 9 0.054097917230186636 0.44999999999999996 >10 0.054097917230186636 0.8 >50 0.0 0.0 >100 0.027048958615093318 4.8500000000000005 >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 GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCTTCGCCTGTGTAGATCT 194 4.8500000000000005 Illumina Single End PCR Primer 1 (96% over 32bp) AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCTTCGCCTGTGTAGATC 20 0.5 Illumina Single End PCR Primer 1 (96% over 33bp) AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 12 0.3 No Hit ATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAAT 9 0.22499999999999998 No Hit AACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAA 9 0.22499999999999998 No Hit GATCGGAAGAGCGTCGTGTATGGAAAGAGTGTCTTCGCCTGTGTAGATCT 8 0.2 Illumina Single End PCR Primer 1 (96% over 32bp) GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCTTCGCCTGTGTCGATCT 5 0.125 Illumina Single End PCR Primer 1 (96% over 32bp) GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCTTCGCCTGTGTTGATCT 5 0.125 Illumina Single End PCR Primer 1 (96% over 32bp) AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 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 0.675 0.0 0.0 0.0 0.0 2 0.7 0.0 0.0 0.0 0.0 3 0.7 0.0 0.0 0.0 0.0 4 0.7 0.0 0.0 0.0 0.0 5 0.7 0.0 0.0 0.0 0.0 6 0.7 0.0 0.0 0.0 0.0 7 0.7 0.0 0.0 0.0 0.0 8 0.7 0.0 0.0 0.0 0.0 9 0.7 0.0 0.0 0.0 0.0 10-11 0.7 0.0 0.0 0.0 0.0 12-13 0.7 0.0 0.0 0.0 0.0 14-15 0.7 0.0 0.0 0.0 0.0 16-17 0.7 0.0 0.0 0.0 0.0 18-19 0.7 0.0 0.0 0.0 0.0 20-21 0.7 0.0 0.0 0.0 0.0 22-23 0.7 0.0 0.0 0.0 0.0 24-25 0.7 0.0 0.0 0.0 0.0 26-27 0.7 0.0 0.0 0.0 0.0 28-29 0.7 0.0 0.0 0.0 0.0 30-31 0.7 0.0 0.0 0.0 0.0 32-33 0.7 0.0 0.0 0.0 0.0 34-35 0.7 0.0 0.0 0.0 0.0 36-37 0.7 0.0 0.0 0.0 0.0 38-39 0.7 0.0 0.0 0.0 0.0 40-41 0.7 0.0 0.0 0.0 0.0 42-43 0.7 0.0 0.0 0.0 0.0 44-45 0.7 0.0 0.0 0.0 0.0 46-47 0.7 0.0 0.0 0.0 0.0 48-49 0.725 0.0 0.0 0.0 0.0 50-51 0.725 0.0 0.0 0.0 0.0 52-53 0.725 0.0 0.0 0.0 0.0 54-55 0.7375 0.0 0.0 0.0 0.0 56-57 0.75 0.0 0.0 0.0 0.0 58-59 0.75 0.0 0.0 0.0 0.0 60-61 0.75 0.0 0.0 0.0 0.0 62-63 0.7625 0.0 0.0 0.0 0.0 64-65 0.8 0.0 0.0 0.0 0.0 66-67 0.8 0.0 0.0 0.0 0.0 68-69 0.825 0.0 0.0 0.0 0.0 70-71 0.875 0.0 0.0 0.0 0.0 72-73 0.9125000000000001 0.0 0.0 0.0 0.0 74-75 0.975 0.0 0.0 0.0 0.0 76-77 0.9875 0.0 0.0 0.0 0.0 78-79 1.1124999999999998 0.0 0.0 0.0 0.0 80-81 1.25 0.0 0.0 0.0 0.0 82-83 1.3 0.0 0.0 0.0 0.0 84-85 1.3875000000000002 0.0 0.0 0.0 0.0 86-87 1.5875 0.0 0.0 0.0 0.0 88-89 1.825 0.0 0.0 0.0 0.0 90-91 2.0625 0.0 0.0 0.0 0.0 92-93 2.35 0.0 0.0 0.0 0.0 94-95 2.5999999999999996 0.0 0.0 0.0 0.0 96-97 2.8875 0.0 0.0 0.0 0.0 98-99 3.175 0.0 0.0 0.0 0.0 100-101 3.5125 0.0 0.0 0.0 0.0 102-103 3.7125 0.0 0.0 0.0 0.0 104-105 4.125 0.0 0.0 0.0 0.0 106-107 4.5875 0.0 0.0 0.0 0.0 108-109 4.975 0.0 0.0 0.0 0.0 110-111 5.3875 0.0 0.0 0.0 0.0 112-113 5.8375 0.0 0.0 0.0 0.0 114-115 6.325 0.0 0.0 0.0 0.0 116-117 7.0625 0.0 0.0 0.0 0.0 118-119 7.775 0.0 0.0 0.0 0.0 120-121 8.4 0.0 0.0 0.0 0.0 122-123 9.1375 0.0 0.0 0.0 0.0 124-125 9.575 0.0 0.0 0.0 0.0 126-127 10.1375 0.0 0.0 0.0 0.0 128-129 10.7875 0.0 0.0 0.0 0.0 130-131 11.425 0.0 0.0 0.0 0.0 132-133 12.1875 0.0 0.0 0.0 0.0 134-135 12.975000000000001 0.0 0.0 0.0 0.0 136-137 13.775 0.0 0.0 0.0 0.0 138-139 14.3875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAGCGTC 90 1.8189894E-12 72.5 9 CGGAAGA 90 1.8189894E-12 72.5 4 AAGAGCG 95 3.6379788E-12 68.68421 7 GATCGGA 95 3.6379788E-12 68.68421 1 TCGGAAG 95 3.6379788E-12 68.68421 3 AGAGCGT 95 3.6379788E-12 68.68421 8 GGAAGAG 95 3.6379788E-12 68.68421 5 GAAGAGC 100 5.456968E-12 65.25 6 ATCGGAA 100 5.456968E-12 65.25 2 TGGTCGC 50 7.0600436E-8 26.1 50-54 CATTAAA 50 7.0600436E-8 26.1 65-69 ATTAAAA 50 7.0600436E-8 26.1 65-69 ATCATTA 50 7.0600436E-8 26.1 60-64 GGTGGTC 50 7.0600436E-8 26.1 50-54 GTGGTCG 50 7.0600436E-8 26.1 50-54 TCATTAA 50 7.0600436E-8 26.1 65-69 TTAAAAA 50 7.0600436E-8 26.1 65-69 GTCGCCG 40 9.990927E-6 25.375 55-59 CCGTATC 40 9.990927E-6 25.375 60-64 TCGCCGT 40 9.990927E-6 25.375 55-59 >>END_MODULE Read 581316 spots for SRR7171119.sra Written 581316 spots for SRR7171119.sra Read 581316 spots for SRR7171119.sra Written 581316 spots for SRR7171119.sra Read 581316 spots for SRR7171119.sra Written 581316 spots for SRR7171119.sra Read 581316 spots for SRR7171119.sra Written 581316 spots for SRR7171119.sra Read 581316 spots for SRR7171119.sra Written 581316 spots for SRR7171119.sra Read 581316 spots for SRR7171119.sra Written 581316 spots for SRR7171119.sra Read 581316 spots for SRR7171119.sra Written 581316 spots for SRR7171119.sra Read 581316 spots for SRR7171119.sra Written 581316 spots for SRR7171119.sra Read 581316 spots for SRR7171119.sra Written 581316 spots for SRR7171119.sra Read 581316 spots for SRR7171119.sra Written 581316 spots for SRR7171119.sra Read 581316 spots for SRR7171119.sra Written 581316 spots for SRR7171119.sra Read 581316 spots for SRR7171119.sra Written 581316 spots for SRR7171119.sra Read 581322 spots for SRR7171119.sra Written 581322 spots for SRR7171119.sra Read 581316 spots for SRR7171119.sra Written 581316 spots for SRR7171119.sra Read 581316 spots for SRR7171119.sra Written 581316 spots for SRR7171119.sra Read 581316 spots for SRR7171119.sra Written 581316 spots for SRR7171119.sra Read 581316 spots for SRR7171119.sra Written 581316 spots for SRR7171119.sra Read 581316 spots for SRR7171119.sra Written 581316 spots for SRR7171119.sra Read 581316 spots for SRR7171119.sra Written 581316 spots for SRR7171119.sra Read 581316 spots for SRR7171119.sra Written 581316 spots for SRR7171119.sra SRR ids: ['SRR7171119.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_y84_ww3p SRR7171119.sra spots: 11626326 blocks: [[1, 581316], [581317, 1162632], [1162633, 1743948], [1743949, 2325264], [2325265, 2906580], [2906581, 3487896], [3487897, 4069212], [4069213, 4650528], [4650529, 5231844], [5231845, 5813160], [5813161, 6394476], [6394477, 6975792], [6975793, 7557108], [7557109, 8138424], [8138425, 8719740], [8719741, 9301056], [9301057, 9882372], [9882373, 10463688], [10463689, 11045004], [11045005, 11626326]] SRR7171119 file size 3918080 SRR7171119 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 SRR7171119 SRR7171119_1.fastq SRR7171119_2.fastq Input file: SRR7171119_1.fastq Paired file: SRR7171119_2.fastq trimmed: SRR7171119-trimmed-pair1.fastq, SRR7171119-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 Fri Feb 14 06:41:40 2025 >> started Fri Feb 14 06:42:01 2025 >> done (20.588s) 11626326 read pairs processed; of these: 26320 ( 0.23%) short read pairs filtered out after trimming by size control 909640 ( 7.82%) empty read pairs filtered out after trimming by size control 10690366 (91.95%) read pairs available; of these: 6830024 (63.89%) trimmed read pairs available after processing 3860342 (36.11%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 39 0.00% 19 55 0.00% 20 58 0.00% 21 74 0.00% 22 55 0.00% 23 60 0.00% 24 68 0.00% 25 82 0.00% 26 67 0.00% 27 104 0.00% 28 101 0.00% 29 87 0.00% 30 98 0.00% 31 150 0.00% 32 110 0.00% 33 88 0.00% 34 119 0.00% 35 112 0.00% 36 113 0.00% 37 143 0.00% 38 175 0.00% 39 165 0.00% 40 201 0.00% 41 221 0.00% 42 284 0.00% 43 352 0.00% 44 393 0.00% 45 674 0.01% 46 873 0.01% 47 849 0.01% 48 864 0.01% 49 880 0.01% 50 922 0.01% 51 930 0.01% 52 927 0.01% 53 909 0.01% 54 974 0.01% 55 1047 0.01% 56 1089 0.01% 57 1072 0.01% 58 1303 0.01% 59 1381 0.01% 60 1545 0.01% 61 2010 0.02% 62 1817 0.02% 63 2149 0.02% 64 1976 0.02% 65 2044 0.02% 66 2004 0.02% 67 2141 0.02% 68 2414 0.02% 69 2670 0.02% 70 3003 0.03% 71 3591 0.03% 72 5440 0.05% 73 5691 0.05% 74 7250 0.07% 75 11008 0.10% 76 36402 0.34% 77 33534 0.31% 78 11862 0.11% 79 9223 0.09% 80 9094 0.09% 81 9424 0.09% 82 9952 0.09% 83 10525 0.10% 84 12089 0.11% 85 12731 0.12% 86 13415 0.13% 87 14407 0.13% 88 15735 0.15% 89 16077 0.15% 90 17370 0.16% 91 18357 0.17% 92 18878 0.18% 93 21034 0.20% 94 21347 0.20% 95 22616 0.21% 96 22481 0.21% 97 22859 0.21% 98 23078 0.22% 99 24039 0.22% 100 26051 0.24% 101 25510 0.24% 102 27665 0.26% 103 28197 0.26% 104 29782 0.28% 105 31420 0.29% 106 31383 0.29% 107 31341 0.29% 108 31621 0.30% 109 33085 0.31% 110 33297 0.31% 111 34098 0.32% 112 35438 0.33% 113 37621 0.35% 114 37859 0.35% 115 40328 0.38% 116 40895 0.38% 117 40520 0.38% 118 40705 0.38% 119 40296 0.38% 120 42037 0.39% 121 41951 0.39% 122 43825 0.41% 123 45702 0.43% 124 46673 0.44% 125 47587 0.45% 126 48494 0.45% 127 49735 0.47% 128 50234 0.47% 129 50848 0.48% 130 52442 0.49% 131 52755 0.49% 132 54683 0.51% 133 57907 0.54% 134 61169 0.57% 135 64178 0.60% 136 66400 0.62% 137 71796 0.67% 138 73883 0.69% 139 78188 0.73% 140 82393 0.77% 141 89645 0.84% 142 96531 0.90% 143 104709 0.98% 144 119605 1.12% 145 136117 1.27% 146 167004 1.56% 147 215091 2.01% 148 313679 2.93% 149 595018 5.57% 150 2631083 24.61% 151 3860342 36.11% 10690366 reads passed initial QC criterion=sequence-density sequence-density=0.41 sequence-density-rank=1 fanout-score=1.96 fanout-score-rank=30 prefix-density=0.41 prefix-fanout=1.9 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=94.98 fanout-score-rank=1 prefix-density=0.10 prefix-fanout=11.4 sequence=AAACAGAATATTTACTTTTAGCGCAAGTTTCAATTCATGAGCTCGTTACATCACAAGTTAACATTACAAGCCAATAGTCCCAGCACAGAAAAAACTCTTTTGTTGCTCACTTTCCGGGAACGAAGTTTGTGGCATATGCCCAGGCGTTGTTGTTTACTGGGTCAGAAAGGTGGTCAGC criterion=sequence-density sequence-density=0.39 sequence-density-rank=1 fanout-score=2.29 fanout-score-rank=23 prefix-density=0.42 prefix-fanout=2.1 sequence=GCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATG criterion=fanout-score sequence-density=0.01 sequence-density-rank=32 fanout-score=34.57 fanout-score-rank=1 prefix-density=0.05 prefix-fanout=4.3 sequence=CCAAAGCTCAAAAAAAATCTTAACTGCACCCGCTCATCCAGCAATGGCAGCAGCAACAATGGCCCTCTC SRR7171119 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 14 06:43:00 Started mapping on | Feb 14 06:43:00 Finished on | Feb 14 06:44:33 Mapping speed, Million of reads per hour | 413.82 Number of input reads | 10690366 Average input read length | 284 UNIQUE READS: Uniquely mapped reads number | 9660917 Uniquely mapped reads % | 90.37% Average mapped length | 285.62 Number of splices: Total | 8822075 Number of splices: Annotated (sjdb) | 8608795 Number of splices: GT/AG | 8654422 Number of splices: GC/AG | 127003 Number of splices: AT/AC | 6201 Number of splices: Non-canonical | 34449 Mismatch rate per base, % | 0.39% Deletion rate per base | 0.03% Deletion average length | 2.45 Insertion rate per base | 0.02% Insertion average length | 1.99 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 260382 % of reads mapped to multiple loci | 2.44% Number of reads mapped to too many loci | 27713 % of reads mapped to too many loci | 0.26% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.81% % of reads unmapped: other | 0.12% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 793189 793189 793189 N_multimapping 260382 260382 260382 N_noFeature 414763 9379404 500968 N_ambiguous 262079 851 66551 UnstrandedReadsAssigned:8984075 PositiveStrandReadsAssigned:280662 NegativeStrandReadsAssigned:9093398 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=141 echo kmer=137 SRR7171119 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: SRR7171119-trimmed-pair1.fastq SRR7171119-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 10,690,366 reads, 9,002,333 reads pseudoaligned [quant] estimated average fragment length: 212.675 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,084 rounds 52401 SRR7171119.ke.tsv 34699 SRR7171119.se.tsv 87100 total ==> SRR7171119.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1806.32 421 16.7084 Potri.005G024800.1.v4.1 1035 823.325 331 28.8207 Potri.004G059700.1.v4.1 961 749.374 9 0.860978 Potri.007G009000.2.v4.1 1416 1204.32 0 0 Potri.003G141000.2.v4.1 2943 2731.32 476.755 12.5132 Potri.016G087400.1.v4.1 270 97.532 713 524.071 Potri.015G069301.1.v4.1 564 356.122 0 0 Potri.010G195200.1.v4.1 1773 1561.32 100 4.5915 Potri.012G127500.1.v4.1 977 765.35 49 4.5897 ==> SRR7171119.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 415 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 299 Potri.001G212900.v4.1 20 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 2 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 13 SRR7171119 completed mapping pipeline successfully