Starting /dee2/code/volunteer_pipeline.sh SRR12670105 current disk space = 3057642225664 free memory = 1463642016 SRR12670105 SRAfilesize 8eb22768128fa9ffe32e20c5d6248452 SRR12670105.sra SRR12670105.sra file validated SRR12670105 is paired end SRR12670105 is conventional basespace SRR12670105 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670105_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 36.621 37.0 37.0 37.0 37.0 37.0 2 36.29225 37.0 37.0 37.0 37.0 37.0 3 36.646 37.0 37.0 37.0 37.0 37.0 4 36.7105 37.0 37.0 37.0 37.0 37.0 5 36.651 37.0 37.0 37.0 37.0 37.0 6 36.6695 37.0 37.0 37.0 37.0 37.0 7 36.5065 37.0 37.0 37.0 37.0 37.0 8 36.6065 37.0 37.0 37.0 37.0 37.0 9 36.677 37.0 37.0 37.0 37.0 37.0 10-14 36.654599999999995 37.0 37.0 37.0 37.0 37.0 15-19 36.5597 37.0 37.0 37.0 37.0 37.0 20-24 36.5363 37.0 37.0 37.0 37.0 37.0 25-29 36.5176 37.0 37.0 37.0 37.0 37.0 30-34 36.5686 37.0 37.0 37.0 37.0 37.0 35-39 36.507600000000004 37.0 37.0 37.0 37.0 37.0 40-44 36.5068 37.0 37.0 37.0 37.0 37.0 45-49 36.477399999999996 37.0 37.0 37.0 37.0 37.0 50-54 36.4291 37.0 37.0 37.0 37.0 37.0 55-59 36.4349 37.0 37.0 37.0 37.0 37.0 60-64 36.378699999999995 37.0 37.0 37.0 37.0 37.0 65-69 36.3557 37.0 37.0 37.0 37.0 37.0 70-74 36.2953 37.0 37.0 37.0 37.0 37.0 75-79 36.32450000000001 37.0 37.0 37.0 37.0 37.0 80-84 36.295 37.0 37.0 37.0 37.0 37.0 85-89 36.293 37.0 37.0 37.0 37.0 37.0 90-94 36.3349 37.0 37.0 37.0 37.0 37.0 95-99 36.2435 37.0 37.0 37.0 37.0 37.0 100-104 36.2747 37.0 37.0 37.0 37.0 37.0 105-109 36.2389 37.0 37.0 37.0 37.0 37.0 110-114 36.165200000000006 37.0 37.0 37.0 37.0 37.0 115-119 36.2411 37.0 37.0 37.0 37.0 37.0 120-124 36.1131 37.0 37.0 37.0 37.0 37.0 125-129 36.027100000000004 37.0 37.0 37.0 37.0 37.0 130-134 36.0459 37.0 37.0 37.0 37.0 37.0 135-139 35.9497 37.0 37.0 37.0 37.0 37.0 140-144 35.82090000000001 37.0 37.0 37.0 37.0 37.0 145-149 35.841899999999995 37.0 37.0 37.0 37.0 37.0 150-151 35.554 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 1.0 24 0.0 25 3.0 26 2.0 27 8.0 28 8.0 29 20.0 30 25.0 31 32.0 32 38.0 33 75.0 34 112.0 35 286.0 36 2987.0 37 403.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 32.425 10.8 5.225 51.55 2 16.587321473314958 13.304936106239037 39.38862440491105 30.719118015534953 3 15.275 14.975 29.025000000000002 40.725 4 22.35 22.775000000000002 23.5 31.374999999999996 5 21.7 32.125 24.0 22.175 6 19.775000000000002 34.475 23.849999999999998 21.9 7 15.225 25.724999999999998 40.5 18.55 8 16.5 27.125 31.8 24.575 9 17.5 24.6 35.225 22.675 10-14 19.39 29.725 27.565 23.32 15-19 19.67 27.99 27.925 24.415 20-24 20.415 27.544999999999998 28.599999999999998 23.44 25-29 20.19 29.134999999999998 27.544999999999998 23.13 30-34 20.525 28.255000000000003 26.805 24.415 35-39 20.26 28.405 27.775 23.56 40-44 19.895 29.044999999999998 27.644999999999996 23.415 45-49 20.155 27.994999999999997 27.665 24.185000000000002 50-54 20.155 27.92 27.615000000000002 24.310000000000002 55-59 20.705000000000002 27.77 27.62 23.905 60-64 20.3 27.79 28.13 23.78 65-69 20.03 28.055000000000003 28.455000000000002 23.46 70-74 20.625 27.485 28.1 23.79 75-79 20.285 27.625 28.475 23.615 80-84 20.78 28.33 27.134999999999998 23.755000000000003 85-89 20.66 28.71 27.375 23.255 90-94 20.565 27.884999999999998 27.605 23.945 95-99 20.580000000000002 27.22 27.975 24.224999999999998 100-104 20.93 28.74 27.41 22.919999999999998 105-109 21.235 27.955000000000002 27.205000000000002 23.605 110-114 21.015 28.175 26.66 24.15 115-119 21.515 27.975 27.215 23.294999999999998 120-124 21.12 28.585 27.055 23.24 125-129 21.015 27.825 27.400000000000002 23.76 130-134 21.075 29.095 26.179999999999996 23.65 135-139 21.05 27.975 27.045 23.93 140-144 21.075 26.875 28.03 24.02 145-149 21.62 27.73 26.91 23.74 150-151 21.5375 26.987499999999997 27.125 24.349999999999998 >>END_MODULE >>Per sequence GC content pass #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 0.0 8 0.0 9 0.0 10 0.5 11 0.5 12 0.0 13 0.0 14 0.5 15 0.5 16 1.0 17 1.0 18 0.0 19 0.0 20 0.5 21 0.5 22 0.5 23 0.5 24 3.5 25 6.0 26 2.5 27 2.5 28 7.0 29 12.5 30 14.5 31 11.0 32 20.0 33 35.0 34 51.0 35 70.5 36 73.0 37 91.0 38 124.0 39 154.0 40 193.0 41 230.5 42 245.0 43 249.0 44 277.5 45 276.5 46 251.0 47 237.0 48 240.0 49 223.5 50 186.0 51 160.5 52 124.0 53 94.0 54 77.5 55 70.0 56 55.0 57 39.5 58 27.5 59 16.0 60 12.5 61 8.5 62 4.5 63 2.5 64 2.5 65 3.5 66 3.0 67 2.0 68 1.5 69 0.5 70 0.0 71 0.0 72 0.0 73 1.0 74 1.0 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 0.0 2 0.22499999999999998 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 79.35 #Duplication Level Percentage of deduplicated Percentage of total 1 80.46628859483302 63.849999999999994 2 14.650283553875237 23.25 3 3.6862003780718333 8.774999999999999 4 0.9136735979836169 2.9000000000000004 5 0.1890359168241966 0.75 6 0.0630119722747322 0.3 7 0.0315059861373661 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >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 GTGGAAGATTTCCCAACTCCTCCTTTGCCCATAACAAGTATGGTCAGTTT 7 0.17500000000000002 No Hit CCTAACAGATAGCTAGGGACTCATCAAATCTTGAAACCTAGACACCCTTC 6 0.15 No Hit GCACGAAATCCAGTTGAATTCCCTTGTTATCTGATGGGAGTTATAGCTTA 6 0.15 No Hit CTTGCATCTTGATTTGACTCAGATTGAGCAGCAGCTTGCCGATTGACCAT 5 0.125 No Hit CCTGCCTTGAGACGAAGGTCATTTTGGACATAAGGCCAAGCCTTCTGGTC 5 0.125 No Hit GTTCCAAGTCAAAGTGGCTCTCGACACGCTGCTTTGTAACAGTCTTGGCA 5 0.125 No Hit GCTTGGGCAGAACTTTGATCACTATTTGAGTTCGCAGTTATTGTTTGCTG 5 0.125 No Hit CCACACCAGAGGCCACAGACATGGCCAATACATAACAATGAAGAAGACAC 5 0.125 No Hit CCAGCAGCTAAATAATGTTTTGCTAGAAAACCCCAGCAAAAGAAACCTAA 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 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.1875 0.0 0.0 0.0 0.0 78-79 0.2625 0.0 0.0 0.0 0.0 80-81 0.6000000000000001 0.0 0.0 0.0 0.0 82-83 0.775 0.0 0.0 0.0 0.0 84-85 0.9875 0.0 0.0 0.0 0.0 86-87 1.1875 0.0 0.0 0.0 0.0 88-89 1.2875 0.0 0.0 0.0 0.0 90-91 1.525 0.0 0.0 0.0 0.0 92-93 1.7375 0.0 0.0 0.0 0.0 94-95 2.175 0.0 0.0 0.0 0.0 96-97 2.375 0.0 0.0 0.0 0.0 98-99 2.8625 0.0 0.0 0.0 0.0 100-101 3.1500000000000004 0.0 0.0 0.0 0.0 102-103 3.4875 0.0 0.0 0.0 0.0 104-105 3.825 0.0 0.0 0.0 0.0 106-107 4.2875 0.0 0.0 0.0 0.0 108-109 4.7625 0.0 0.0 0.0 0.0 110-111 5.3875 0.0 0.0 0.0 0.0 112-113 5.875 0.0 0.0 0.0 0.0 114-115 6.4125 0.0 0.0 0.0 0.0 116-117 6.95 0.0 0.0 0.0 0.0 118-119 7.4375 0.0 0.0 0.0 0.0 120-121 7.9375 0.0 0.0 0.0 0.0 122-123 8.45 0.0 0.0 0.0 0.0 124-125 9.212499999999999 0.0 0.0 0.0 0.0 126-127 9.8375 0.0 0.0 0.0 0.0 128-129 10.399999999999999 0.0 0.0 0.0 0.0 130-131 10.9875 0.0 0.0 0.0 0.0 132-133 11.7 0.0 0.0 0.0 0.0 134-135 12.2 0.0 0.0 0.0 0.0 136-137 12.6875 0.0 0.0 0.0 0.0 138-139 13.537500000000001 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CCCTGAT 10 0.006830828 145.0 1 CAGTCAC 40 0.005621335 54.375 145 >>END_MODULE SRR12670105 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670105_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 36.4015 37.0 37.0 37.0 37.0 37.0 2 36.2825 37.0 37.0 37.0 37.0 37.0 3 36.1855 37.0 37.0 37.0 37.0 37.0 4 36.206 37.0 37.0 37.0 37.0 37.0 5 36.3765 37.0 37.0 37.0 37.0 37.0 6 36.384 37.0 37.0 37.0 37.0 37.0 7 36.301 37.0 37.0 37.0 37.0 37.0 8 36.3295 37.0 37.0 37.0 37.0 37.0 9 36.368 37.0 37.0 37.0 37.0 37.0 10-14 36.4135 37.0 37.0 37.0 37.0 37.0 15-19 36.3986 37.0 37.0 37.0 37.0 37.0 20-24 36.3634 37.0 37.0 37.0 37.0 37.0 25-29 36.3421 37.0 37.0 37.0 37.0 37.0 30-34 36.2889 37.0 37.0 37.0 37.0 37.0 35-39 36.310500000000005 37.0 37.0 37.0 37.0 37.0 40-44 36.307399999999994 37.0 37.0 37.0 37.0 37.0 45-49 36.275299999999994 37.0 37.0 37.0 37.0 37.0 50-54 36.232 37.0 37.0 37.0 37.0 37.0 55-59 36.190999999999995 37.0 37.0 37.0 37.0 37.0 60-64 36.1507 37.0 37.0 37.0 37.0 37.0 65-69 36.14790000000001 37.0 37.0 37.0 37.0 37.0 70-74 36.106 37.0 37.0 37.0 37.0 37.0 75-79 36.1342 37.0 37.0 37.0 37.0 37.0 80-84 36.0868 37.0 37.0 37.0 37.0 37.0 85-89 36.1041 37.0 37.0 37.0 37.0 37.0 90-94 36.0754 37.0 37.0 37.0 37.0 37.0 95-99 35.947500000000005 37.0 37.0 37.0 37.0 37.0 100-104 35.954100000000004 37.0 37.0 37.0 37.0 37.0 105-109 35.9661 37.0 37.0 37.0 37.0 37.0 110-114 35.8555 37.0 37.0 37.0 37.0 37.0 115-119 35.9293 37.0 37.0 37.0 37.0 37.0 120-124 35.8017 37.0 37.0 37.0 37.0 37.0 125-129 35.689099999999996 37.0 37.0 37.0 37.0 37.0 130-134 35.56680000000001 37.0 37.0 37.0 34.6 37.0 135-139 35.490100000000005 37.0 37.0 37.0 37.0 37.0 140-144 35.4009 37.0 37.0 37.0 37.0 37.0 145-149 35.057 37.0 37.0 37.0 25.0 37.0 150-151 34.767624999999995 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 0.0 21 0.0 22 0.0 23 1.0 24 7.0 25 3.0 26 4.0 27 7.0 28 11.0 29 18.0 30 28.0 31 40.0 32 62.0 33 107.0 34 206.0 35 557.0 36 2681.0 37 267.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 33.525 22.15 9.475 34.849999999999994 2 24.075 28.075 33.25 14.6 3 18.475 28.475 32.0 21.05 4 22.1 35.475 23.025000000000002 19.400000000000002 5 23.575 37.075 22.575 16.775000000000002 6 20.25 40.225 23.375 16.150000000000002 7 20.125 21.875 39.0 19.0 8 20.625 25.1 30.325000000000003 23.95 9 22.425 24.224999999999998 29.95 23.400000000000002 10-14 22.645 29.57 26.534999999999997 21.25 15-19 22.965 27.785 28.23 21.02 20-24 22.43 28.610000000000003 27.99 20.97 25-29 22.63 28.175 28.26 20.935000000000002 30-34 22.58 28.105000000000004 27.93 21.385 35-39 22.939999999999998 28.144999999999996 27.77 21.145 40-44 23.035 27.275 27.985 21.705 45-49 22.32 27.83 28.64 21.21 50-54 22.665 27.485 28.32 21.529999999999998 55-59 23.105 28.299999999999997 27.11 21.485000000000003 60-64 22.86 27.644999999999996 28.64 20.855 65-69 23.18 27.615000000000002 27.779999999999998 21.425 70-74 23.195 28.165000000000003 27.575 21.065 75-79 23.275000000000002 27.905 27.265 21.555 80-84 23.18 27.565 27.900000000000002 21.355 85-89 23.54 28.525 26.810000000000002 21.125 90-94 24.560000000000002 27.560000000000002 26.995 20.885 95-99 23.52 28.79 27.11 20.580000000000002 100-104 24.485 28.389999999999997 26.465 20.66 105-109 24.18 28.315 27.389999999999997 20.115 110-114 24.585 28.12 27.005000000000003 20.29 115-119 25.235000000000003 27.839999999999996 27.134999999999998 19.79 120-124 25.900000000000002 27.439999999999998 26.669999999999998 19.99 125-129 25.3 28.42 26.605 19.675 130-134 25.95 28.225 26.08 19.744999999999997 135-139 26.56 27.79 26.540000000000003 19.11 140-144 26.995 26.595000000000002 26.805 19.605 145-149 27.732773277327734 26.72267226722672 26.422642264226422 19.121912191219124 150-151 28.79109888736092 27.590948868608578 25.415676959619955 18.20227528441055 >>END_MODULE >>Per sequence GC content pass #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 0.5 11 0.5 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.5 19 0.5 20 2.5 21 3.0 22 1.5 23 2.0 24 1.5 25 2.0 26 2.0 27 3.5 28 7.5 29 8.5 30 18.0 31 27.5 32 28.0 33 35.5 34 53.5 35 71.0 36 87.0 37 112.0 38 138.0 39 149.0 40 182.0 41 226.0 42 243.0 43 256.0 44 270.0 45 253.0 46 256.5 47 269.0 48 252.5 49 227.0 50 171.0 51 124.5 52 100.0 53 98.5 54 90.0 55 58.0 56 46.5 57 40.5 58 28.5 59 18.5 60 12.0 61 7.5 62 4.0 63 3.0 64 0.0 65 0.0 66 1.0 67 1.0 68 0.0 69 1.0 70 1.5 71 0.5 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 0.5 >>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 0.01 150-151 0.0125 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 79.5 #Duplication Level Percentage of deduplicated Percentage of total 1 80.9748427672956 64.375 2 14.08805031446541 22.400000000000002 3 3.6792452830188678 8.774999999999999 4 0.8805031446540881 2.8000000000000003 5 0.25157232704402516 1.0 6 0.06289308176100629 0.3 7 0.06289308176100629 0.35000000000000003 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >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 CTCTATTTCTCTTCCGCAGTTAGGCGACATATTCAAGAGGCATCAATGGG 7 0.17500000000000002 No Hit AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 7 0.17500000000000002 No Hit GGAAATTGAGTACCTTCTTCGCAACAAGTGGGTTCCTTGCTTGGAATTCG 6 0.15 No Hit GGGAGAGAAATGGGATATAGCCATGGCTGCTGTCTATCTTGCATCTGATG 6 0.15 No Hit GCTGCGGATAGTCTTCTCCCCAGACTTGAAGATATGCTCTTGGGAGTTTT 5 0.125 No Hit TGTAAAGGAGGTGAAGCCAAGACCTGATGGTTCAATTCAGCAAGAGATTG 5 0.125 No Hit CGCATATATTTCCAAGATGAAGGCCTTTCTTATCGTATGCTTTCTCTTAG 5 0.125 No Hit GAACGAATCAAGGAAGAGATCGAAGCCCTTGTTGGGGCTATTCATCCTAA 5 0.125 No Hit CTCTCATCAAGAACCCATTTCCAAGATTTTCAAGAAATGGCAAACCAACT 5 0.125 No Hit GACGGTCTTCAGTATACATTTTCCCATGTTGGTCAGTTGACGGGAATGTA 5 0.125 No Hit CTCAGAACTTGGTTCAAGATCTACAAGAGGAACTTGAGATGAAGGATTCA 5 0.125 No Hit ATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAAT 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 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.025 0.0 32-33 0.025 0.0 0.0 0.025 0.0 34-35 0.025 0.0 0.0 0.025 0.0 36-37 0.025 0.0 0.0 0.025 0.0 38-39 0.025 0.0 0.0 0.025 0.0 40-41 0.025 0.0 0.0 0.025 0.0 42-43 0.025 0.0 0.0 0.025 0.0 44-45 0.025 0.0 0.0 0.025 0.0 46-47 0.025 0.0 0.0 0.025 0.0 48-49 0.025 0.0 0.0 0.025 0.0 50-51 0.025 0.0 0.0 0.025 0.0 52-53 0.025 0.0 0.0 0.025 0.0 54-55 0.025 0.0 0.0 0.025 0.0 56-57 0.025 0.0 0.0 0.025 0.0 58-59 0.037500000000000006 0.0 0.0 0.025 0.0 60-61 0.05 0.0 0.0 0.025 0.0 62-63 0.05 0.0 0.0 0.025 0.0 64-65 0.075 0.0 0.0 0.025 0.0 66-67 0.075 0.0 0.0 0.025 0.0 68-69 0.075 0.0 0.0 0.025 0.0 70-71 0.075 0.0 0.0 0.025 0.0 72-73 0.075 0.0 0.0 0.025 0.0 74-75 0.125 0.0 0.0 0.025 0.0 76-77 0.1875 0.0 0.0 0.025 0.0 78-79 0.2625 0.0 0.0 0.025 0.0 80-81 0.6000000000000001 0.0 0.0 0.025 0.0 82-83 0.775 0.0 0.0 0.025 0.0 84-85 0.9750000000000001 0.0 0.0 0.025 0.0 86-87 1.1625 0.0 0.0 0.025 0.0 88-89 1.2625000000000002 0.0 0.0 0.025 0.0 90-91 1.5 0.0 0.0 0.025 0.0 92-93 1.725 0.0 0.0 0.025 0.0 94-95 2.175 0.0 0.0 0.025 0.0 96-97 2.375 0.0 0.0 0.025 0.0 98-99 2.8625 0.0 0.0 0.025 0.0 100-101 3.1500000000000004 0.0 0.0 0.025 0.0 102-103 3.5125 0.0 0.0 0.025 0.0 104-105 3.85 0.0 0.0 0.025 0.0 106-107 4.3125 0.0 0.0 0.025 0.0 108-109 4.8125 0.0 0.0 0.025 0.0 110-111 5.4375 0.0 0.0 0.025 0.0 112-113 5.95 0.0 0.0 0.025 0.0 114-115 6.5125 0.0 0.0 0.025 0.0 116-117 7.05 0.0 0.0 0.025 0.0 118-119 7.525 0.0 0.0 0.025 0.0 120-121 7.9875 0.0 0.0 0.025 0.0 122-123 8.5125 0.0 0.0 0.025 0.0 124-125 9.3 0.0 0.0 0.025 0.0 126-127 9.9375 0.0 0.0 0.025 0.0 128-129 10.5 0.0 0.0 0.025 0.0 130-131 11.125 0.0 0.0 0.025 0.0 132-133 11.850000000000001 0.0 0.0 0.025 0.0 134-135 12.35 0.0 0.0 0.025 0.0 136-137 12.8375 0.0 0.0 0.025 0.0 138-139 13.662500000000001 0.0 0.0 0.025 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CACCGGG 10 0.006830828 145.0 7 >>END_MODULE Read 578812 spots for SRR12670105.sra Written 578812 spots for SRR12670105.sra Read 578812 spots for SRR12670105.sra Written 578812 spots for SRR12670105.sra Read 578812 spots for SRR12670105.sra Written 578812 spots for SRR12670105.sra Read 578812 spots for SRR12670105.sra Written 578812 spots for SRR12670105.sra Read 578812 spots for SRR12670105.sra Written 578812 spots for SRR12670105.sra Read 578812 spots for SRR12670105.sra Written 578812 spots for SRR12670105.sra Read 578812 spots for SRR12670105.sra Written 578812 spots for SRR12670105.sra Read 578812 spots for SRR12670105.sra Written 578812 spots for SRR12670105.sra Read 578812 spots for SRR12670105.sra Written 578812 spots for SRR12670105.sra Read 578812 spots for SRR12670105.sra Written 578812 spots for SRR12670105.sra Read 578812 spots for SRR12670105.sra Written 578812 spots for SRR12670105.sra Read 578812 spots for SRR12670105.sra Written 578812 spots for SRR12670105.sra Read 578812 spots for SRR12670105.sra Written 578812 spots for SRR12670105.sra Read 578812 spots for SRR12670105.sra Written 578812 spots for SRR12670105.sra Read 578812 spots for SRR12670105.sra Written 578812 spots for SRR12670105.sra Read 578812 spots for SRR12670105.sra Written 578812 spots for SRR12670105.sra Read 578812 spots for SRR12670105.sra Written 578812 spots for SRR12670105.sra Read 578812 spots for SRR12670105.sra Written 578812 spots for SRR12670105.sra Read 578812 spots for SRR12670105.sra Written 578812 spots for SRR12670105.sra Read 578828 spots for SRR12670105.sra Written 578828 spots for SRR12670105.sra SRR ids: ['SRR12670105.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_dj766waf SRR12670105.sra spots: 11576256 blocks: [[1, 578812], [578813, 1157624], [1157625, 1736436], [1736437, 2315248], [2315249, 2894060], [2894061, 3472872], [3472873, 4051684], [4051685, 4630496], [4630497, 5209308], [5209309, 5788120], [5788121, 6366932], [6366933, 6945744], [6945745, 7524556], [7524557, 8103368], [8103369, 8682180], [8682181, 9260992], [9260993, 9839804], [9839805, 10418616], [10418617, 10997428], [10997429, 11576256]] SRR12670105 file size 3912417 SRR12670105 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 SRR12670105 SRR12670105_1.fastq SRR12670105_2.fastq Input file: SRR12670105_1.fastq Paired file: SRR12670105_2.fastq trimmed: SRR12670105-trimmed-pair1.fastq, SRR12670105-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 23:09:24 2025 >> started Mon Feb 10 23:09:45 2025 >> done (20.674s) 11576256 read pairs processed; of these: 46 ( 0.00%) short read pairs filtered out after trimming by size control 555 ( 0.00%) empty read pairs filtered out after trimming by size control 11575655 (99.99%) read pairs available; of these: 1910935 (16.51%) trimmed read pairs available after processing 9664720 (83.49%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 5 0.00% 20 1 0.00% 21 3 0.00% 22 3 0.00% 23 4 0.00% 24 16 0.00% 25 13 0.00% 26 17 0.00% 27 14 0.00% 28 11 0.00% 29 20 0.00% 30 18 0.00% 31 39 0.00% 32 41 0.00% 33 34 0.00% 34 35 0.00% 35 46 0.00% 36 47 0.00% 37 49 0.00% 38 63 0.00% 39 84 0.00% 40 72 0.00% 41 79 0.00% 42 97 0.00% 43 96 0.00% 44 103 0.00% 45 93 0.00% 46 129 0.00% 47 164 0.00% 48 154 0.00% 49 172 0.00% 50 217 0.00% 51 272 0.00% 52 296 0.00% 53 312 0.00% 54 351 0.00% 55 332 0.00% 56 390 0.00% 57 452 0.00% 58 520 0.00% 59 637 0.01% 60 712 0.01% 61 799 0.01% 62 865 0.01% 63 967 0.01% 64 1098 0.01% 65 1213 0.01% 66 1264 0.01% 67 1446 0.01% 68 1595 0.01% 69 1763 0.02% 70 2105 0.02% 71 2276 0.02% 72 2558 0.02% 73 2926 0.03% 74 3269 0.03% 75 3522 0.03% 76 3850 0.03% 77 4050 0.03% 78 4420 0.04% 79 4991 0.04% 80 5293 0.05% 81 5907 0.05% 82 6632 0.06% 83 7201 0.06% 84 7738 0.07% 85 8603 0.07% 86 9469 0.08% 87 9647 0.08% 88 10123 0.09% 89 10542 0.09% 90 11332 0.10% 91 12131 0.10% 92 12382 0.11% 93 13459 0.12% 94 14383 0.12% 95 15181 0.13% 96 15962 0.14% 97 16468 0.14% 98 16802 0.15% 99 17364 0.15% 100 18454 0.16% 101 18231 0.16% 102 19503 0.17% 103 19948 0.17% 104 20694 0.18% 105 21248 0.18% 106 22105 0.19% 107 22679 0.20% 108 23078 0.20% 109 23788 0.21% 110 23940 0.21% 111 24416 0.21% 112 25058 0.22% 113 25476 0.22% 114 26083 0.23% 115 27591 0.24% 116 27742 0.24% 117 28730 0.25% 118 29032 0.25% 119 29604 0.26% 120 30002 0.26% 121 30532 0.26% 122 30927 0.27% 123 31076 0.27% 124 32398 0.28% 125 32690 0.28% 126 33371 0.29% 127 34181 0.30% 128 34088 0.29% 129 34458 0.30% 130 35285 0.30% 131 35634 0.31% 132 35163 0.30% 133 36030 0.31% 134 36608 0.32% 135 36642 0.32% 136 37274 0.32% 137 38403 0.33% 138 38432 0.33% 139 39847 0.34% 140 40055 0.35% 141 40034 0.35% 142 40552 0.35% 143 40681 0.35% 144 41674 0.36% 145 41535 0.36% 146 42595 0.37% 147 42965 0.37% 148 44066 0.38% 149 43504 0.38% 150 45022 0.39% 151 9664720 83.49% 11575655 reads passed initial QC criterion=sequence-density sequence-density=0.52 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=21 prefix-density=0.50 prefix-fanout=2.0 sequence=GTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTG criterion=fanout-score sequence-density=0.02 sequence-density-rank=25 fanout-score=233.46 fanout-score-rank=1 prefix-density=0.25 prefix-fanout=16.1 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTC criterion=sequence-density sequence-density=0.47 sequence-density-rank=1 fanout-score=2.32 fanout-score-rank=22 prefix-density=0.49 prefix-fanout=2.2 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.12 sequence-density-rank=24 fanout-score=18.56 fanout-score-rank=1 prefix-density=0.50 prefix-fanout=4.4 sequence=AATGGCAGCCTCAGTTATGGCTTCACTGAACCTGAAACCATCTCCATTCACGGTTGAGAAGTCTTCAGTGAGAGGCCTCCCAACTCTTTCAAGGAGATCTTTCAAGATTGAAGCCAGTGGTGTCAAGAAGATCAAGACCGATACGCCTTATGGAACTGGTGGTGGCATGAACCT SRR12670105 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 10 23:10:34 Started mapping on | Feb 10 23:10:34 Finished on | Feb 10 23:14:07 Mapping speed, Million of reads per hour | 195.64 Number of input reads | 11575655 Average input read length | 292 UNIQUE READS: Uniquely mapped reads number | 10816764 Uniquely mapped reads % | 93.44% Average mapped length | 291.43 Number of splices: Total | 10878922 Number of splices: Annotated (sjdb) | 10624173 Number of splices: GT/AG | 10654408 Number of splices: GC/AG | 172633 Number of splices: AT/AC | 6839 Number of splices: Non-canonical | 45042 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.03% Deletion average length | 2.87 Insertion rate per base | 0.02% Insertion average length | 2.42 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 277985 % of reads mapped to multiple loci | 2.40% Number of reads mapped to too many loci | 103696 % of reads mapped to too many loci | 0.90% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.05% % of reads unmapped: other | 0.21% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 480906 480906 480906 N_multimapping 277985 277985 277985 N_noFeature 472014 10641862 534867 N_ambiguous 180624 665 68191 UnstrandedReadsAssigned:10164126 PositiveStrandReadsAssigned:174237 NegativeStrandReadsAssigned:10213706 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12670105 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: SRR12670105-trimmed-pair1.fastq SRR12670105-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 11,575,655 reads, 10,237,957 reads pseudoaligned [quant] estimated average fragment length: 232.741 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,063 rounds 52401 SRR12670105.ke.tsv 34699 SRR12670105.se.tsv 87100 total ==> SRR12670105.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1786.26 526 26.3254 Potri.005G024800.1.v4.1 1035 803.259 167 18.5864 Potri.004G059700.1.v4.1 961 729.315 3 0.367739 Potri.007G009000.2.v4.1 1416 1184.26 0 0 Potri.003G141000.2.v4.1 2943 2711.26 527 17.3769 Potri.016G087400.1.v4.1 270 93.9781 575 546.984 Potri.015G069301.1.v4.1 564 340.463 0 0 Potri.010G195200.1.v4.1 1773 1541.26 75 4.3503 Potri.012G127500.1.v4.1 977 745.285 82 9.83615 ==> SRR12670105.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 59 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 130 Potri.001G212900.v4.1 89 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 2 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 11 SRR12670105 completed mapping pipeline successfully