Starting /dee2/code/volunteer_pipeline.sh SRR12670108 current disk space = 3057609252864 free memory = 1058928112 SRR12670108 SRAfilesize 424c2f929024c642f26880e4fcd86c4d SRR12670108.sra SRR12670108.sra file validated SRR12670108 is paired end SRR12670108 is conventional basespace SRR12670108 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670108_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.5995 37.0 37.0 37.0 37.0 37.0 2 36.57075 37.0 37.0 37.0 37.0 37.0 3 36.64 37.0 37.0 37.0 37.0 37.0 4 36.6325 37.0 37.0 37.0 37.0 37.0 5 36.7135 37.0 37.0 37.0 37.0 37.0 6 36.649 37.0 37.0 37.0 37.0 37.0 7 36.6725 37.0 37.0 37.0 37.0 37.0 8 36.608 37.0 37.0 37.0 37.0 37.0 9 36.5955 37.0 37.0 37.0 37.0 37.0 10-14 36.616400000000006 37.0 37.0 37.0 37.0 37.0 15-19 36.6335 37.0 37.0 37.0 37.0 37.0 20-24 36.5653 37.0 37.0 37.0 37.0 37.0 25-29 36.5453 37.0 37.0 37.0 37.0 37.0 30-34 36.502 37.0 37.0 37.0 37.0 37.0 35-39 36.5346 37.0 37.0 37.0 37.0 37.0 40-44 36.4607 37.0 37.0 37.0 37.0 37.0 45-49 36.423199999999994 37.0 37.0 37.0 37.0 37.0 50-54 36.437799999999996 37.0 37.0 37.0 37.0 37.0 55-59 36.3605 37.0 37.0 37.0 37.0 37.0 60-64 36.3411 37.0 37.0 37.0 37.0 37.0 65-69 36.35 37.0 37.0 37.0 37.0 37.0 70-74 36.3295 37.0 37.0 37.0 37.0 37.0 75-79 36.3192 37.0 37.0 37.0 37.0 37.0 80-84 36.2945 37.0 37.0 37.0 37.0 37.0 85-89 36.2651 37.0 37.0 37.0 37.0 37.0 90-94 36.290200000000006 37.0 37.0 37.0 37.0 37.0 95-99 36.2399 37.0 37.0 37.0 37.0 37.0 100-104 36.233999999999995 37.0 37.0 37.0 37.0 37.0 105-109 36.238600000000005 37.0 37.0 37.0 37.0 37.0 110-114 36.103300000000004 37.0 37.0 37.0 37.0 37.0 115-119 36.146699999999996 37.0 37.0 37.0 37.0 37.0 120-124 36.0315 37.0 37.0 37.0 37.0 37.0 125-129 35.9304 37.0 37.0 37.0 37.0 37.0 130-134 35.830200000000005 37.0 37.0 37.0 37.0 37.0 135-139 35.714 37.0 37.0 37.0 37.0 37.0 140-144 35.4905 37.0 37.0 37.0 37.0 37.0 145-149 35.2819 37.0 37.0 37.0 34.6 37.0 150-151 35.02525 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 1.0 19 0.0 20 0.0 21 1.0 22 0.0 23 2.0 24 2.0 25 2.0 26 3.0 27 1.0 28 14.0 29 16.0 30 20.0 31 26.0 32 50.0 33 95.0 34 150.0 35 357.0 36 2886.0 37 374.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 36.9 10.75 6.7250000000000005 45.625 2 18.04755944931164 13.316645807259073 37.947434292866085 30.688360450563202 3 17.5 16.675 26.174999999999997 39.65 4 22.325 23.925 22.425 31.324999999999996 5 23.150000000000002 30.9 24.75 21.2 6 21.65 33.725 23.150000000000002 21.475 7 15.9 26.424999999999997 39.45 18.224999999999998 8 16.950000000000003 25.724999999999998 33.324999999999996 24.0 9 18.4 23.375 35.15 23.075000000000003 10-14 20.655 28.89 27.810000000000002 22.645 15-19 20.165 27.12 28.425 24.29 20-24 20.335 28.13 28.095 23.44 25-29 20.315 27.74 28.09 23.855 30-34 20.0 27.775 28.285 23.94 35-39 20.785 28.615000000000002 26.715 23.885 40-44 19.62 28.884999999999998 27.415 24.08 45-49 20.84 27.96 27.825 23.375 50-54 20.755000000000003 28.18 27.145000000000003 23.919999999999998 55-59 20.925 28.055000000000003 27.1 23.919999999999998 60-64 20.52 27.310000000000002 28.194999999999997 23.974999999999998 65-69 20.43 28.384999999999998 26.955000000000002 24.23 70-74 20.765 28.050000000000004 27.735 23.45 75-79 20.9 28.08 26.779999999999998 24.240000000000002 80-84 20.685000000000002 28.455000000000002 27.655 23.205000000000002 85-89 21.475 28.64 26.765 23.119999999999997 90-94 21.65 27.860000000000003 27.62 22.869999999999997 95-99 21.02 28.410000000000004 27.04 23.53 100-104 20.815 28.325 27.284999999999997 23.575 105-109 21.455 28.494999999999997 26.534999999999997 23.515 110-114 21.740000000000002 28.884999999999998 26.165 23.21 115-119 21.425 27.965 26.52 24.09 120-124 21.72 27.810000000000002 25.935000000000002 24.535 125-129 21.39 28.83 25.924999999999997 23.855 130-134 21.845 27.584999999999997 26.06 24.51 135-139 21.775 28.244999999999997 25.624999999999996 24.355 140-144 22.35 27.495000000000005 26.135 24.02 145-149 22.29 27.76 26.169999999999998 23.78 150-151 24.05 26.987499999999997 25.5125 23.45 >>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 0.0 11 0.0 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 1.5 21 1.5 22 1.0 23 2.5 24 1.5 25 2.0 26 3.5 27 4.5 28 6.0 29 7.0 30 14.0 31 20.5 32 27.0 33 44.5 34 51.0 35 54.0 36 75.0 37 91.0 38 108.0 39 145.0 40 179.5 41 208.5 42 228.5 43 251.5 44 268.5 45 245.5 46 259.5 47 270.0 48 236.0 49 226.5 50 200.0 51 163.5 52 127.0 53 97.0 54 89.5 55 74.0 56 57.5 57 49.5 58 36.0 59 22.5 60 15.5 61 9.5 62 8.0 63 6.0 64 2.5 65 1.5 66 3.0 67 1.5 68 0.0 69 0.0 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 0.0 2 0.125 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 80.85 #Duplication Level Percentage of deduplicated Percentage of total 1 82.06555349412493 66.35 2 13.729128014842301 22.2 3 3.0921459492888066 7.5 4 0.7730364873222016 2.5 5 0.27829313543599254 1.125 6 0.030921459492888066 0.15 7 0.030921459492888066 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 CCCTAAACTAGCAAGAAGAACAAGCAAAAAGAATGGCTCCTGTTCTAATA 7 0.17500000000000002 No Hit CTTGGCGGCGAGAGATCTGAGAATTGTGCTCGCATTTGCAGTGGGTGGTG 6 0.15 No Hit GGATCTGATACGCCAATAATATAATCTACCATGGTTGACTTGTCATTATT 5 0.125 No Hit CACTAACATCTTGATGTCCTCTCTATCCATGTTAGCTTCCTCGCCAGTAT 5 0.125 No Hit CCCATCTTTACAAGTTATACGAGCATGTGTTTTTGAAACCTGCGGTGCAG 5 0.125 No Hit CAGGGATCAATTGTTGAAGGTAGCCACAAAGCTAATGGGACCTTTTCCTG 5 0.125 No Hit GGTTAGTTCCTCCTCATCCCCTCTGCCTCCAGCAGGCAATGCAACTGCAT 5 0.125 No Hit TGGAGGGTTAGTGGGTTTCTTTTTCTCATTCTTGGTTTCAGAACGGAGCC 5 0.125 No Hit ACAAAATTGTGCACGAGTTCGTAAGATTCGCTGACGAGCACATATTGCAG 5 0.125 No Hit GCTGAGACTTGAGCTGTTCAATAACTTGTTCTCTCACGAATTTGTGGTGC 5 0.125 No Hit GAGGAAGCTTGTCAACATCATCGGTAGCAGGAAGAGCATCTGATGGAGGA 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 0.0 0.0 0.0 0.0 0.0 48-49 0.0125 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 0.0875 0.0 0.0 0.0 0.0 62-63 0.1375 0.0 0.0 0.0 0.0 64-65 0.175 0.0 0.0 0.0 0.0 66-67 0.2 0.0 0.0 0.0 0.0 68-69 0.2375 0.0 0.0 0.0 0.0 70-71 0.2875 0.0 0.0 0.0 0.0 72-73 0.35 0.0 0.0 0.0 0.0 74-75 0.4625 0.0 0.0 0.0 0.0 76-77 0.5874999999999999 0.0 0.0 0.0 0.0 78-79 0.8374999999999999 0.0 0.0 0.0 0.0 80-81 1.1 0.0 0.0 0.0 0.0 82-83 1.3375 0.0 0.0 0.0 0.0 84-85 1.6 0.0 0.0 0.0 0.0 86-87 2.0375 0.0 0.0 0.0 0.0 88-89 2.425 0.0 0.0 0.0 0.0 90-91 2.7875 0.0 0.0 0.0 0.0 92-93 3.2625 0.0 0.0 0.0 0.0 94-95 3.65 0.0 0.0 0.0 0.0 96-97 4.0875 0.0 0.0 0.0 0.0 98-99 4.55 0.0 0.0 0.0 0.0 100-101 5.325 0.0 0.0 0.0 0.0 102-103 6.0 0.0 0.0 0.0 0.0 104-105 6.9875 0.0 0.0 0.0 0.0 106-107 7.775 0.0 0.0 0.0 0.0 108-109 8.662500000000001 0.0 0.0 0.0 0.0 110-111 9.475 0.0 0.0 0.0 0.0 112-113 9.925 0.0 0.0 0.0 0.0 114-115 10.9875 0.0 0.0 0.0 0.0 116-117 12.2 0.0 0.0 0.0 0.0 118-119 13.175 0.0 0.0 0.0 0.0 120-121 14.1875 0.0 0.0 0.0 0.0 122-123 15.2875 0.0 0.0 0.0 0.0 124-125 16.3375 0.0 0.0 0.0 0.0 126-127 17.325 0.0 0.0 0.0 0.0 128-129 18.625 0.0 0.0 0.0 0.0 130-131 19.65 0.0 0.0 0.0 0.0 132-133 20.5 0.0 0.0 0.0 0.0 134-135 21.4625 0.0 0.0 0.0 0.0 136-137 22.575 0.0 0.0 0.0 0.0 138-139 23.5 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTTGGAA 10 0.006830828 145.0 1 TCCATTG 15 1.1411342E-4 145.0 2 AAAGAAC 10 0.006830828 145.0 6 GGGGGGG 65 0.0076375785 22.307692 145 >>END_MODULE SRR12670108 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670108_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.345 37.0 37.0 37.0 37.0 37.0 2 36.337 37.0 37.0 37.0 37.0 37.0 3 36.4475 37.0 37.0 37.0 37.0 37.0 4 36.3575 37.0 37.0 37.0 37.0 37.0 5 36.459 37.0 37.0 37.0 37.0 37.0 6 36.371 37.0 37.0 37.0 37.0 37.0 7 36.414 37.0 37.0 37.0 37.0 37.0 8 36.4355 37.0 37.0 37.0 37.0 37.0 9 36.4085 37.0 37.0 37.0 37.0 37.0 10-14 36.435500000000005 37.0 37.0 37.0 37.0 37.0 15-19 36.4369 37.0 37.0 37.0 37.0 37.0 20-24 36.3343 37.0 37.0 37.0 37.0 37.0 25-29 36.315200000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.3043 37.0 37.0 37.0 37.0 37.0 35-39 36.3001 37.0 37.0 37.0 37.0 37.0 40-44 36.2692 37.0 37.0 37.0 37.0 37.0 45-49 36.3107 37.0 37.0 37.0 37.0 37.0 50-54 36.2251 37.0 37.0 37.0 37.0 37.0 55-59 36.2392 37.0 37.0 37.0 37.0 37.0 60-64 36.1445 37.0 37.0 37.0 37.0 37.0 65-69 36.202299999999994 37.0 37.0 37.0 37.0 37.0 70-74 36.154900000000005 37.0 37.0 37.0 37.0 37.0 75-79 36.1074 37.0 37.0 37.0 37.0 37.0 80-84 36.061400000000006 37.0 37.0 37.0 37.0 37.0 85-89 36.034800000000004 37.0 37.0 37.0 37.0 37.0 90-94 36.0816 37.0 37.0 37.0 37.0 37.0 95-99 35.981700000000004 37.0 37.0 37.0 37.0 37.0 100-104 35.9908 37.0 37.0 37.0 37.0 37.0 105-109 35.89960000000001 37.0 37.0 37.0 37.0 37.0 110-114 35.876 37.0 37.0 37.0 37.0 37.0 115-119 35.891000000000005 37.0 37.0 37.0 37.0 37.0 120-124 35.7727 37.0 37.0 37.0 37.0 37.0 125-129 35.6524 37.0 37.0 37.0 37.0 37.0 130-134 35.5043 37.0 37.0 37.0 34.6 37.0 135-139 35.373999999999995 37.0 37.0 37.0 37.0 37.0 140-144 35.1873 37.0 37.0 37.0 32.2 37.0 145-149 34.851600000000005 37.0 37.0 37.0 27.4 37.0 150-151 34.43925 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 1.0 15 2.0 16 3.0 17 0.0 18 2.0 19 4.0 20 0.0 21 3.0 22 1.0 23 4.0 24 2.0 25 4.0 26 5.0 27 9.0 28 11.0 29 12.0 30 15.0 31 35.0 32 54.0 33 101.0 34 207.0 35 552.0 36 2699.0 37 274.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 35.449999999999996 21.875 12.475 30.2 2 25.974999999999998 27.3 30.7 16.025 3 20.525 28.225 32.025 19.225 4 23.75 34.175 23.724999999999998 18.35 5 24.675 35.65 23.075000000000003 16.6 6 18.875 40.0 22.975 18.15 7 20.549999999999997 22.2 37.775 19.475 8 20.525 25.4 28.749999999999996 25.324999999999996 9 22.3 24.55 31.574999999999996 21.575 10-14 23.06 29.56 25.995 21.385 15-19 23.125 28.02 26.845000000000002 22.009999999999998 20-24 22.6 29.49 26.88 21.029999999999998 25-29 23.115 27.355 28.565 20.965 30-34 22.795 27.445000000000004 28.139999999999997 21.62 35-39 23.23 28.33 27.63 20.810000000000002 40-44 22.7 28.215 27.439999999999998 21.645 45-49 23.515 28.27 27.095000000000002 21.12 50-54 23.16 28.255000000000003 27.72 20.865000000000002 55-59 23.365 28.08 27.43 21.125 60-64 22.545 27.66 28.515 21.279999999999998 65-69 23.695 27.555000000000003 27.555000000000003 21.195 70-74 23.474999999999998 27.63 26.669999999999998 22.225 75-79 23.415 26.995 28.044999999999998 21.545 80-84 24.34 27.200000000000003 27.310000000000002 21.15 85-89 23.549999999999997 27.48 27.255000000000003 21.715 90-94 24.83 27.935 26.3 20.935000000000002 95-99 24.355 27.42 27.02 21.205 100-104 24.51 28.43 26.645000000000003 20.415 105-109 25.155 27.105 27.034999999999997 20.705000000000002 110-114 26.145000000000003 28.34 25.905 19.61 115-119 26.27 28.01 26.25 19.470000000000002 120-124 27.195000000000004 28.044999999999998 25.255 19.505 125-129 27.685 28.860000000000003 24.795 18.66 130-134 27.66 27.685 25.674999999999997 18.98 135-139 27.85 27.794999999999998 25.974999999999998 18.38 140-144 29.104999999999997 27.36 24.884999999999998 18.65 145-149 29.94 26.935 25.44 17.685000000000002 150-151 30.45 27.224999999999998 25.387500000000003 16.9375 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 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 0.5 14 0.5 15 0.5 16 0.5 17 0.5 18 0.5 19 0.5 20 0.5 21 0.0 22 0.0 23 0.5 24 2.0 25 2.5 26 3.0 27 4.5 28 7.0 29 9.0 30 8.5 31 12.5 32 22.5 33 30.0 34 35.5 35 54.5 36 72.0 37 103.5 38 145.0 39 159.5 40 181.5 41 214.0 42 230.0 43 264.5 44 285.5 45 271.0 46 279.5 47 286.0 48 254.0 49 204.5 50 159.0 51 127.5 52 119.0 53 108.5 54 82.0 55 62.0 56 51.5 57 45.0 58 31.0 59 17.0 60 11.5 61 10.0 62 8.0 63 3.5 64 2.0 65 0.0 66 1.0 67 1.0 68 0.0 69 0.0 70 0.5 71 1.5 72 1.0 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 0.5 82 0.5 83 1.0 84 1.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.5 90 0.5 91 0.5 92 1.0 93 0.5 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 1.5 >>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 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 81.05 #Duplication Level Percentage of deduplicated Percentage of total 1 82.449105490438 66.825 2 13.325107958050586 21.6 3 3.0228254164096238 7.35 4 0.8945095619987662 2.9000000000000004 5 0.24676125848241826 1.0 6 0.030845157310302282 0.15 7 0.030845157310302282 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 CAATGAAGTTCTAACCGAGCTTGACTTAGGATTTAATGAAATAAGAGATG 7 0.17500000000000002 No Hit ATGATATTGGCCAAGCTGCCGGCTTGCTTCGTCTCCATTTCCACGACTGC 6 0.15 No Hit CTGCATAGCTTATAAGCTTGTAAGAGATGGCTTCCTCCTCTATGATCTCA 5 0.125 No Hit GAAAAACGGTTAACGCTAGAATCATTATGGAGATTGACAAAATTGCCGAG 5 0.125 No Hit AACACATCTAGCATACATACAAGATGGTGAGCTGAAGAGGGCTAAGAAGT 5 0.125 No Hit ATTTTTAATAGCAATGTCTTTTCTTTTTTATTAGGTTAAAGTTATATAAT 5 0.125 No Hit CAGTACCCATCTAAGTCTAACATCATCCCTCTTTCTTCTTCTTCCTCTTC 5 0.125 No Hit CAAGAATTCCCCACCTGATTTCCAAAAAACTAAGCTTATGACACGTTTAA 5 0.125 No Hit AGCTGATTGAGGGGTCATCCTACCTTGGCCAGCCACTTCCTTTCTCCTTG 5 0.125 No Hit TGAAGCCCCGAAGAGCTTTGAAGAATTTTGTGCAATATTGGAGAATTGTT 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 0.0 0.0 0.0 0.0 0.0 48-49 0.0125 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 0.0875 0.0 0.0 0.0 0.0 62-63 0.1375 0.0 0.0 0.0 0.0 64-65 0.175 0.0 0.0 0.0 0.0 66-67 0.2 0.0 0.0 0.0 0.0 68-69 0.2375 0.0 0.0 0.0 0.0 70-71 0.2875 0.0 0.0 0.0 0.0 72-73 0.35 0.0 0.0 0.0 0.0 74-75 0.4625 0.0 0.0 0.0 0.0 76-77 0.5874999999999999 0.0 0.0 0.0 0.0 78-79 0.8374999999999999 0.0 0.0 0.0 0.0 80-81 1.1 0.0 0.0 0.0 0.0 82-83 1.3375 0.0 0.0 0.0 0.0 84-85 1.6125 0.0 0.0 0.0 0.0 86-87 2.0375 0.0 0.0 0.0 0.0 88-89 2.4125 0.0 0.0 0.0 0.0 90-91 2.7625 0.0 0.0 0.0 0.0 92-93 3.2625 0.0 0.0 0.0 0.0 94-95 3.65 0.0 0.0 0.0 0.0 96-97 4.0875 0.0 0.0 0.0 0.0 98-99 4.55 0.0 0.0 0.0 0.0 100-101 5.325 0.0 0.0 0.0 0.0 102-103 6.0 0.0 0.0 0.0 0.0 104-105 7.0125 0.0 0.0 0.0 0.0 106-107 7.8375 0.0 0.0 0.0 0.0 108-109 8.712499999999999 0.0 0.0 0.0 0.0 110-111 9.525 0.0 0.0 0.0 0.0 112-113 10.0 0.0 0.0 0.0 0.0 114-115 11.087499999999999 0.0 0.0 0.0 0.0 116-117 12.3 0.0 0.0 0.0 0.0 118-119 13.274999999999999 0.0 0.0 0.0 0.0 120-121 14.3 0.0 0.0 0.0 0.0 122-123 15.3875 0.0 0.0 0.0 0.0 124-125 16.4375 0.0 0.0 0.0 0.0 126-127 17.425 0.0 0.0 0.0 0.0 128-129 18.725 0.0 0.0 0.0 0.0 130-131 19.75 0.0 0.0 0.0 0.0 132-133 20.6 0.0 0.0 0.0 0.0 134-135 21.612499999999997 0.0 0.0 0.0 0.0 136-137 22.7375 0.0 0.0 0.0 0.0 138-139 23.675 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACAAGGT 10 0.006830828 145.0 2 >>END_MODULE Read 676298 spots for SRR12670108.sra Written 676298 spots for SRR12670108.sra Read 676298 spots for SRR12670108.sra Written 676298 spots for SRR12670108.sra Read 676298 spots for SRR12670108.sra Written 676298 spots for SRR12670108.sra Read 676298 spots for SRR12670108.sra Written 676298 spots for SRR12670108.sra Read 676298 spots for SRR12670108.sra Written 676298 spots for SRR12670108.sra Read 676298 spots for SRR12670108.sra Written 676298 spots for SRR12670108.sra Read 676298 spots for SRR12670108.sra Written 676298 spots for SRR12670108.sra Read 676298 spots for SRR12670108.sra Written 676298 spots for SRR12670108.sra Read 676298 spots for SRR12670108.sra Written 676298 spots for SRR12670108.sra Read 676298 spots for SRR12670108.sra Written 676298 spots for SRR12670108.sra Read 676298 spots for SRR12670108.sra Written 676298 spots for SRR12670108.sra Read 676298 spots for SRR12670108.sra Written 676298 spots for SRR12670108.sra Read 676298 spots for SRR12670108.sra Written 676298 spots for SRR12670108.sra Read 676306 spots for SRR12670108.sra Written 676306 spots for SRR12670108.sra Read 676298 spots for SRR12670108.sra Written 676298 spots for SRR12670108.sra Read 676298 spots for SRR12670108.sra Written 676298 spots for SRR12670108.sra Read 676298 spots for SRR12670108.sra Written 676298 spots for SRR12670108.sra Read 676298 spots for SRR12670108.sra Written 676298 spots for SRR12670108.sra Read 676298 spots for SRR12670108.sra Written 676298 spots for SRR12670108.sra Read 676298 spots for SRR12670108.sra Written 676298 spots for SRR12670108.sra SRR ids: ['SRR12670108.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_zzmvl07l SRR12670108.sra spots: 13525968 blocks: [[1, 676298], [676299, 1352596], [1352597, 2028894], [2028895, 2705192], [2705193, 3381490], [3381491, 4057788], [4057789, 4734086], [4734087, 5410384], [5410385, 6086682], [6086683, 6762980], [6762981, 7439278], [7439279, 8115576], [8115577, 8791874], [8791875, 9468172], [9468173, 10144470], [10144471, 10820768], [10820769, 11497066], [11497067, 12173364], [12173365, 12849662], [12849663, 13525968]] SRR12670108 file size 4575015 SRR12670108 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 SRR12670108 SRR12670108_1.fastq SRR12670108_2.fastq Input file: SRR12670108_1.fastq Paired file: SRR12670108_2.fastq trimmed: SRR12670108-trimmed-pair1.fastq, SRR12670108-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 23:07:15 2025 >> started Mon Feb 10 23:07:30 2025 >> done (14.827s) 13525968 read pairs processed; of these: 53 ( 0.00%) short read pairs filtered out after trimming by size control 7818 ( 0.06%) empty read pairs filtered out after trimming by size control 13518097 (99.94%) read pairs available; of these: 3885820 (28.75%) trimmed read pairs available after processing 9632277 (71.25%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 19 4 0.00% 20 2 0.00% 21 6 0.00% 22 16 0.00% 23 16 0.00% 24 24 0.00% 25 28 0.00% 26 35 0.00% 27 30 0.00% 28 57 0.00% 29 58 0.00% 30 66 0.00% 31 70 0.00% 32 59 0.00% 33 77 0.00% 34 101 0.00% 35 79 0.00% 36 131 0.00% 37 124 0.00% 38 144 0.00% 39 171 0.00% 40 185 0.00% 41 192 0.00% 42 182 0.00% 43 250 0.00% 44 261 0.00% 45 249 0.00% 46 299 0.00% 47 311 0.00% 48 454 0.00% 49 489 0.00% 50 545 0.00% 51 636 0.00% 52 782 0.01% 53 778 0.01% 54 809 0.01% 55 895 0.01% 56 942 0.01% 57 1208 0.01% 58 1349 0.01% 59 1548 0.01% 60 1900 0.01% 61 2179 0.02% 62 2512 0.02% 63 2691 0.02% 64 2922 0.02% 65 2988 0.02% 66 3384 0.03% 67 3760 0.03% 68 4153 0.03% 69 4685 0.03% 70 5551 0.04% 71 6360 0.05% 72 7301 0.05% 73 7808 0.06% 74 8955 0.07% 75 9717 0.07% 76 10346 0.08% 77 10750 0.08% 78 11913 0.09% 79 13216 0.10% 80 14424 0.11% 81 16252 0.12% 82 18323 0.14% 83 19965 0.15% 84 21799 0.16% 85 23221 0.17% 86 24754 0.18% 87 25721 0.19% 88 27165 0.20% 89 28411 0.21% 90 30526 0.23% 91 32479 0.24% 92 34915 0.26% 93 37150 0.27% 94 39763 0.29% 95 42380 0.31% 96 42750 0.32% 97 44893 0.33% 98 44311 0.33% 99 45649 0.34% 100 48080 0.36% 101 48377 0.36% 102 50794 0.38% 103 52399 0.39% 104 53812 0.40% 105 55599 0.41% 106 56762 0.42% 107 56999 0.42% 108 57067 0.42% 109 57217 0.42% 110 56927 0.42% 111 58036 0.43% 112 59811 0.44% 113 59873 0.44% 114 61357 0.45% 115 62782 0.46% 116 63479 0.47% 117 63771 0.47% 118 63411 0.47% 119 62986 0.47% 120 63323 0.47% 121 63094 0.47% 122 64214 0.48% 123 63606 0.47% 124 64885 0.48% 125 64889 0.48% 126 66653 0.49% 127 66494 0.49% 128 65158 0.48% 129 64751 0.48% 130 64217 0.48% 131 63449 0.47% 132 63004 0.47% 133 64733 0.48% 134 63872 0.47% 135 64607 0.48% 136 65051 0.48% 137 65058 0.48% 138 64069 0.47% 139 64562 0.48% 140 63634 0.47% 141 63114 0.47% 142 63023 0.47% 143 62639 0.46% 144 63180 0.47% 145 63759 0.47% 146 63453 0.47% 147 63344 0.47% 148 64405 0.48% 149 61949 0.46% 150 62488 0.46% 151 9632277 71.25% 13518097 reads passed initial QC criterion=sequence-density sequence-density=0.58 sequence-density-rank=1 fanout-score=1.97 fanout-score-rank=23 prefix-density=0.59 prefix-fanout=2.0 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTTCGAGCGAAGAAGGT criterion=fanout-score sequence-density=0.03 sequence-density-rank=24 fanout-score=134.29 fanout-score-rank=1 prefix-density=0.28 prefix-fanout=12.5 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTC criterion=sequence-density sequence-density=0.79 sequence-density-rank=1 fanout-score=2.05 fanout-score-rank=22 prefix-density=0.79 prefix-fanout=2.0 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=29 fanout-score=97.14 fanout-score-rank=1 prefix-density=0.11 prefix-fanout=10.1 sequence=AAACCCAAAGCTCAAAAAAAATCTTAACTGCACCCGCTCATCCAGCAATGGCAGCAGCAACAATGGCCCTCTCCTCCCCTTCGCTAGCCGGAAAGGCGGTGAAGCTCAACCCCTCCTCCTCTGAGATCATGGGCAATGGCCGTGTCTCCATGAGGAAAACCACCAAGCCTGTTCCCTCCGGGAGCCCATGGTACGGACCAGACCGTGTTAAATACTTGGGCCCGTTCTCTGGTGAGCCCCCATCCTACTTGACTGGTGAGTTCCCTGGTGACTACGGCTGGGACACTGCTGG SRR12670108 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 10 23:08:13 Started mapping on | Feb 10 23:08:25 Finished on | Feb 10 23:09:37 Mapping speed, Million of reads per hour | 675.90 Number of input reads | 13518097 Average input read length | 283 UNIQUE READS: Uniquely mapped reads number | 12848894 Uniquely mapped reads % | 95.05% Average mapped length | 282.02 Number of splices: Total | 12233501 Number of splices: Annotated (sjdb) | 11986371 Number of splices: GT/AG | 11978372 Number of splices: GC/AG | 210698 Number of splices: AT/AC | 7456 Number of splices: Non-canonical | 36975 Mismatch rate per base, % | 0.33% Deletion rate per base | 0.02% Deletion average length | 2.78 Insertion rate per base | 0.02% Insertion average length | 2.39 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 291711 % of reads mapped to multiple loci | 2.16% Number of reads mapped to too many loci | 56579 % of reads mapped to too many loci | 0.42% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.27% % of reads unmapped: other | 0.11% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 377492 377492 377492 N_multimapping 291711 291711 291711 N_noFeature 394211 12663062 469068 N_ambiguous 182301 775 70793 UnstrandedReadsAssigned:12272382 PositiveStrandReadsAssigned:185057 NegativeStrandReadsAssigned:12309033 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=132 echo kmer=127 SRR12670108 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: SRR12670108-trimmed-pair1.fastq SRR12670108-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,518,097 reads, 12,335,987 reads pseudoaligned [quant] estimated average fragment length: 204.391 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,178 rounds 52401 SRR12670108.ke.tsv 34699 SRR12670108.se.tsv 87100 total ==> SRR12670108.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1814.61 373 16.7015 Potri.005G024800.1.v4.1 1035 831.609 118 11.529 Potri.004G059700.1.v4.1 961 757.671 12 1.28686 Potri.007G009000.2.v4.1 1416 1212.61 0 0 Potri.003G141000.2.v4.1 2943 2739.61 535.115 15.8704 Potri.016G087400.1.v4.1 270 111.303 497 362.811 Potri.015G069301.1.v4.1 564 367.678 0 0 Potri.010G195200.1.v4.1 1773 1569.61 20 1.03531 Potri.012G127500.1.v4.1 977 773.64 88 9.24217 ==> SRR12670108.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 438 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 147 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 1 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 3 SRR12670108 completed mapping pipeline successfully