Starting /dee2/code/volunteer_pipeline.sh SRR7166140 current disk space = 3112313495552 free memory = 1414831992 SRR7166140 SRAfilesize 7f2f4e311697199443814943139f29e0 SRR7166140.sra SRR7166140.sra file validated SRR7166140 is paired end SRR7166140 is conventional basespace SRR7166140 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7166140_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 42 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.58075 33.0 31.0 33.0 25.0 34.0 2 31.21875 33.0 30.0 33.0 27.0 34.0 3 32.39425 33.0 33.0 33.0 31.0 34.0 4 32.20125 33.0 31.0 33.0 31.0 34.0 5 32.66825 33.0 33.0 33.0 32.0 34.0 6 36.97425 38.0 37.0 38.0 35.0 38.0 7 37.21475 38.0 38.0 38.0 36.0 38.0 8 37.36125 38.0 38.0 38.0 37.0 38.0 9 37.508 38.0 38.0 38.0 37.0 38.0 10-14 37.54415 38.0 38.0 38.0 37.8 38.0 15-19 37.5495 38.0 38.0 38.0 38.0 38.0 20-24 37.49405 38.0 38.0 38.0 38.0 38.0 25-29 37.4894 38.0 38.0 38.0 37.6 38.0 30-34 37.4327 38.0 38.0 38.0 37.8 38.0 35-39 37.3949 38.0 38.0 38.0 37.0 38.0 40-44 37.34735 38.0 38.0 38.0 37.0 38.0 45-49 37.3268 38.0 38.0 38.0 37.0 38.0 50-54 37.0301 38.0 38.0 38.0 36.6 38.0 55-59 36.7013 38.0 38.0 38.0 36.0 38.0 60-64 36.88635 38.0 38.0 38.0 36.0 38.0 65-69 37.06115 38.0 38.0 38.0 36.2 38.0 70-74 36.96935 38.0 38.0 38.0 36.0 38.0 75-79 36.86285 38.0 38.0 38.0 35.8 38.0 80-84 36.7512 38.0 38.0 38.0 35.0 38.0 85-89 36.6569 38.0 38.0 38.0 35.0 38.0 90-94 36.578649999999996 38.0 38.0 38.0 34.8 38.0 95-99 36.40795 38.0 38.0 38.0 34.0 38.0 100-104 36.26904999999999 38.0 38.0 38.0 34.0 38.0 105-109 35.986599999999996 38.0 37.8 38.0 33.6 38.0 110-114 36.017849999999996 38.0 37.4 38.0 33.4 38.0 115-119 35.876200000000004 38.0 37.0 38.0 33.0 38.0 120-124 35.69025 38.0 37.0 38.0 31.2 38.0 125-129 35.47175 38.0 36.2 38.0 30.6 38.0 130-134 35.3457 38.0 36.2 38.0 30.0 38.0 135-139 35.1013 38.0 36.0 38.0 29.4 38.0 140-144 34.9091 38.0 36.0 38.0 29.0 38.0 145-149 34.217200000000005 38.0 35.2 38.0 25.2 38.0 150-151 30.880625000000002 36.5 31.0 38.0 8.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 4 1.0 5 0.0 6 1.0 7 4.0 8 3.0 9 1.0 10 1.0 11 0.0 12 1.0 13 1.0 14 3.0 15 2.0 16 4.0 17 2.0 18 2.0 19 6.0 20 2.0 21 5.0 22 4.0 23 8.0 24 7.0 25 10.0 26 9.0 27 20.0 28 33.0 29 27.0 30 40.0 31 44.0 32 76.0 33 84.0 34 129.0 35 244.0 36 694.0 37 2532.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 35.30901722391084 19.427558257345492 14.58966565349544 30.673758865248228 2 18.825 26.05 37.55 17.575 3 17.4 35.175 26.700000000000003 20.724999999999998 4 18.75 37.775 24.25 19.225 5 18.23190583521162 39.093413473578764 25.36939644377661 17.305284247433008 6 15.775 39.4 26.924999999999997 17.9 7 12.9 22.775000000000002 45.75 18.575 8 16.55 23.95 30.85 28.65 9 17.974999999999998 24.0 32.725 25.3 10-14 19.215 32.910000000000004 26.16 21.715 15-19 18.645 31.885 27.575 21.895 20-24 18.55 32.06 27.284999999999997 22.105 25-29 19.32 31.514999999999997 27.51 21.654999999999998 30-34 19.27 31.59 27.189999999999998 21.95 35-39 18.77 31.52 27.67 22.040000000000003 40-44 19.645000000000003 31.445 27.0 21.91 45-49 20.119999999999997 31.535000000000004 26.655 21.69 50-54 18.933721923521432 31.581327571478816 27.440832118988993 22.04411838601075 55-59 18.455629674550234 32.19122700626642 27.445926824337985 21.90721649484536 60-64 19.010795882500627 31.539040923926688 27.436605573688173 22.01355761988451 65-69 18.66 30.95 28.134999999999998 22.255 70-74 19.416795878557494 31.185915070274596 26.88440954334017 22.51287950782774 75-79 19.82 31.295 26.69 22.195 80-84 19.765 30.775000000000002 26.875 22.585 85-89 19.705000000000002 30.955 27.295 22.045 90-94 19.305 31.1 27.339999999999996 22.255 95-99 20.32 30.94 27.07 21.67 100-104 20.45067601402103 30.175262894341515 26.354531797696545 23.01952929394091 105-109 20.071396249182964 30.97692191663734 26.290914575896224 22.660767258283474 110-114 20.04 31.335 25.919999999999998 22.705000000000002 115-119 20.517698893506235 30.581284734391428 26.42567466079207 22.475341711310268 120-124 20.171008550427523 30.736536826841345 25.881294064703237 23.211160558027903 125-129 20.362398638502352 31.01912103313645 25.87346080688758 22.745019521473623 130-134 20.885 30.645 25.435000000000002 23.035 135-139 20.845 30.78 25.595000000000002 22.78 140-144 20.66 29.685 26.38 23.275000000000002 145-149 20.945 30.585 24.755 23.715 150-151 21.434831601352197 28.358582696882433 25.57906598222111 24.62751971954426 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.5 4 1.5 5 1.0 6 0.5 7 1.0 8 1.0 9 1.0 10 1.0 11 0.5 12 0.0 13 0.0 14 0.0 15 0.5 16 0.5 17 0.5 18 1.0 19 3.0 20 3.0 21 4.0 22 3.5 23 4.5 24 9.0 25 7.5 26 11.5 27 22.0 28 28.5 29 47.0 30 69.5 31 85.5 32 102.0 33 118.5 34 141.0 35 160.0 36 169.5 37 186.5 38 217.5 39 219.0 40 201.5 41 192.0 42 198.5 43 191.5 44 184.5 45 182.0 46 168.5 47 152.5 48 143.5 49 139.0 50 112.5 51 100.5 52 89.0 53 76.0 54 61.5 55 41.5 56 30.0 57 22.5 58 20.5 59 17.0 60 11.0 61 7.0 62 9.0 63 9.5 64 4.0 65 2.0 66 1.0 67 1.5 68 1.5 69 0.0 70 0.5 71 1.5 72 2.0 73 1.0 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 1.3 2 0.0 3 0.0 4 0.0 5 0.17500000000000002 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 0.49500000000000005 55-59 1.06 60-64 0.42500000000000004 65-69 0.0 70-74 0.034999999999999996 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.15 105-109 0.555 110-114 0.0 115-119 0.135 120-124 0.005 125-129 0.11 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.1625 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 94.55 #Duplication Level Percentage of deduplicated Percentage of total 1 96.43046007403491 91.175 2 2.4061343204653625 4.55 3 0.6874669487043892 1.95 4 0.23796932839767318 0.8999999999999999 5 0.10576414595452141 0.5 6 0.07932310946589106 0.44999999999999996 7 0.0 0.0 8 0.026441036488630353 0.2 9 0.0 0.0 >10 0.026441036488630353 0.27499999999999997 >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 GTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGAGTAGGGA 11 0.27499999999999997 No Hit GTAGGGATGAGCATAAACCAACAACTCTCAAAGAAGATGGGAAGCTATAC 8 0.2 No Hit CTTAGCAGTAGTTTATAAGGAATATATCCCATTTTTAGTTATAATGATGC 6 0.15 No Hit GTTATGAGTAGGGATGAGCATAAACCAACAACTCTCAAAGAAGATGGGAA 6 0.15 No Hit GTGGATGTTGTTGTTAGACACTTCTTTTTGTCTTTAAATATAAGGCGTGG 6 0.15 No Hit CTTATATTGAAGTATAAACCAATGAGAGAGCCTCACTTAGTTACAGTTTT 5 0.125 No Hit ATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGAGTAGGGATGA 5 0.125 No Hit GCCTCTTTAAAATATCTAAGTGCTGGGGTTATGAGTAGGGATGAGCATAA 5 0.125 No Hit GATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGAGTAGGGATG 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 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0125 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.0875 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.2625 0.0 0.0 0.0 0.0 82-83 0.30000000000000004 0.0 0.0 0.0 0.0 84-85 0.375 0.0 0.0 0.0 0.0 86-87 0.42500000000000004 0.0 0.0 0.0 0.0 88-89 0.5125 0.0 0.0 0.0 0.0 90-91 0.6875 0.0 0.0 0.0 0.0 92-93 0.95 0.0 0.0 0.0 0.0 94-95 1.2125 0.0 0.0 0.0 0.0 96-97 1.6125 0.0 0.0 0.0 0.0 98-99 2.0125 0.0 0.0 0.0 0.0 100-101 2.3125 0.0 0.0 0.0 0.0 102-103 2.6 0.0 0.0 0.0 0.0 104-105 3.1625 0.0 0.0 0.0 0.0 106-107 3.7625 0.0 0.0 0.0 0.0 108-109 4.25 0.0 0.0 0.0 0.0 110-111 4.7125 0.0 0.0 0.0 0.0 112-113 5.300000000000001 0.0 0.0 0.0 0.0 114-115 5.8625 0.0 0.0 0.0 0.0 116-117 6.5 0.0 0.0 0.0 0.0 118-119 7.175000000000001 0.0 0.0 0.0 0.0 120-121 7.8375 0.0 0.0 0.0 0.0 122-123 8.5625 0.0 0.0 0.0 0.0 124-125 9.25 0.0 0.0 0.0 0.0 126-127 9.9625 0.0 0.0 0.0 0.0 128-129 10.675 0.0 0.0 0.0 0.0 130-131 11.5375 0.0 0.0 0.0 0.0 132-133 12.525 0.0 0.0 0.0 0.0 134-135 13.4 0.0 0.0 0.0 0.0 136-137 14.225 0.0 0.0 0.0 0.0 138-139 15.1875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTTTTTT 10 0.0064039123 148.11537 1 TTTTTTA 10 0.006914255 144.41249 2 >>END_MODULE SRR7166140 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7166140_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 42 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.71925 33.0 33.0 34.0 32.0 34.0 2 32.822 33.0 33.0 34.0 32.0 34.0 3 32.87475 33.0 33.0 34.0 32.0 34.0 4 32.8735 33.0 33.0 34.0 32.0 34.0 5 32.84375 33.0 33.0 34.0 32.0 34.0 6 37.163 38.0 38.0 38.0 36.0 38.0 7 37.2245 38.0 38.0 38.0 37.0 38.0 8 37.1025 38.0 38.0 38.0 36.0 38.0 9 37.113 38.0 38.0 38.0 36.0 38.0 10-14 37.0767 38.0 38.0 38.0 36.0 38.0 15-19 37.07165 38.0 38.0 38.0 36.0 38.0 20-24 37.0105 38.0 38.0 38.0 36.0 38.0 25-29 36.88905 38.0 38.0 38.0 36.0 38.0 30-34 36.85065 38.0 38.0 38.0 35.8 38.0 35-39 36.70345 38.0 38.0 38.0 35.0 38.0 40-44 36.63435 38.0 38.0 38.0 34.8 38.0 45-49 36.53205 38.0 38.0 38.0 34.0 38.0 50-54 36.32575 38.0 37.8 38.0 33.8 38.0 55-59 36.25705 38.0 37.6 38.0 33.4 38.0 60-64 36.23855 38.0 37.6 38.0 33.4 38.0 65-69 36.1274 38.0 37.2 38.0 33.2 38.0 70-74 35.91075000000001 38.0 37.0 38.0 31.2 38.0 75-79 35.7382 38.0 37.0 38.0 30.8 38.0 80-84 35.60785 38.0 37.0 38.0 29.8 38.0 85-89 35.35565 38.0 36.2 38.0 29.0 38.0 90-94 35.06855 38.0 36.0 38.0 28.4 38.0 95-99 34.86735 38.0 35.6 38.0 27.6 38.0 100-104 34.52935000000001 38.0 35.0 38.0 25.4 38.0 105-109 34.162549999999996 38.0 34.6 38.0 23.6 38.0 110-114 33.6822 38.0 34.0 38.0 19.4 38.0 115-119 33.3549 38.0 34.0 38.0 16.6 38.0 120-124 32.824200000000005 37.6 33.0 38.0 15.0 38.0 125-129 32.3091 37.0 32.4 38.0 14.8 38.0 130-134 31.56635 36.4 30.6 38.0 14.2 38.0 135-139 30.82635 36.0 28.2 38.0 13.4 38.0 140-144 29.338750000000005 35.2 24.2 38.0 6.4 38.0 145-149 27.705000000000002 34.6 18.6 38.0 2.0 38.0 150-151 22.441000000000003 28.5 2.0 35.5 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 4.0 3 3.0 4 2.0 5 2.0 6 1.0 7 2.0 8 0.0 9 1.0 10 3.0 11 0.0 12 1.0 13 3.0 14 4.0 15 3.0 16 11.0 17 9.0 18 13.0 19 15.0 20 13.0 21 17.0 22 19.0 23 19.0 24 20.0 25 29.0 26 41.0 27 50.0 28 52.0 29 71.0 30 88.0 31 129.0 32 186.0 33 231.0 34 306.0 35 580.0 36 967.0 37 1105.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.709927481870466 16.204051012753187 16.35408852213053 27.731932983245812 2 26.0 22.375 34.525 17.1 3 21.3 25.525 33.050000000000004 20.125 4 24.725 34.849999999999994 23.0 17.424999999999997 5 24.0 36.725 21.325 17.95 6 18.125 36.275 24.65 20.95 7 17.1 16.275000000000002 44.525 22.1 8 20.849999999999998 22.1 27.075 29.975 9 22.45 23.075000000000003 29.799999999999997 24.675 10-14 22.945 28.110000000000003 27.735 21.21 15-19 23.990000000000002 27.095000000000002 28.79 20.125 20-24 23.919999999999998 27.425 28.610000000000003 20.044999999999998 25-29 23.79 27.560000000000002 28.78 19.869999999999997 30-34 22.93 27.01 29.57 20.49 35-39 23.075000000000003 27.195000000000004 29.849999999999998 19.88 40-44 23.465 28.000000000000004 29.115000000000002 19.42 45-49 22.759999999999998 27.145000000000003 29.645 20.45 50-54 22.235 27.13 30.25 20.385 55-59 23.01 27.075 30.025000000000002 19.89 60-64 22.365 27.915 30.285 19.435 65-69 22.345000000000002 27.88 29.53 20.244999999999997 70-74 22.220000000000002 27.87 29.725 20.185 75-79 22.1 27.42 30.19 20.29 80-84 22.56 27.925 30.5 19.015 85-89 22.785 27.99 29.975 19.25 90-94 22.795 28.525 29.915000000000003 18.765 95-99 22.855 27.944999999999997 29.925 19.275000000000002 100-104 22.264999999999997 28.139999999999997 29.64 19.955000000000002 105-109 22.555 28.27 29.37 19.805 110-114 22.365 28.475 29.69 19.470000000000002 115-119 23.055 28.675 29.425 18.845 120-124 23.48 27.800000000000004 29.544999999999998 19.175 125-129 24.135 27.650000000000002 29.265 18.95 130-134 24.63 27.625 29.01 18.735 135-139 24.715 28.03 29.225 18.029999999999998 140-144 25.505 27.74 28.694999999999997 18.060000000000002 145-149 25.674999999999997 27.689999999999998 28.57 18.065 150-151 27.51157262604779 26.498185912673588 28.287251344926812 17.702990116351806 >>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 0.5 15 0.5 16 0.0 17 0.5 18 0.5 19 0.5 20 1.0 21 1.5 22 1.0 23 0.5 24 1.5 25 5.0 26 7.5 27 8.0 28 11.5 29 14.0 30 25.0 31 41.5 32 52.5 33 62.5 34 84.0 35 110.0 36 127.5 37 165.0 38 219.5 39 229.0 40 205.0 41 198.5 42 232.0 43 236.0 44 219.5 45 225.0 46 205.0 47 205.5 48 198.0 49 155.0 50 135.0 51 120.0 52 102.0 53 89.0 54 71.5 55 55.5 56 45.5 57 32.5 58 23.5 59 24.0 60 17.5 61 11.0 62 7.0 63 5.5 64 4.0 65 2.0 66 2.0 67 1.5 68 0.5 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 0.025 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 0.08750000000000001 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 93.95 #Duplication Level Percentage of deduplicated Percentage of total 1 97.09952102182011 91.225 2 1.9425226184140503 3.65 3 0.37253858435337944 1.05 4 0.15965939329430548 0.6 5 0.10643959552953698 0.5 6 0.10643959552953698 0.6 7 0.05321979776476849 0.35000000000000003 8 0.05321979776476849 0.4 9 0.0 0.0 >10 0.10643959552953698 1.625 >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 GAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCC 22 0.5499999999999999 No Hit GCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCC 17 0.42500000000000004 No Hit GGGAGGTATCCCAATAGGAGGTTTCCTCCTATGGTTTTCAAAACAATCAC 14 0.35000000000000003 No Hit TGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTC 12 0.3 No Hit AGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGATGGTTTTTACTA 8 0.2 No Hit TTTGCACTTGTGGTAACGGTATTTGCATTATTGATGGTTTTTACTATGTT 8 0.2 No Hit CGGGCGTCGGCATCCAGACCGTCGGCTGATCGTGGTTTTACTAGGCTAGA 7 0.17500000000000002 No Hit CGGGAGGTATCCCAATAGGAGGTTTCCTCCTATGGTTTTCAAAACAATCA 7 0.17500000000000002 No Hit ATTTGCACTTGTGGTAACGGTATTTGCATTATTGATGGTTTTTACTATGT 6 0.15 No Hit CAATTATCCATAAAACTGTAACTAAGTGAGGCTCTCTCATTGGTTTATAC 6 0.15 No Hit GTTTCCTCCTATGGTTTTCAAAACAATCACCATCATGCTATTAATGATAT 6 0.15 No Hit GGAGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGATGGTTTTTAC 6 0.15 No Hit TGGGAGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGATGGTTTTT 5 0.125 No Hit CTTGAGCAAATTCAGTTTCTAAGCAAAAGCTTTCCAGGCCCCTTTATCCT 5 0.125 No Hit CTCTCATTGGTTTATACTTCAATATAAGCCTTGGTAGGGATAGATAGCCA 5 0.125 No Hit CCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATGGT 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 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0125 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.0875 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.2625 0.0 0.0 0.0 0.0 82-83 0.30000000000000004 0.0 0.0 0.0 0.0 84-85 0.4 0.0 0.0 0.0 0.0 86-87 0.44999999999999996 0.0 0.0 0.0 0.0 88-89 0.5375 0.0 0.0 0.0 0.0 90-91 0.7125 0.0 0.0 0.0 0.0 92-93 0.95 0.0 0.0 0.0 0.0 94-95 1.2125 0.0 0.0 0.0 0.0 96-97 1.6125 0.0 0.0 0.0 0.0 98-99 1.975 0.0 0.0 0.0 0.0 100-101 2.2875 0.0 0.0 0.0 0.0 102-103 2.55 0.0 0.0 0.0 0.0 104-105 3.0999999999999996 0.0 0.0 0.0 0.0 106-107 3.65 0.0 0.0 0.0 0.0 108-109 4.0625 0.0 0.0 0.0 0.0 110-111 4.5375 0.0 0.0 0.0 0.0 112-113 5.1 0.0 0.0 0.0 0.0 114-115 5.6 0.0 0.0 0.0 0.0 116-117 6.25 0.0 0.0 0.0 0.0 118-119 6.9 0.0 0.0 0.0 0.0 120-121 7.525 0.0 0.0 0.0 0.0 122-123 8.175 0.0 0.0 0.0 0.0 124-125 8.8375 0.0 0.0 0.0 0.0 126-127 9.45 0.0 0.0 0.0 0.0 128-129 10.05 0.0 0.0 0.0 0.0 130-131 10.85 0.0 0.0 0.0 0.0 132-133 11.7 0.0 0.0 0.0 0.0 134-135 12.425 0.0 0.0 0.0 0.0 136-137 13.125 0.0 0.0 0.0 0.0 138-139 13.9375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAATTCA 10 0.006830828 145.0 3 AATTCAG 10 0.006830828 145.0 4 CAAATTC 10 0.006830828 145.0 2 CAAATCT 10 0.006830828 145.0 4 >>END_MODULE Read 547578 spots for SRR7166140.sra Written 547578 spots for SRR7166140.sra Read 547578 spots for SRR7166140.sra Written 547578 spots for SRR7166140.sra Read 547578 spots for SRR7166140.sra Written 547578 spots for SRR7166140.sra Read 547578 spots for SRR7166140.sra Written 547578 spots for SRR7166140.sra Read 547578 spots for SRR7166140.sra Written 547578 spots for SRR7166140.sra Read 547578 spots for SRR7166140.sra Written 547578 spots for SRR7166140.sra Read 547578 spots for SRR7166140.sra Written 547578 spots for SRR7166140.sra Read 547578 spots for SRR7166140.sra Written 547578 spots for SRR7166140.sra Read 547578 spots for SRR7166140.sra Written 547578 spots for SRR7166140.sra Read 547578 spots for SRR7166140.sra Written 547578 spots for SRR7166140.sra Read 547578 spots for SRR7166140.sra Written 547578 spots for SRR7166140.sra Read 547578 spots for SRR7166140.sra Written 547578 spots for SRR7166140.sra Read 547585 spots for SRR7166140.sra Written 547585 spots for SRR7166140.sra Read 547578 spots for SRR7166140.sra Written 547578 spots for SRR7166140.sra Read 547578 spots for SRR7166140.sra Written 547578 spots for SRR7166140.sra Read 547578 spots for SRR7166140.sra Written 547578 spots for SRR7166140.sra Read 547578 spots for SRR7166140.sra Written 547578 spots for SRR7166140.sra Read 547578 spots for SRR7166140.sra Written 547578 spots for SRR7166140.sra Read 547578 spots for SRR7166140.sra Written 547578 spots for SRR7166140.sra Read 547578 spots for SRR7166140.sra Written 547578 spots for SRR7166140.sra SRR ids: ['SRR7166140.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ruy152mz SRR7166140.sra spots: 10951567 blocks: [[1, 547578], [547579, 1095156], [1095157, 1642734], [1642735, 2190312], [2190313, 2737890], [2737891, 3285468], [3285469, 3833046], [3833047, 4380624], [4380625, 4928202], [4928203, 5475780], [5475781, 6023358], [6023359, 6570936], [6570937, 7118514], [7118515, 7666092], [7666093, 8213670], [8213671, 8761248], [8761249, 9308826], [9308827, 9856404], [9856405, 10403982], [10403983, 10951567]] SRR7166140 file size 3689426 SRR7166140 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 SRR7166140 SRR7166140_1.fastq SRR7166140_2.fastq Input file: SRR7166140_1.fastq Paired file: SRR7166140_2.fastq trimmed: SRR7166140-trimmed-pair1.fastq, SRR7166140-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 14:39:00 2025 >> started Fri Feb 14 14:39:13 2025 >> done (13.705s) 10951567 read pairs processed; of these: 7490 ( 0.07%) short read pairs filtered out after trimming by size control 9064 ( 0.08%) empty read pairs filtered out after trimming by size control 10935013 (99.85%) read pairs available; of these: 5487453 (50.18%) trimmed read pairs available after processing 5447560 (49.82%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 4 0.00% 19 1 0.00% 20 3 0.00% 21 6 0.00% 22 8 0.00% 23 0 0.00% 24 9 0.00% 25 3 0.00% 26 3 0.00% 27 6 0.00% 28 12 0.00% 29 4 0.00% 30 10 0.00% 31 5 0.00% 32 4 0.00% 33 4 0.00% 34 7 0.00% 35 10 0.00% 36 11 0.00% 37 5 0.00% 38 11 0.00% 39 4 0.00% 40 11 0.00% 41 17 0.00% 42 15 0.00% 43 16 0.00% 44 32 0.00% 45 31 0.00% 46 46 0.00% 47 47 0.00% 48 63 0.00% 49 71 0.00% 50 53 0.00% 51 76 0.00% 52 98 0.00% 53 95 0.00% 54 118 0.00% 55 116 0.00% 56 142 0.00% 57 191 0.00% 58 178 0.00% 59 232 0.00% 60 297 0.00% 61 314 0.00% 62 375 0.00% 63 356 0.00% 64 506 0.00% 65 508 0.00% 66 558 0.01% 67 674 0.01% 68 811 0.01% 69 876 0.01% 70 1055 0.01% 71 1261 0.01% 72 1440 0.01% 73 1638 0.01% 74 1811 0.02% 75 2045 0.02% 76 2505 0.02% 77 2608 0.02% 78 2820 0.03% 79 3300 0.03% 80 3670 0.03% 81 4263 0.04% 82 4917 0.04% 83 5529 0.05% 84 6553 0.06% 85 7155 0.07% 86 8019 0.07% 87 8860 0.08% 88 9703 0.09% 89 10330 0.09% 90 11035 0.10% 91 11898 0.11% 92 13369 0.12% 93 14152 0.13% 94 15256 0.14% 95 16008 0.15% 96 16975 0.16% 97 17338 0.16% 98 18377 0.17% 99 20010 0.18% 100 20208 0.18% 101 21986 0.20% 102 23064 0.21% 103 24644 0.23% 104 26054 0.24% 105 27494 0.25% 106 28147 0.26% 107 28802 0.26% 108 29753 0.27% 109 30237 0.28% 110 31387 0.29% 111 32728 0.30% 112 34600 0.32% 113 39245 0.36% 114 38844 0.36% 115 40532 0.37% 116 41415 0.38% 117 40982 0.37% 118 41834 0.38% 119 42639 0.39% 120 43514 0.40% 121 45730 0.42% 122 47050 0.43% 123 48693 0.45% 124 50235 0.46% 125 52361 0.48% 126 52660 0.48% 127 52813 0.48% 128 53040 0.49% 129 55033 0.50% 130 56058 0.51% 131 56926 0.52% 132 59058 0.54% 133 60884 0.56% 134 63627 0.58% 135 65141 0.60% 136 67947 0.62% 137 68849 0.63% 138 71447 0.65% 139 73381 0.67% 140 76427 0.70% 141 80276 0.73% 142 86122 0.79% 143 90803 0.83% 144 100365 0.92% 145 115010 1.05% 146 135598 1.24% 147 168546 1.54% 148 236295 2.16% 149 417691 3.82% 150 1940325 17.74% 151 5447560 49.82% 10935013 reads passed initial QC criterion=sequence-density sequence-density=0.90 sequence-density-rank=1 fanout-score=2.12 fanout-score-rank=34 prefix-density=0.95 prefix-fanout=2.0 sequence=CAGGTGCAGTTTGATCC criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=75.70 fanout-score-rank=1 prefix-density=0.19 prefix-fanout=3.1 sequence=TTTTTTTTCTCGTTCTTTGGTCGCAATCCTGCGTAATCAACGCCGCAACTTTACGTCGGATTAGCTCTTCTTTGATTAGCATGAAACTCCAAGGTCCGGGGGGGTCACTTATCCTGGGCTTCATCCAATGGTGGGTGCTAACTCTTTAATAGCCTTCAGTGACTGTGAGATGCCGTCTACGAGTGGCACGAATCGCACGGATGTTTGGTTAAAGAACAGTCGCAGTTTTCCTCAAATCCCGCCACGAAACTAAGCGATTGAACTCTTGCCTGGTTACTGTATGCCCCTGTGTTATTGCAGCGTCTCGATTAGGGGGAAACCTTGTCACCGTCAGCTTATTCCCGAGGCATATGGCCCTACTTAACTGATCTGAAGTATTACGGTAACCGCGACGATAATAACCCGGACCAAATATAGCCTGATATGAGCGTGCCCGTCCATAGTCCCAGAGACGGGCGGAGGCTCTTAACC criterion=sequence-density sequence-density=1.08 sequence-density-rank=1 fanout-score=2.08 fanout-score-rank=26 prefix-density=1.09 prefix-fanout=2.1 sequence=ATGTACCCTGACTTAGGTTTCTCAGA criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=11.51 fanout-score-rank=1 prefix-density=0.02 prefix-fanout=2.7 sequence=GAGATTGTCTCGTACGGTTAAGAGCCTCCGCCCGTCTCTGGGACTATGGACGGGCACGCTCATATCAGGCTATATTTGGTCCGGGTTATTATCGTCGCGGTTACCGTAATACTTCAGATCAGTTAAGTAGGGCCATATGCCTCGGGAATAAGCTGACGGTGACAAGGTTTCCCCCTAATCGAGACGCTGCAATAACACAGGGGCATACAGTAACCAGGCAAGAGTTCAATCGCTTAGTTTCGTGGCGGGATTTGAGGAAAACTGCGACTGTTCTTTAACCAAACATCCGTGCGATTCGTGCCACTCGTAGACGGCATCTCACAGTCACTGAAGGCTATTAAAGAGTTAGCACCCACCATTGGATGAAGCCCAGGATAAGTGACCCCCCCGGACCTTGGAGTTTCAT SRR7166140 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 14 14:40:42 Started mapping on | Feb 14 14:40:42 Finished on | Feb 14 14:46:59 Mapping speed, Million of reads per hour | 104.42 Number of input reads | 10935013 Average input read length | 288 UNIQUE READS: Uniquely mapped reads number | 8148443 Uniquely mapped reads % | 74.52% Average mapped length | 286.87 Number of splices: Total | 5500412 Number of splices: Annotated (sjdb) | 5359225 Number of splices: GT/AG | 5398748 Number of splices: GC/AG | 71031 Number of splices: AT/AC | 4500 Number of splices: Non-canonical | 26133 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.06% Deletion average length | 2.37 Insertion rate per base | 0.04% Insertion average length | 2.17 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 239493 % of reads mapped to multiple loci | 2.19% Number of reads mapped to too many loci | 37770 % of reads mapped to too many loci | 0.35% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 22.84% % of reads unmapped: other | 0.11% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2555310 2555310 2555310 N_multimapping 239493 239493 239493 N_noFeature 320292 8025196 375962 N_ambiguous 109115 746 41172 UnstrandedReadsAssigned:7719036 PositiveStrandReadsAssigned:122501 NegativeStrandReadsAssigned:7731309 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=143 echo kmer=139 SRR7166140 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: SRR7166140-trimmed-pair1.fastq SRR7166140-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 10,935,013 reads, 7,689,221 reads pseudoaligned [quant] estimated average fragment length: 200.899 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,124 rounds 52401 SRR7166140.ke.tsv 34699 SRR7166140.se.tsv 87100 total ==> SRR7166140.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1818.1 524 27.3985 Potri.005G024800.1.v4.1 1035 835.101 176 20.0349 Potri.004G059700.1.v4.1 961 761.101 20 2.49805 Potri.007G009000.2.v4.1 1416 1216.1 0 0 Potri.003G141000.2.v4.1 2943 2743.1 223.346 7.74018 Potri.016G087400.1.v4.1 270 98.4414 602 581.343 Potri.015G069301.1.v4.1 564 365.235 0 0 Potri.010G195200.1.v4.1 1773 1573.1 270 16.3163 Potri.012G127500.1.v4.1 977 777.101 3107 380.082 ==> SRR7166140.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 6 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 485 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 134 SRR7166140 completed mapping pipeline successfully