Starting /dee2/code/volunteer_pipeline.sh SRR6958255 current disk space = 1550714294272 free memory = 1393641732 SRR6958255 SRAfilesize e81e7f2e2e611c8932b6fa24daa46e27 SRR6958255.sra SRR6958255.sra file validated SRR6958255 is paired end SRR6958255 is conventional basespace SRR6958255 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958255_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 26.1685 31.0 18.0 33.0 18.0 33.0 2 30.4035 31.0 29.0 33.0 27.0 34.0 3 30.69075 33.0 29.0 33.0 27.0 34.0 4 31.128 33.0 31.0 33.0 28.0 33.0 5 31.39675 33.0 32.0 33.0 28.0 33.0 6 36.5115 38.0 37.0 38.0 34.0 38.0 7 37.08525 38.0 38.0 38.0 36.0 38.0 8 37.0765 38.0 38.0 38.0 36.0 38.0 9 37.131 38.0 38.0 38.0 36.0 38.0 10-14 37.330200000000005 38.0 38.0 38.0 37.0 38.0 15-19 37.401300000000006 38.0 38.0 38.0 37.0 38.0 20-24 37.32925 38.0 38.0 38.0 36.8 38.0 25-29 37.09665 38.0 38.0 38.0 36.0 38.0 30-34 37.02185 38.0 38.0 38.0 36.0 38.0 35-39 36.786500000000004 38.0 38.0 38.0 35.0 38.0 40-44 36.880250000000004 38.0 38.0 38.0 35.4 38.0 45-49 36.8694 38.0 38.0 38.0 35.0 38.0 50-54 36.477250000000005 38.0 38.0 38.0 33.6 38.0 55-59 36.5221 38.0 38.0 38.0 34.0 38.0 60-64 36.784299999999995 38.0 38.0 38.0 34.6 38.0 65-69 36.7285 38.0 38.0 38.0 34.4 38.0 70-74 36.482150000000004 38.0 38.0 38.0 34.0 38.0 75-79 35.957100000000004 38.0 37.0 38.0 31.8 38.0 80-84 35.758399999999995 38.0 36.8 38.0 30.6 38.0 85-89 36.11105 38.0 37.0 38.0 32.4 38.0 90-94 36.15525 38.0 37.0 38.0 33.0 38.0 95-99 35.83865 38.0 36.6 38.0 32.0 38.0 100-104 34.98245 38.0 35.4 38.0 27.4 38.0 105-109 34.6858 38.0 34.8 38.0 25.8 38.0 110-114 34.846799999999995 38.0 34.8 38.0 26.8 38.0 115-119 34.6533 38.0 35.0 38.0 26.4 38.0 120-124 34.516600000000004 38.0 34.4 38.0 26.0 38.0 125-129 34.2196 38.0 34.2 38.0 24.2 38.0 130-134 34.01220000000001 38.0 34.0 38.0 23.0 38.0 135-139 33.294 38.0 33.6 38.0 20.2 38.0 140-144 32.0547 36.4 31.8 38.0 14.2 38.0 145-149 30.33415 35.8 28.8 38.0 8.6 38.0 150-151 25.264875 32.5 12.5 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 1.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 3.0 15 2.0 16 3.0 17 0.0 18 0.0 19 4.0 20 4.0 21 2.0 22 4.0 23 12.0 24 17.0 25 28.0 26 36.0 27 47.0 28 55.0 29 70.0 30 70.0 31 104.0 32 143.0 33 203.0 34 302.0 35 503.0 36 1015.0 37 1372.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 47.98803697661773 10.576400217509516 7.3409461663947795 34.09461663947798 2 23.849999999999998 12.049999999999999 33.125 30.975 3 20.275000000000002 17.349999999999998 26.450000000000003 35.925000000000004 4 25.4 22.900000000000002 22.925 28.775000000000002 5 26.5 27.950000000000003 21.825 23.724999999999998 6 23.125 32.425 22.025 22.425 7 18.325 26.325 37.0 18.35 8 20.925 24.425 28.449999999999996 26.200000000000003 9 20.625 21.925 32.05 25.4 10-14 22.67 26.66 25.755 24.915000000000003 15-19 23.200000000000003 25.465 25.669999999999998 25.665 20-24 22.73 25.679999999999996 25.655 25.935000000000002 25-29 22.875 25.505 25.75 25.869999999999997 30-34 22.8 25.130000000000003 26.43 25.64 35-39 23.21 25.295 25.759999999999998 25.735000000000003 40-44 22.855 25.814999999999998 25.465 25.865 45-49 23.05 25.240000000000002 25.755 25.955000000000002 50-54 23.119999999999997 25.09 25.955000000000002 25.835 55-59 23.26 24.740000000000002 25.485000000000003 26.515 60-64 22.99 24.529999999999998 26.16 26.32 65-69 22.895 25.47 25.75 25.885 70-74 23.29 25.295 25.535000000000004 25.88 75-79 23.150000000000002 25.135 25.4 26.314999999999998 80-84 23.125 25.445 25.505 25.924999999999997 85-89 22.770000000000003 25.900000000000002 25.055 26.275 90-94 23.405 25.52 25.435000000000002 25.64 95-99 23.189999999999998 25.135 25.36 26.314999999999998 100-104 23.150000000000002 25.369999999999997 25.435000000000002 26.045 105-109 23.494999999999997 25.095 25.380000000000003 26.029999999999998 110-114 23.835 25.145 25.085 25.935000000000002 115-119 23.57 25.755 25.205 25.47 120-124 24.125 24.765 25.040000000000003 26.07 125-129 23.395 25.264999999999997 25.130000000000003 26.21 130-134 23.41 24.93 25.55 26.11 135-139 22.97 25.45 25.240000000000002 26.340000000000003 140-144 23.785 24.81 25.36 26.045 145-149 23.585 25.41 25.240000000000002 25.765 150-151 23.6125 25.137500000000003 25.7 25.55 >>END_MODULE >>Per sequence GC content fail #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 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.5 24 0.5 25 1.5 26 2.0 27 0.5 28 1.5 29 3.5 30 7.0 31 11.5 32 19.0 33 21.5 34 25.0 35 37.5 36 51.5 37 63.5 38 72.0 39 94.0 40 120.5 41 152.5 42 168.5 43 187.5 44 208.0 45 218.0 46 218.5 47 198.5 48 186.5 49 167.5 50 153.0 51 154.5 52 145.5 53 122.0 54 115.0 55 109.0 56 96.5 57 87.5 58 77.5 59 74.5 60 75.5 61 69.0 62 57.5 63 53.0 64 47.5 65 38.0 66 38.0 67 43.5 68 43.5 69 33.5 70 24.0 71 22.5 72 21.0 73 15.5 74 12.0 75 9.0 76 5.0 77 7.0 78 6.0 79 2.5 80 1.5 81 0.5 82 0.5 83 0.5 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 warn #Base N-Count 1 8.05 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 99.775 #Duplication Level Percentage of deduplicated Percentage of total 1 99.79954898521673 99.575 2 0.17539463793535454 0.35000000000000003 3 0.025056376847907794 0.075 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 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 pass >>END_MODULE >>Adapter Content pass #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 0.025 0.0 0.0 52-53 0.0 0.0 0.025 0.0 0.0 54-55 0.0 0.0 0.025 0.0 0.0 56-57 0.0 0.0 0.025 0.0 0.0 58-59 0.0 0.0 0.025 0.0 0.0 60-61 0.0 0.0 0.025 0.0 0.0 62-63 0.0 0.0 0.025 0.0 0.0 64-65 0.0 0.0 0.025 0.0 0.0 66-67 0.0 0.0 0.025 0.0 0.0 68-69 0.0 0.0 0.025 0.0 0.0 70-71 0.0 0.0 0.025 0.0 0.0 72-73 0.0 0.0 0.025 0.0 0.0 74-75 0.0 0.0 0.025 0.0 0.0 76-77 0.0 0.0 0.025 0.0 0.0 78-79 0.025 0.0 0.025 0.0 0.0 80-81 0.025 0.0 0.025 0.0 0.0 82-83 0.025 0.0 0.025 0.0 0.0 84-85 0.037500000000000006 0.0 0.025 0.0 0.0 86-87 0.05 0.0 0.025 0.0 0.0 88-89 0.05 0.0 0.025 0.0 0.0 90-91 0.0625 0.0 0.025 0.0 0.0 92-93 0.1 0.0 0.025 0.0 0.0 94-95 0.16249999999999998 0.0 0.025 0.0 0.0 96-97 0.2 0.0 0.025 0.0 0.0 98-99 0.21250000000000002 0.0 0.025 0.0 0.0 100-101 0.25 0.0 0.025 0.0 0.0 102-103 0.3375 0.0 0.025 0.0 0.0 104-105 0.3875 0.0 0.025 0.0 0.0 106-107 0.55 0.0 0.025 0.0 0.0 108-109 0.65 0.0 0.025 0.0 0.0 110-111 0.725 0.0 0.025 0.0 0.0 112-113 0.825 0.0 0.025 0.0 0.0 114-115 1.0125 0.0 0.025 0.0 0.0 116-117 1.0625 0.0 0.025 0.0 0.0 118-119 1.2125 0.0 0.025 0.0 0.0 120-121 1.4625 0.0 0.025 0.0 0.0 122-123 1.65 0.0 0.025 0.0 0.0 124-125 1.8375 0.0 0.025 0.0 0.0 126-127 2.0375 0.0 0.025 0.0 0.0 128-129 2.25 0.0 0.025 0.0 0.0 130-131 2.4375 0.0 0.025 0.0 0.0 132-133 2.6875 0.0 0.025 0.0 0.0 134-135 3.1125 0.0 0.025 0.0 0.0 136-137 3.375 0.0 0.025 0.0 0.0 138-139 3.7750000000000004 0.0 0.025 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CAAGATT 10 0.006841402 144.925 8 AAGATTA 10 0.006841402 144.925 9 CTTCTCG 35 0.0035472352 20.703571 30-34 >>END_MODULE SRR6958255 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958255_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.4445 33.0 33.0 34.0 32.0 34.0 2 32.5205 33.0 33.0 34.0 31.0 34.0 3 32.41325 33.0 33.0 34.0 31.0 34.0 4 32.38 33.0 33.0 34.0 31.0 34.0 5 32.33125 33.0 33.0 34.0 31.0 34.0 6 36.11775 38.0 38.0 38.0 33.0 38.0 7 36.207 38.0 38.0 38.0 33.0 38.0 8 36.205 38.0 38.0 38.0 33.0 38.0 9 36.1635 38.0 38.0 38.0 33.0 38.0 10-14 36.2678 38.0 38.0 38.0 33.4 38.0 15-19 36.46445000000001 38.0 38.0 38.0 34.4 38.0 20-24 36.63055000000001 38.0 38.0 38.0 35.0 38.0 25-29 36.61825 38.0 38.0 38.0 34.8 38.0 30-34 36.538599999999995 38.0 38.0 38.0 34.4 38.0 35-39 36.3523 38.0 38.0 38.0 34.0 38.0 40-44 36.2944 38.0 38.0 38.0 33.6 38.0 45-49 36.1207 38.0 38.0 38.0 33.2 38.0 50-54 36.28055 38.0 38.0 38.0 33.6 38.0 55-59 36.3583 38.0 38.0 38.0 34.0 38.0 60-64 36.17985 38.0 38.0 38.0 33.6 38.0 65-69 36.0598 38.0 37.8 38.0 33.2 38.0 70-74 35.997600000000006 38.0 38.0 38.0 33.0 38.0 75-79 35.73895 38.0 37.0 38.0 31.0 38.0 80-84 35.666799999999995 38.0 37.2 38.0 30.6 38.0 85-89 35.65925 38.0 37.0 38.0 30.8 38.0 90-94 35.4519 38.0 37.0 38.0 30.2 38.0 95-99 35.265299999999996 38.0 36.6 38.0 29.0 38.0 100-104 35.0015 38.0 36.0 38.0 27.8 38.0 105-109 34.64935 38.0 35.2 38.0 26.0 38.0 110-114 34.62779999999999 38.0 35.0 38.0 26.0 38.0 115-119 34.43175 38.0 35.0 38.0 25.2 38.0 120-124 34.1883 38.0 34.8 38.0 23.6 38.0 125-129 33.73725 38.0 34.2 38.0 20.6 38.0 130-134 33.31565 38.0 34.0 38.0 18.6 38.0 135-139 32.888850000000005 38.0 33.6 38.0 14.6 38.0 140-144 32.15785 37.8 31.6 38.0 13.2 38.0 145-149 30.73275 36.2 30.2 38.0 8.6 38.0 150-151 25.125375 33.5 15.0 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 10.0 3 10.0 4 2.0 5 4.0 6 1.0 7 3.0 8 0.0 9 1.0 10 4.0 11 4.0 12 2.0 13 4.0 14 3.0 15 5.0 16 6.0 17 10.0 18 10.0 19 7.0 20 8.0 21 12.0 22 9.0 23 27.0 24 21.0 25 23.0 26 43.0 27 43.0 28 48.0 29 73.0 30 76.0 31 80.0 32 119.0 33 168.0 34 227.0 35 397.0 36 763.0 37 1777.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.150000000000006 18.125 11.525 30.2 2 27.41370685342671 23.761880940470235 27.41370685342671 21.410705352676338 3 21.96098049024512 26.91345672836418 28.91445722861431 22.211105552776388 4 27.070302727045288 28.971728796597446 20.84063047285464 23.117338003502628 5 26.713356678339167 33.291645822911455 19.18459229614807 20.810405202601302 6 23.905976494123532 35.483870967741936 19.504876219054765 21.10527631907977 7 22.080520130032507 20.05501375343836 34.98374593648413 22.88072018004501 8 25.35633908477119 24.131032758189548 23.1807951987997 27.33183295823956 9 24.356089022255563 23.755938984746187 26.081520380095025 25.806451612903224 10-14 26.377913374012202 24.93748124437331 23.452035610683204 25.232569770931278 15-19 25.735294117647058 25.570228091236498 24.029611844737893 24.66486594637855 20-24 25.697709312793837 25.507652295688704 24.827448234470342 23.967190157047114 25-29 26.04281284385316 25.307592277683305 24.29728918675603 24.352305691707514 30-34 26.186546636659163 25.751437859464865 24.20105026256564 23.86096524131033 35-39 25.66641660415104 25.55138784696174 24.18104526131533 24.601150287571894 40-44 25.775155031006204 25.340068013602718 24.16983396679336 24.71494298859772 45-49 26.47029405881176 25.10502100420084 24.90498099619924 23.51970394078816 50-54 25.811452863215806 25.531382845711427 24.90622655663916 23.75093773443361 55-59 26.811702925731435 24.921230307576895 25.0112528132033 23.25581395348837 60-64 26.257877363208966 24.74742422726818 25.517655296588977 23.477043112933877 65-69 26.22286686005802 24.572371711513455 24.852455736721016 24.352305691707514 70-74 26.57930275596459 25.34387035462412 24.89871455009253 23.178112339318762 75-79 26.03650912728182 24.66116529132283 25.23130782695674 24.07101775443861 80-84 25.67141785446362 25.06626656664166 24.756189047261813 24.50612653163291 85-89 26.886721680420106 24.846211552888224 24.751187796949235 23.515878969742435 90-94 26.15784735420626 25.01750525157547 25.192557767330197 23.632089626888067 95-99 25.955382152861144 24.759903961584634 25.34013605442177 23.944577831132452 100-104 26.211552888222055 25.381345336334082 24.921230307576895 23.485871467866968 105-109 26.14653663415854 25.34133533383346 24.596149037259316 23.915978994748688 110-114 26.906726681670417 25.851462865716428 24.566141535383846 22.67566891722931 115-119 26.43292987896369 24.75742722816845 24.827448234470342 23.982194658397518 120-124 26.690338067613524 25.3000600120024 24.5499099819964 23.459691938387678 125-129 26.875375075015 25.520104020804162 24.55491098219644 23.049609921984395 130-134 27.016754188547136 25.41635408852213 24.241060265066267 23.325831457864467 135-139 26.616654163540886 25.36134033508377 25.03125781445361 22.99074768692173 140-144 27.090418083616726 25.595119023804763 24.989997999599918 22.324464892978597 145-149 27.016754188547136 25.7664416104026 24.691172793198298 22.52563140785196 150-151 27.66941735433858 25.656414103525883 24.06851712928232 22.605651412853213 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.5 3 0.5 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.5 20 1.0 21 0.5 22 0.0 23 0.0 24 0.0 25 0.5 26 1.0 27 0.5 28 0.5 29 2.0 30 5.0 31 6.5 32 8.5 33 13.5 34 18.5 35 26.5 36 33.0 37 48.5 38 83.5 39 105.5 40 120.0 41 146.5 42 171.5 43 181.5 44 175.0 45 180.0 46 196.5 47 196.0 48 173.5 49 176.5 50 179.0 51 144.5 52 133.5 53 130.5 54 107.0 55 96.0 56 92.0 57 95.5 58 94.0 59 83.0 60 90.0 61 89.5 62 74.0 63 60.0 64 52.5 65 51.5 66 48.0 67 45.0 68 47.5 69 48.5 70 40.0 71 31.5 72 29.0 73 22.0 74 19.5 75 13.0 76 3.5 77 2.5 78 1.5 79 1.0 80 0.5 81 0.5 82 0.5 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 0.05 3 0.05 4 0.075 5 0.05 6 0.025 7 0.025 8 0.025 9 0.025 10-14 0.03 15-19 0.04 20-24 0.03 25-29 0.03 30-34 0.025 35-39 0.025 40-44 0.02 45-49 0.02 50-54 0.025 55-59 0.025 60-64 0.03 65-69 0.03 70-74 0.034999999999999996 75-79 0.025 80-84 0.025 85-89 0.025 90-94 0.03 95-99 0.04 100-104 0.025 105-109 0.025 110-114 0.025 115-119 0.03 120-124 0.02 125-129 0.02 130-134 0.025 135-139 0.025 140-144 0.02 145-149 0.025 150-151 0.025 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.65 #Duplication Level Percentage of deduplicated Percentage of total 1 99.69894631209232 99.35000000000001 2 0.2508780732563974 0.5 3 0.050175614651279475 0.15 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 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 pass >>END_MODULE >>Adapter Content pass #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 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 82-83 0.025 0.0 0.0 0.0 0.0 84-85 0.037500000000000006 0.0 0.0 0.0 0.0 86-87 0.05 0.0 0.0 0.0 0.0 88-89 0.05 0.0 0.0 0.0 0.0 90-91 0.0625 0.0 0.0 0.0 0.0 92-93 0.1 0.0 0.0 0.0 0.0 94-95 0.16249999999999998 0.0 0.0 0.0 0.0 96-97 0.2 0.0 0.0 0.0 0.0 98-99 0.21250000000000002 0.0 0.0 0.0 0.0 100-101 0.25 0.0 0.0 0.0 0.0 102-103 0.3375 0.0 0.0 0.0 0.0 104-105 0.3875 0.0 0.0 0.0 0.0 106-107 0.5249999999999999 0.0 0.0 0.0 0.0 108-109 0.625 0.0 0.0 0.0 0.0 110-111 0.7124999999999999 0.0 0.0 0.0 0.0 112-113 0.825 0.0 0.0 0.0 0.0 114-115 1.0 0.0 0.0 0.0 0.0 116-117 1.0625 0.0 0.0 0.0 0.0 118-119 1.2125 0.0 0.0 0.0 0.0 120-121 1.4625 0.0 0.0 0.0 0.0 122-123 1.65 0.0 0.0 0.0 0.0 124-125 1.8375 0.0 0.0 0.0 0.0 126-127 2.0375 0.0 0.0 0.0 0.0 128-129 2.25 0.0 0.0 0.0 0.0 130-131 2.4124999999999996 0.0 0.0 0.0 0.0 132-133 2.6625 0.0 0.0 0.0 0.0 134-135 3.0625 0.0 0.0 0.0 0.0 136-137 3.35 0.0 0.0 0.0 0.0 138-139 3.7750000000000004 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GATGATG 10 0.0068378756 144.95 145 ATGCCAC 10 0.0068378756 144.95 6 >>END_MODULE Read 1024090 spots for SRR6958255.sra Written 1024090 spots for SRR6958255.sra Read 1024090 spots for SRR6958255.sra Written 1024090 spots for SRR6958255.sra Read 1024090 spots for SRR6958255.sra Written 1024090 spots for SRR6958255.sra Read 1024090 spots for SRR6958255.sra Written 1024090 spots for SRR6958255.sra Read 1024090 spots for SRR6958255.sra Written 1024090 spots for SRR6958255.sra Read 1024090 spots for SRR6958255.sra Written 1024090 spots for SRR6958255.sra Read 1024090 spots for SRR6958255.sra Written 1024090 spots for SRR6958255.sra Read 1024090 spots for SRR6958255.sra Written 1024090 spots for SRR6958255.sra Read 1024090 spots for SRR6958255.sra Written 1024090 spots for SRR6958255.sra Read 1024090 spots for SRR6958255.sra Written 1024090 spots for SRR6958255.sra Read 1024090 spots for SRR6958255.sra Written 1024090 spots for SRR6958255.sra Read 1024107 spots for SRR6958255.sra Written 1024107 spots for SRR6958255.sra Read 1024090 spots for SRR6958255.sra Written 1024090 spots for SRR6958255.sra Read 1024090 spots for SRR6958255.sra Written 1024090 spots for SRR6958255.sra Read 1024090 spots for SRR6958255.sra Written 1024090 spots for SRR6958255.sra Read 1024090 spots for SRR6958255.sra Written 1024090 spots for SRR6958255.sra Read 1024090 spots for SRR6958255.sra Written 1024090 spots for SRR6958255.sra Read 1024090 spots for SRR6958255.sra Written 1024090 spots for SRR6958255.sra Read 1024090 spots for SRR6958255.sra Written 1024090 spots for SRR6958255.sra Read 1024090 spots for SRR6958255.sra Written 1024090 spots for SRR6958255.sra SRR ids: ['SRR6958255.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_bp_c9gf4 SRR6958255.sra spots: 20481817 blocks: [[1, 1024090], [1024091, 2048180], [2048181, 3072270], [3072271, 4096360], [4096361, 5120450], [5120451, 6144540], [6144541, 7168630], [7168631, 8192720], [8192721, 9216810], [9216811, 10240900], [10240901, 11264990], [11264991, 12289080], [12289081, 13313170], [13313171, 14337260], [14337261, 15361350], [15361351, 16385440], [16385441, 17409530], [17409531, 18433620], [18433621, 19457710], [19457711, 20481817]] SRR6958255 file size 6918915 SRR6958255 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 SRR6958255 SRR6958255_1.fastq SRR6958255_2.fastq Input file: SRR6958255_1.fastq Paired file: SRR6958255_2.fastq trimmed: SRR6958255-trimmed-pair1.fastq, SRR6958255-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 Dec 6 17:51:00 2024 >> started Fri Dec 6 17:51:27 2024 >> done (26.306s) 20481817 read pairs processed; of these: 39458 ( 0.19%) short read pairs filtered out after trimming by size control 41772 ( 0.20%) empty read pairs filtered out after trimming by size control 20400587 (99.60%) read pairs available; of these: 8910737 (43.68%) trimmed read pairs available after processing 11489850 (56.32%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 2 0.00% 20 2 0.00% 21 2 0.00% 22 4 0.00% 23 2 0.00% 24 2 0.00% 25 4 0.00% 26 3 0.00% 27 3 0.00% 28 13 0.00% 29 6 0.00% 30 8 0.00% 31 5 0.00% 32 16 0.00% 33 4 0.00% 34 11 0.00% 35 13 0.00% 36 12 0.00% 37 14 0.00% 38 17 0.00% 39 11 0.00% 40 19 0.00% 41 16 0.00% 42 23 0.00% 43 25 0.00% 44 25 0.00% 45 22 0.00% 46 32 0.00% 47 24 0.00% 48 36 0.00% 49 34 0.00% 50 31 0.00% 51 46 0.00% 52 61 0.00% 53 49 0.00% 54 69 0.00% 55 78 0.00% 56 81 0.00% 57 98 0.00% 58 93 0.00% 59 88 0.00% 60 105 0.00% 61 135 0.00% 62 148 0.00% 63 156 0.00% 64 188 0.00% 65 188 0.00% 66 222 0.00% 67 292 0.00% 68 297 0.00% 69 325 0.00% 70 352 0.00% 71 430 0.00% 72 521 0.00% 73 569 0.00% 74 599 0.00% 75 677 0.00% 76 758 0.00% 77 808 0.00% 78 1015 0.00% 79 1119 0.01% 80 1218 0.01% 81 1380 0.01% 82 1630 0.01% 83 1872 0.01% 84 3511 0.02% 85 4454 0.02% 86 4466 0.02% 87 4567 0.02% 88 4778 0.02% 89 4722 0.02% 90 5059 0.02% 91 5176 0.03% 92 5668 0.03% 93 5866 0.03% 94 6480 0.03% 95 7009 0.03% 96 7332 0.04% 97 7838 0.04% 98 7970 0.04% 99 8910 0.04% 100 9311 0.05% 101 10015 0.05% 102 10640 0.05% 103 11449 0.06% 104 12292 0.06% 105 13177 0.06% 106 13909 0.07% 107 14611 0.07% 108 15145 0.07% 109 15857 0.08% 110 17177 0.08% 111 18150 0.09% 112 19353 0.09% 113 20545 0.10% 114 21896 0.11% 115 23190 0.11% 116 24714 0.12% 117 25965 0.13% 118 26931 0.13% 119 28097 0.14% 120 29416 0.14% 121 30953 0.15% 122 32393 0.16% 123 34253 0.17% 124 36403 0.18% 125 38584 0.19% 126 40677 0.20% 127 42661 0.21% 128 45088 0.22% 129 47182 0.23% 130 49343 0.24% 131 52075 0.26% 132 54877 0.27% 133 58630 0.29% 134 61924 0.30% 135 65902 0.32% 136 69792 0.34% 137 73879 0.36% 138 78906 0.39% 139 85119 0.42% 140 92143 0.45% 141 99964 0.49% 142 111828 0.55% 143 127323 0.62% 144 147939 0.73% 145 175945 0.86% 146 220238 1.08% 147 298487 1.46% 148 453144 2.22% 149 936630 4.59% 150 4756700 23.32% 151 11489850 56.32% 20400587 reads passed initial QC criterion=sequence-density sequence-density=0.30 sequence-density-rank=1 fanout-score=3.05 fanout-score-rank=27 prefix-density=0.32 prefix-fanout=2.9 sequence=GGTGTTGTCGAAGCCGATGATGCGGAC criterion=fanout-score sequence-density=0.03 sequence-density-rank=37 fanout-score=243.21 fanout-score-rank=1 prefix-density=0.50 prefix-fanout=12.6 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.26 sequence-density-rank=1 fanout-score=11.99 fanout-score-rank=10 prefix-density=0.46 prefix-fanout=6.8 sequence=AAGATCAAGGAGAAGCTCCCTGGTGGTGGC criterion=fanout-score sequence-density=0.12 sequence-density-rank=23 fanout-score=128.67 fanout-score-rank=1 prefix-density=0.70 prefix-fanout=21.5 sequence=CAAGAAGAAGGT SRR6958255 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 17:53:51 Started mapping on | Dec 06 17:53:51 Finished on | Dec 06 17:55:11 Mapping speed, Million of reads per hour | 918.03 Number of input reads | 20400587 Average input read length | 296 UNIQUE READS: Uniquely mapped reads number | 19723855 Uniquely mapped reads % | 96.68% Average mapped length | 296.13 Number of splices: Total | 19597283 Number of splices: Annotated (sjdb) | 18219058 Number of splices: GT/AG | 19353394 Number of splices: GC/AG | 212695 Number of splices: AT/AC | 8962 Number of splices: Non-canonical | 22232 Mismatch rate per base, % | 0.12% Deletion rate per base | 0.00% Deletion average length | 1.39 Insertion rate per base | 0.00% Insertion average length | 1.12 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 138887 % of reads mapped to multiple loci | 0.68% Number of reads mapped to too many loci | 29355 % of reads mapped to too many loci | 0.14% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.45% % of reads unmapped: other | 1.04% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 560475 560475 560475 N_multimapping 138887 138887 138887 N_noFeature 947097 19103960 1190924 N_ambiguous 450922 3252 75633 UnstrandedReadsAssigned:18325836 PositiveStrandReadsAssigned:616643 NegativeStrandReadsAssigned:18457298 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=149 echo kmer=145 SRR6958255 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: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in paired-end mode [quant] will process pair 1: SRR6958255-trimmed-pair1.fastq SRR6958255-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 20,400,587 reads, 18,467,779 reads pseudoaligned [quant] estimated average fragment length: 257.326 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,204 rounds 52973 SRR6958255.ke.tsv 35125 SRR6958255.se.tsv 88098 total ==> SRR6958255.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 680.038 166.137 19.5238 PNS24247 1044 787.674 90.7242 9.20463 PNS24249 1928 1671.67 177.064 8.46465 PNS24246 1044 787.674 90.7242 9.20463 PNS24248 1044 787.674 90.7242 9.20463 PNS24244 1471 1214.67 117.626 7.73882 PNS24243 293 85.4619 0 0 KQK14069 1603 1346.67 1103.24 65.469 KQK14071 474 230.874 14.8519 5.14087 ==> SRR6958255.se.tsv <== BRADI_1g14170v3 1221 BRADI_1g53295v3 631 BRADI_1g59795v3 173 BRADI_1g07683v3 0 BRADI_1g00485v3 24 BRADI_1g20270v3 755 BRADI_1g74790v3 792 BRADI_1g09890v3 2 BRADI_1g77505v3 174 BRADI_1g48960v3 0 SRR6958255 completed mapping pipeline successfully