Starting /dee2/code/volunteer_pipeline.sh SRR11445638 current disk space = 3051733274624 free memory = 1580754060 SRR11445638 SRAfilesize 50c2834b2900611d8a1a0944ce201bb8 SRR11445638.sra SRR11445638.sra file validated SRR11445638 is paired end SRR11445638 is conventional basespace SRR11445638 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11445638_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 38 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 23.31625 32.0 2.0 32.0 2.0 32.0 2 30.97375 32.0 32.0 32.0 32.0 32.0 3 34.335 37.0 32.0 37.0 32.0 37.0 4 34.92625 37.0 32.0 37.0 32.0 37.0 5 36.16375 37.0 37.0 37.0 32.0 37.0 6 39.4995 41.0 41.0 41.0 37.0 41.0 7 39.9475 41.0 41.0 41.0 37.0 41.0 8 39.61225 41.0 41.0 41.0 37.0 41.0 9 39.986 41.0 41.0 41.0 37.0 41.0 10-14 39.8998 41.0 41.0 41.0 37.0 41.0 15-19 38.96225 41.0 40.2 41.0 35.0 41.0 20-24 38.715 41.0 38.6 41.0 33.0 41.0 25-29 38.486599999999996 41.0 39.4 41.0 34.0 41.0 30-34 38.84355 41.0 39.4 41.0 35.0 41.0 35-39 39.269349999999996 41.0 41.0 41.0 37.0 41.0 40-44 38.773999999999994 41.0 40.2 41.0 34.0 41.0 45-49 38.20485000000001 41.0 38.6 41.0 32.0 41.0 50-54 38.773700000000005 41.0 40.2 41.0 34.0 41.0 55-59 38.299899999999994 41.0 38.6 41.0 31.0 41.0 60-64 38.381750000000004 41.0 38.6 41.0 32.0 41.0 65-69 38.034349999999996 41.0 38.6 41.0 30.0 41.0 70-74 36.92265 41.0 36.0 41.0 27.0 41.0 75-79 37.3948 41.0 37.0 41.0 29.0 41.0 80-84 36.8038 41.0 36.0 41.0 26.0 41.0 85-89 34.6974 38.6 32.0 41.0 20.0 41.0 90-94 35.76665 40.2 34.0 41.0 21.0 41.0 95-99 35.7077 41.0 35.0 41.0 20.0 41.0 100-104 33.5769 38.6 28.0 41.0 16.0 41.0 105-109 35.82834999999999 41.0 34.0 41.0 22.0 41.0 110-114 36.456250000000004 41.0 37.0 41.0 22.0 41.0 115-119 35.8985 41.0 35.0 41.0 22.0 41.0 120-124 33.28075 37.8 29.0 41.0 14.0 41.0 125-129 33.634 37.8 30.0 41.0 16.0 41.0 130-134 33.21235 37.8 29.0 41.0 12.0 41.0 135-139 33.32065 37.0 30.0 41.0 12.0 41.0 140-144 32.24555 37.0 27.0 41.0 12.0 41.0 145-149 29.043950000000002 33.0 18.0 39.4 12.0 41.0 150 30.79625 37.0 22.0 41.0 12.0 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 1.0 19 1.0 20 9.0 21 8.0 22 14.0 23 17.0 24 31.0 25 43.0 26 43.0 27 55.0 28 94.0 29 90.0 30 100.0 31 94.0 32 125.0 33 180.0 34 206.0 35 267.0 36 340.0 37 443.0 38 619.0 39 748.0 40 472.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 25.034435261707987 24.862258953168045 25.10330578512397 25.0 2 24.224999999999998 25.224999999999998 23.9 26.650000000000002 3 23.45 28.000000000000004 24.5 24.05 4 25.374999999999996 27.975 21.05 25.6 5 25.424999999999997 28.7 23.400000000000002 22.475 6 27.0 25.924999999999997 24.55 22.525000000000002 7 26.25 26.450000000000003 24.575 22.725 8 26.700000000000003 26.650000000000002 30.275000000000002 16.375 9 28.15 27.450000000000003 28.275 16.125 10-14 25.795 28.7 28.205000000000002 17.299999999999997 15-19 22.49 30.159999999999997 30.564999999999998 16.785 20-24 21.525 30.709999999999997 30.759999999999998 17.005 25-29 21.98 28.985 31.230000000000004 17.805 30-34 22.175 30.39 30.264999999999997 17.169999999999998 35-39 21.295 29.64 31.395 17.669999999999998 40-44 21.584999999999997 30.29 30.95 17.175 45-49 20.805 30.395 31.119999999999997 17.68 50-54 21.05 29.54 31.935000000000002 17.474999999999998 55-59 20.605 30.404999999999998 31.405 17.585 60-64 20.068010201530228 30.544581687253086 31.43971595739361 17.947692153823073 65-69 20.385 29.439999999999998 32.4 17.775 70-74 20.825 30.29 31.624999999999996 17.26 75-79 20.525 29.81 31.965 17.7 80-84 20.525 29.65 32.32 17.505000000000003 85-89 20.495 30.04 32.015 17.45 90-94 20.630000000000003 30.654999999999998 31.585 17.130000000000003 95-99 20.26 30.930000000000003 31.879999999999995 16.93 100-104 20.125 30.285 32.595 16.994999999999997 105-109 19.945 30.42 32.785 16.85 110-114 19.8 31.064999999999998 32.41 16.725 115-119 19.655 31.005 32.49 16.85 120-124 21.02 29.395 32.89 16.695 125-129 20.135 30.099999999999998 33.045 16.72 130-134 19.97 30.185000000000002 33.040000000000006 16.805 135-139 19.98 30.404999999999998 32.295 17.32 140-144 19.585 30.575000000000003 33.410000000000004 16.43 145-149 19.759999999999998 30.165 33.975 16.1 150 19.05 29.9 33.125 17.925 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 5.0 1 4.0 2 3.5 3 6.0 4 7.0 5 4.5 6 2.5 7 4.0 8 5.5 9 4.5 10 4.0 11 5.5 12 7.0 13 6.0 14 5.5 15 6.5 16 5.5 17 4.0 18 5.0 19 6.0 20 6.5 21 6.0 22 7.0 23 8.5 24 10.5 25 18.5 26 32.0 27 34.5 28 39.0 29 61.0 30 66.5 31 78.5 32 108.0 33 132.5 34 169.0 35 177.5 36 180.5 37 191.5 38 208.0 39 208.0 40 212.0 41 238.0 42 219.0 43 197.5 44 178.0 45 165.0 46 151.5 47 138.0 48 126.5 49 104.5 50 86.0 51 66.0 52 64.5 53 52.0 54 28.5 55 28.0 56 25.0 57 16.5 58 12.0 59 10.5 60 9.5 61 6.5 62 6.0 63 4.0 64 3.0 65 4.0 66 2.0 67 0.5 68 0.0 69 0.0 70 1.5 71 1.5 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 0.0 >>END_MODULE >>Per base N content fail #Base N-Count 1 27.400000000000002 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 0.015 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 95.42500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 95.7296305999476 91.35 2 3.851192035630076 7.35 3 0.36678019386953103 1.05 4 0.026198585276395077 0.1 5 0.0 0.0 6 0.026198585276395077 0.15 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 warn #Sequence Count Percentage Possible Source AAAAAAAAAAAAAAAAAAAAGATCGGAAGAGCACACGTCTGAACTCCAGT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) >>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 0.0125 0.0 0.0 0.0 0.0 18-19 0.05 0.0 0.0 0.0 0.0 20-21 0.35 0.0 0.0 0.0 0.0 22-23 1.0375 0.0 0.0 0.0 0.0 24-25 1.4875 0.0 0.0 0.0 0.0 26-27 1.75 0.0 0.0 0.0 0.0 28-29 2.0125 0.0 0.0 0.0 0.0 30-31 2.0625 0.0 0.0 0.0 0.0 32-33 2.3 0.0 0.0 0.0 0.0 34-35 2.475 0.0 0.0 0.0 0.0 36-37 2.6 0.0 0.0 0.0 0.0 38-39 2.75 0.0 0.0 0.0 0.0 40-41 2.925 0.0 0.0 0.0 0.0 42-43 3.0375 0.0 0.0 0.0 0.0 44-45 3.1375 0.0 0.0 0.0 0.0 46-47 3.3625 0.0 0.0 0.0 0.0 48-49 3.6375 0.0 0.0 0.0 0.0 50-51 3.7750000000000004 0.0 0.0 0.0 0.0 52-53 3.9875000000000003 0.0 0.0 0.0 0.0 54-55 4.137499999999999 0.0 0.0 0.0 0.0 56-57 4.262499999999999 0.0 0.0 0.0 0.0 58-59 4.475 0.0 0.0 0.0 0.0 60-61 4.625 0.0 0.0 0.0 0.0 62-63 4.8 0.0 0.0 0.0 0.0 64-65 4.9625 0.0 0.0 0.0 0.0 66-67 5.125 0.0 0.0 0.0 0.0 68-69 5.275 0.0 0.0 0.0 0.0 70-71 5.4875 0.0 0.0 0.0 0.0 72-73 5.775 0.0 0.0 0.0 0.0 74-75 5.9625 0.0 0.0 0.0 0.0 76-77 6.075 0.0 0.0 0.0 0.0 78-79 6.300000000000001 0.0 0.0 0.0 0.0 80-81 6.5625 0.0 0.0 0.0 0.0 82-83 6.737500000000001 0.0 0.0 0.0 0.0 84-85 6.9125 0.0 0.0 0.0 0.0 86-87 7.125 0.0 0.0 0.0 0.0 88-89 7.3 0.0 0.0 0.0 0.0 90-91 7.575 0.0 0.0 0.0 0.0 92-93 7.7375 0.0 0.0 0.0 0.0 94-95 7.8125 0.0 0.0 0.0 0.0 96-97 7.95 0.0 0.0 0.0 0.0 98-99 8.15 0.0 0.0 0.0 0.0 100-101 8.2625 0.0 0.0 0.0 0.0 102-103 8.3875 0.0 0.0 0.0 0.0 104-105 8.625 0.0 0.0 0.0 0.0 106-107 8.875 0.0 0.0 0.0 0.0 108-109 9.1125 0.0 0.0 0.0 0.0 110-111 9.2625 0.0 0.0 0.0 0.0 112-113 9.5125 0.0 0.0 0.0 0.0 114-115 9.6875 0.0 0.0 0.0 0.0 116-117 9.8125 0.0 0.0 0.0 0.0 118-119 9.9625 0.0 0.0 0.0 0.0 120-121 10.125 0.0 0.0 0.0 0.0 122-123 10.3 0.0 0.0 0.0 0.0 124-125 10.5 0.0 0.0 0.0 0.0 126-127 10.7875 0.0 0.0 0.0 0.0 128-129 10.975000000000001 0.0 0.0 0.0 0.0 130-131 11.1375 0.0 0.0 0.0 0.0 132-133 11.3125 0.0 0.0 0.0 0.0 134-135 11.5 0.0 0.0 0.0 0.0 136-137 11.6875 0.0 0.0 0.0 0.0 138 11.9 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTCACAA 10 0.0070099696 143.75 9 >>END_MODULE SRR11445638 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11445638_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 28 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 18.6775 27.0 2.0 32.0 2.0 32.0 2 31.06875 32.0 32.0 32.0 32.0 32.0 3 33.0875 32.0 32.0 37.0 32.0 37.0 4 34.2725 37.0 32.0 37.0 32.0 37.0 5 35.7475 37.0 37.0 37.0 32.0 37.0 6 38.625 41.0 41.0 41.0 32.0 41.0 7 39.42575 41.0 41.0 41.0 37.0 41.0 8 38.9355 41.0 41.0 41.0 37.0 41.0 9 36.5065 41.0 37.0 41.0 22.0 41.0 10-14 39.18150000000001 41.0 41.0 41.0 36.0 41.0 15-19 36.95745 40.2 36.6 41.0 28.0 41.0 20-24 26.6282 29.0 14.0 38.6 12.0 41.0 25-29 29.934199999999997 34.0 20.0 40.2 12.0 41.0 30-34 29.4052 33.0 18.0 41.0 12.0 41.0 35-39 28.383499999999998 33.0 18.0 39.4 12.0 41.0 40-44 27.804399999999998 31.0 12.0 38.6 12.0 41.0 45-49 27.20965 29.0 14.0 38.6 12.0 41.0 50-54 25.86925 24.0 12.0 37.0 12.0 41.0 55-59 25.6764 27.0 12.0 36.0 12.0 41.0 60-64 27.700049999999997 31.0 14.0 38.6 12.0 41.0 65-69 27.437400000000004 30.0 12.0 37.8 12.0 41.0 70-74 25.41415 26.0 12.0 36.0 12.0 41.0 75-79 24.491350000000004 23.0 12.0 35.0 12.0 39.4 80-84 25.307550000000003 24.0 12.0 37.0 12.0 41.0 85-89 24.688650000000003 22.0 12.0 37.0 12.0 41.0 90-94 23.7008 22.0 12.0 34.0 12.0 39.4 95-99 23.95235 22.0 12.0 35.0 12.0 39.4 100-104 22.431900000000002 22.0 12.0 32.0 12.0 37.8 105-109 23.058799999999998 22.0 12.0 34.0 12.0 38.6 110-114 21.37855 20.0 12.0 31.0 12.0 37.8 115-119 21.77355 22.0 12.0 32.0 12.0 37.8 120-124 22.23225 22.0 12.0 32.0 12.0 37.8 125-129 19.941899999999997 16.0 12.0 28.0 12.0 35.0 130-134 19.8921 18.0 12.0 27.0 12.0 36.0 135-139 20.02025 18.0 12.0 27.0 12.0 36.0 140-144 19.31855 14.0 12.0 27.0 12.0 35.0 145-149 19.10265 12.0 12.0 26.0 12.0 34.0 150 19.4075 12.0 12.0 27.0 12.0 37.0 >>END_MODULE >>Per sequence quality scores warn #Quality Count 14 1.0 15 2.0 16 13.0 17 57.0 18 115.0 19 209.0 20 283.0 21 314.0 22 320.0 23 333.0 24 285.0 25 306.0 26 274.0 27 255.0 28 216.0 29 194.0 30 179.0 31 146.0 32 132.0 33 102.0 34 82.0 35 68.0 36 54.0 37 30.0 38 19.0 39 10.0 40 1.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 4.533333333333333 0.0380952380952381 91.92380952380952 3.5047619047619047 2 0.4 0.1 99.325 0.17500000000000002 3 0.125 0.075 99.65 0.15 4 0.775 0.025 98.97500000000001 0.22499999999999998 5 0.1 0.15 99.65 0.1 6 0.42500000000000004 0.1 99.4 0.075 7 0.27499999999999997 0.1 99.47500000000001 0.15 8 0.325 0.15 99.3 0.22499999999999998 9 1.9254813703425855 0.07501875468867217 97.69942485621405 0.30007501875468867 10-14 0.2900580116023205 0.1850370074014803 99.35987197439488 0.16503300660132028 15-19 2.94 2.0650000000000004 93.345 1.6500000000000001 20-24 19.45 29.865000000000002 34.54 16.145 25-29 12.335 44.285000000000004 31.095 12.285 30-34 13.850000000000001 35.085 35.975 15.09 35-39 12.941294129412942 29.182918291829186 43.154315431543154 14.72147214721472 40-44 12.025 29.215000000000003 45.785 12.975 45-49 12.67 32.72 41.455 13.155 50-54 15.260000000000002 33.550000000000004 37.505 13.685 55-59 16.455000000000002 33.32 35.725 14.499999999999998 60-64 16.07 34.37 33.71 15.85 65-69 16.32 34.415 32.84 16.425 70-74 16.64 33.765 32.455 17.14 75-79 16.14 34.455000000000005 33.025 16.38 80-84 15.597339600940142 34.88023203480522 33.32499874981247 16.197429614442164 85-89 16.17 34.79 33.129999999999995 15.909999999999998 90-94 16.72 34.36 33.73 15.190000000000001 95-99 16.8 34.755 32.2 16.245 100-104 16.935 34.705000000000005 32.245000000000005 16.115 105-109 17.294999999999998 35.260000000000005 31.695 15.75 110-114 17.03 35.67 31.509999999999998 15.790000000000001 115-119 17.1 36.425000000000004 29.84 16.634999999999998 120-124 16.87421855463866 35.58389597399349 30.02750687671918 17.514378594648665 125-129 17.69265389808471 34.46516977546632 30.99464919737961 16.847527129069363 130-134 17.605 33.87 30.975 17.549999999999997 135-139 16.6 35.135 30.39 17.875 140-144 18.195 33.495000000000005 30.545 17.765 145-149 17.845 33.975 30.285 17.895 150 16.35 33.225 31.25 19.175 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 77.0 1 65.0 2 58.0 3 44.0 4 20.0 5 14.0 6 16.5 7 16.5 8 16.0 9 15.5 10 16.0 11 23.0 12 32.5 13 39.0 14 33.5 15 42.0 16 51.5 17 49.0 18 65.0 19 90.0 20 109.0 21 126.0 22 147.5 23 170.5 24 199.5 25 222.0 26 230.0 27 243.0 28 255.5 29 246.0 30 212.5 31 180.0 32 156.5 33 143.0 34 117.0 35 87.0 36 77.0 37 60.0 38 50.0 39 44.5 40 35.5 41 28.5 42 21.5 43 16.5 44 11.5 45 12.5 46 12.5 47 7.0 48 5.0 49 5.5 50 4.0 51 3.0 52 1.5 53 3.5 54 4.0 55 2.0 56 1.0 57 0.0 58 0.0 59 0.0 60 0.0 61 0.0 62 0.5 63 0.5 64 0.0 65 0.5 66 0.5 67 0.0 68 0.0 69 0.0 70 0.0 71 0.0 72 0.0 73 0.5 74 0.5 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 fail #Base N-Count 1 34.375 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.025 10-14 0.02 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.01 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 0.015 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 0.025 125-129 0.015 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 93.5 #Duplication Level Percentage of deduplicated Percentage of total 1 98.55614973262033 92.15 2 0.8823529411764706 1.6500000000000001 3 0.1336898395721925 0.375 4 0.10695187165775401 0.4 5 0.026737967914438502 0.125 6 0.026737967914438502 0.15 7 0.0 0.0 8 0.026737967914438502 0.2 9 0.026737967914438502 0.22499999999999998 >10 0.18716577540106952 3.375 >50 0.026737967914438502 1.35 >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 fail #Sequence Count Percentage Possible Source NTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 54 1.35 No Hit TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 50 1.25 No Hit TTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 19 0.475 No Hit TTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 16 0.4 No Hit TTTTTTTTTTTTTTTTTTTCCTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 15 0.375 No Hit NTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 13 0.325 No Hit NTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 11 0.27499999999999997 No Hit TTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 11 0.27499999999999997 No Hit NTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 9 0.22499999999999998 No Hit TTTTTTTTTTTTTTTTTTTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 8 0.2 No Hit TTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 6 0.15 No Hit TTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #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 0.037500000000000006 0.0 0.0 0.0 0.0 18-19 0.07500000000000001 0.0 0.0 0.0 0.0 20-21 0.3125 0.0 0.0 0.0 0.0 22-23 0.8875 0.0 0.0 0.0 0.0 24-25 1.2125 0.0 0.0 0.0 0.0 26-27 1.4125 0.0 0.0 0.0 0.0 28-29 1.6125 0.0 0.0 0.0 0.0 30-31 1.6625 0.0 0.0 0.0 0.0 32-33 1.8125 0.0 0.0 0.0 0.0 34-35 1.9874999999999998 0.0 0.0 0.0 0.0 36-37 2.0875000000000004 0.0 0.0 0.0 0.0 38-39 2.2 0.0 0.0 0.0 0.0 40-41 2.275 0.0 0.0 0.0 0.0 42-43 2.375 0.0 0.0 0.0 0.0 44-45 2.55 0.0 0.0 0.0 0.0 46-47 2.675 0.0 0.0 0.0 0.0 48-49 2.925 0.0 0.0 0.0 0.0 50-51 3.0 0.0 0.0 0.0 0.0 52-53 3.175 0.0 0.0 0.0 0.0 54-55 3.25 0.0 0.0 0.0 0.0 56-57 3.375 0.0 0.0 0.0 0.0 58-59 3.55 0.0 0.0 0.0 0.0 60-61 3.7 0.0 0.0 0.0 0.0 62-63 3.8499999999999996 0.0 0.0 0.0 0.0 64-65 3.95 0.0 0.0 0.0 0.0 66-67 4.1125 0.0 0.0 0.0 0.0 68-69 4.225 0.0 0.0 0.0 0.0 70-71 4.4 0.0 0.0 0.0 0.0 72-73 4.612500000000001 0.0 0.0 0.0 0.0 74-75 4.7875 0.0 0.0 0.0 0.0 76-77 4.9625 0.0 0.0 0.0 0.0 78-79 5.225 0.0 0.0 0.0 0.0 80-81 5.475 0.0 0.0 0.0 0.0 82-83 5.6625 0.0 0.0 0.0 0.0 84-85 5.8125 0.0 0.0 0.0 0.0 86-87 5.95 0.0 0.0 0.0 0.0 88-89 6.0625 0.0 0.0 0.0 0.0 90-91 6.3375 0.0 0.0 0.0 0.0 92-93 6.5125 0.0 0.0 0.0 0.0 94-95 6.6125 0.0 0.0 0.0 0.0 96-97 6.737500000000001 0.0 0.0 0.0 0.0 98-99 6.875 0.0 0.0 0.0 0.0 100-101 6.9625 0.0 0.0 0.0 0.0 102-103 7.050000000000001 0.0 0.0 0.0 0.0 104-105 7.1875 0.0 0.0 0.0 0.0 106-107 7.4 0.0 0.0 0.0 0.0 108-109 7.525 0.0 0.0 0.0 0.0 110-111 7.6375 0.0 0.0 0.0 0.0 112-113 7.8375 0.0 0.0 0.0 0.0 114-115 7.975 0.0 0.0 0.0 0.0 116-117 8.1375 0.0 0.0 0.0 0.0 118-119 8.25 0.0 0.0 0.0 0.0 120-121 8.4 0.0 0.0 0.0 0.0 122-123 8.6125 0.0 0.0 0.0 0.0 124-125 8.7875 0.0 0.0 0.0 0.0 126-127 9.024999999999999 0.0 0.0 0.0 0.0 128-129 9.1875 0.0 0.0 0.0 0.0 130-131 9.325 0.0 0.0 0.0 0.0 132-133 9.425 0.0 0.0 0.0 0.0 134-135 9.5625 0.0 0.0 0.0 0.0 136-137 9.662500000000001 0.0 0.0 0.0 0.0 138 9.8 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTTGGAA 20 0.0062073963 28.735 15-19 TTTTTGG 85 3.135756E-8 18.593235 15-19 TTTTGGG 40 0.008071216 17.959375 15-19 TTTTTGC 50 0.0014142258 17.241001 15-19 TTTTTTG 285 0.0 13.611316 10-14 TTTTTTC 130 2.6135058E-7 13.262308 10-14 TTTTTAG 65 0.00811574 13.262308 15-19 TTTTTTA 245 4.7293724E-10 10.555715 10-14 TTTTTTT 8190 0.0 6.929381 2 >>END_MODULE Read 1074585 spots for SRR11445638.sra Written 1074585 spots for SRR11445638.sra Read 1074585 spots for SRR11445638.sra Written 1074585 spots for SRR11445638.sra Read 1074585 spots for SRR11445638.sra Written 1074585 spots for SRR11445638.sra Read 1074585 spots for SRR11445638.sra Written 1074585 spots for SRR11445638.sra Read 1074585 spots for SRR11445638.sra Written 1074585 spots for SRR11445638.sra Read 1074585 spots for SRR11445638.sra Written 1074585 spots for SRR11445638.sra Read 1074585 spots for SRR11445638.sra Written 1074585 spots for SRR11445638.sra Read 1074585 spots for SRR11445638.sra Written 1074585 spots for SRR11445638.sra Read 1074585 spots for SRR11445638.sra Written 1074585 spots for SRR11445638.sra Read 1074585 spots for SRR11445638.sra Written 1074585 spots for SRR11445638.sra Read 1074585 spots for SRR11445638.sra Written 1074585 spots for SRR11445638.sra Read 1074585 spots for SRR11445638.sra Written 1074585 spots for SRR11445638.sra Read 1074585 spots for SRR11445638.sra Written 1074585 spots for SRR11445638.sra Read 1074585 spots for SRR11445638.sra Written 1074585 spots for SRR11445638.sra Read 1074585 spots for SRR11445638.sra Written 1074585 spots for SRR11445638.sra Read 1074585 spots for SRR11445638.sra Written 1074585 spots for SRR11445638.sra Read 1074585 spots for SRR11445638.sra Written 1074585 spots for SRR11445638.sra Read 1074585 spots for SRR11445638.sra Written 1074585 spots for SRR11445638.sra Read 1074585 spots for SRR11445638.sra Written 1074585 spots for SRR11445638.sra Read 1074591 spots for SRR11445638.sra Written 1074591 spots for SRR11445638.sra SRR ids: ['SRR11445638.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_k0okrm06 SRR11445638.sra spots: 21491706 blocks: [[1, 1074585], [1074586, 2149170], [2149171, 3223755], [3223756, 4298340], [4298341, 5372925], [5372926, 6447510], [6447511, 7522095], [7522096, 8596680], [8596681, 9671265], [9671266, 10745850], [10745851, 11820435], [11820436, 12895020], [12895021, 13969605], [13969606, 15044190], [15044191, 16118775], [16118776, 17193360], [17193361, 18267945], [18267946, 19342530], [19342531, 20417115], [20417116, 21491706]] SRR11445638 file size 7240145 SRR11445638 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 SRR11445638 SRR11445638_1.fastq SRR11445638_2.fastq Input file: SRR11445638_1.fastq Paired file: SRR11445638_2.fastq trimmed: SRR11445638-trimmed-pair1.fastq, SRR11445638-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 Wed Feb 12 15:25:40 2025 >> started Wed Feb 12 15:26:03 2025 >> done (23.125s) 21491706 read pairs processed; of these: 16175 ( 0.08%) short read pairs filtered out after trimming by size control 1783 ( 0.01%) empty read pairs filtered out after trimming by size control 21473748 (99.92%) read pairs available; of these: 4369161 (20.35%) trimmed read pairs available after processing 17104587 (79.65%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 11738 0.05% 19 32379 0.15% 20 39393 0.18% 21 60177 0.28% 22 48441 0.23% 23 33420 0.16% 24 28213 0.13% 25 24632 0.11% 26 22875 0.11% 27 20545 0.10% 28 19595 0.09% 29 19468 0.09% 30 17441 0.08% 31 17756 0.08% 32 18005 0.08% 33 18342 0.09% 34 19867 0.09% 35 19338 0.09% 36 19137 0.09% 37 19233 0.09% 38 19663 0.09% 39 19223 0.09% 40 18871 0.09% 41 18844 0.09% 42 18390 0.09% 43 17662 0.08% 44 17608 0.08% 45 17226 0.08% 46 16578 0.08% 47 16554 0.08% 48 16472 0.08% 49 16704 0.08% 50 16398 0.08% 51 16573 0.08% 52 16723 0.08% 53 16920 0.08% 54 17090 0.08% 55 17395 0.08% 56 17440 0.08% 57 17428 0.08% 58 17510 0.08% 59 18076 0.08% 60 18768 0.09% 61 19102 0.09% 62 19894 0.09% 63 18526 0.09% 64 18623 0.09% 65 19282 0.09% 66 19505 0.09% 67 20364 0.09% 68 19622 0.09% 69 19166 0.09% 70 18979 0.09% 71 18885 0.09% 72 19076 0.09% 73 18948 0.09% 74 19166 0.09% 75 19082 0.09% 76 19619 0.09% 77 19864 0.09% 78 19957 0.09% 79 19936 0.09% 80 20282 0.09% 81 20061 0.09% 82 19857 0.09% 83 19671 0.09% 84 19795 0.09% 85 19967 0.09% 86 19969 0.09% 87 19865 0.09% 88 20064 0.09% 89 20121 0.09% 90 20134 0.09% 91 19898 0.09% 92 19882 0.09% 93 19551 0.09% 94 19588 0.09% 95 19548 0.09% 96 19875 0.09% 97 19745 0.09% 98 20219 0.09% 99 20219 0.09% 100 20075 0.09% 101 19847 0.09% 102 19747 0.09% 103 19893 0.09% 104 19578 0.09% 105 19578 0.09% 106 19618 0.09% 107 19659 0.09% 108 19961 0.09% 109 20208 0.09% 110 19992 0.09% 111 20080 0.09% 112 20749 0.10% 113 19801 0.09% 114 19969 0.09% 115 20144 0.09% 116 20544 0.10% 117 20685 0.10% 118 20365 0.09% 119 20615 0.10% 120 21422 0.10% 121 20805 0.10% 122 20879 0.10% 123 20853 0.10% 124 20749 0.10% 125 21928 0.10% 126 21469 0.10% 127 21054 0.10% 128 21091 0.10% 129 20951 0.10% 130 21534 0.10% 131 21590 0.10% 132 21887 0.10% 133 21782 0.10% 134 21259 0.10% 135 21088 0.10% 136 21246 0.10% 137 21020 0.10% 138 21327 0.10% 139 21648 0.10% 140 21237 0.10% 141 22233 0.10% 142 22800 0.11% 143 23618 0.11% 144 24877 0.12% 145 30293 0.14% 146 44520 0.21% 147 93572 0.44% 148 269018 1.25% 149 1310285 6.10% 150 17104587 79.65% 21473748 reads passed initial QC criterion=sequence-density sequence-density=1.06 sequence-density-rank=1 fanout-score=1.10 fanout-score-rank=41 prefix-density=0.49 prefix-fanout=1.1 sequence=ACTCCAGTCACC criterion=fanout-score sequence-density=0.05 sequence-density-rank=30 fanout-score=80.05 fanout-score-rank=1 prefix-density=0.55 prefix-fanout=7.7 sequence=GATGATGATGATAGTGATTATGACTATGCTCCTGCAGCGCCCATGGAGGGTGACGATGACGATGATGGAGACTACGATTATGCTCCTGCTGCCTAGTTAATTATAGAATTATATTTAGCTCATAATAAATCACAGTACTAAACTTTGTTAGCTTGCTCCATGCACTAATATTTGTATGGCTTAATGCCCTAAAGTTTTTGTAGGTTATCGTGACTACATTAATTAAAGCTCTTAATTATGTTACCC criterion=sequence-density sequence-density=0.13 sequence-density-rank=1 fanout-score=2.14 fanout-score-rank=31 prefix-density=0.02 prefix-fanout=2.1 sequence=TTTTTTTTTTGG criterion=fanout-score sequence-density=0.01 sequence-density-rank=46 fanout-score=3.96 fanout-score-rank=1 prefix-density=0.02 prefix-fanout=2.1 sequence=TTTTTTTTTCAG SRR11445638 testing PE reads STAR mapping to Ensembl genome Unpaired reads removal Started job on | Feb 12 15:39:14 Started mapping on | Feb 12 15:39:14 Finished on | Feb 12 15:46:14 Mapping speed, Million of reads per hour | 179.69 Number of input reads | 20963753 Average input read length | 268 UNIQUE READS: Uniquely mapped reads number | 9474667 Uniquely mapped reads % | 45.20% Average mapped length | 248.94 Number of splices: Total | 934902 Number of splices: Annotated (sjdb) | 857276 Number of splices: GT/AG | 888155 Number of splices: GC/AG | 11055 Number of splices: AT/AC | 1085 Number of splices: Non-canonical | 34607 Mismatch rate per base, % | 2.80% Deletion rate per base | 0.03% Deletion average length | 2.10 Insertion rate per base | 0.02% Insertion average length | 2.09 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 558922 % of reads mapped to multiple loci | 2.67% Number of reads mapped to too many loci | 15385 % of reads mapped to too many loci | 0.07% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 51.51% % of reads unmapped: other | 0.55% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 10930431 10930431 10930431 N_multimapping 558922 558922 558922 N_noFeature 414246 502834 9197236 N_ambiguous 276212 87187 2039 UnstrandedReadsAssigned:8784209 PositiveStrandReadsAssigned:8884646 NegativeStrandReadsAssigned:275392 Dataset is classified positive stranded MeadianReadLen=150 20thPercentileLength=150 echo kmer=145 SRR11445638 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: SRR11445638-trimmed-pair1.fastq SRR11445638-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 20,963,753 reads, 16,438,953 reads pseudoaligned [quant] estimated average fragment length: 201.038 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,156 rounds 52401 SRR11445638.ke.tsv 34699 SRR11445638.se.tsv 87100 total ==> SRR11445638.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1817.96 1470 46.9637 Potri.005G024800.1.v4.1 1035 834.962 706 49.1098 Potri.004G059700.1.v4.1 961 760.962 16 1.2212 Potri.007G009000.2.v4.1 1416 1215.96 0 0 Potri.003G141000.2.v4.1 2943 2742.96 676 14.3139 Potri.016G087400.1.v4.1 270 97.5481 132 78.5932 Potri.015G069301.1.v4.1 564 364.344 0 0 Potri.010G195200.1.v4.1 1773 1572.96 208 7.68025 Potri.012G127500.1.v4.1 977 776.962 4004 299.312 ==> SRR11445638.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 97 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 269 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 45 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 12 SRR11445638 completed mapping pipeline successfully