Starting /dee2/code/volunteer_pipeline.sh SRR14040102 current disk space = 3050329260032 free memory = 1440710632 SRR14040102 SRAfilesize fdab28febce0c011149a0b9a971a8363 SRR14040102.sra SRR14040102.sra file validated SRR14040102 is paired end SRR14040102 is conventional basespace SRR14040102 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR14040102_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.8475 37.0 37.0 37.0 37.0 37.0 2 36.169 37.0 37.0 37.0 37.0 37.0 3 36.1665 37.0 37.0 37.0 37.0 37.0 4 36.294 37.0 37.0 37.0 37.0 37.0 5 36.353 37.0 37.0 37.0 37.0 37.0 6 36.3175 37.0 37.0 37.0 37.0 37.0 7 36.291 37.0 37.0 37.0 37.0 37.0 8 36.3125 37.0 37.0 37.0 37.0 37.0 9 36.2785 37.0 37.0 37.0 37.0 37.0 10-14 36.3284 37.0 37.0 37.0 37.0 37.0 15-19 36.28679999999999 37.0 37.0 37.0 37.0 37.0 20-24 36.3244 37.0 37.0 37.0 37.0 37.0 25-29 36.2472 37.0 37.0 37.0 37.0 37.0 30-34 36.1913 37.0 37.0 37.0 37.0 37.0 35-39 36.1803 37.0 37.0 37.0 37.0 37.0 40-44 36.160900000000005 37.0 37.0 37.0 37.0 37.0 45-49 35.916199999999996 37.0 37.0 37.0 37.0 37.0 50-54 35.8977 37.0 37.0 37.0 37.0 37.0 55-59 35.7334 37.0 37.0 37.0 37.0 37.0 60-64 35.7829 37.0 37.0 37.0 37.0 37.0 65-69 35.75019999999999 37.0 37.0 37.0 37.0 37.0 70-74 35.9191 37.0 37.0 37.0 37.0 37.0 75-79 35.947500000000005 37.0 37.0 37.0 37.0 37.0 80-84 35.9104 37.0 37.0 37.0 37.0 37.0 85-89 35.889300000000006 37.0 37.0 37.0 37.0 37.0 90-94 35.9071 37.0 37.0 37.0 37.0 37.0 95-99 35.8717 37.0 37.0 37.0 37.0 37.0 100-104 35.8321 37.0 37.0 37.0 37.0 37.0 105-109 35.8022 37.0 37.0 37.0 37.0 37.0 110-114 35.7512 37.0 37.0 37.0 37.0 37.0 115-119 35.6279 37.0 37.0 37.0 37.0 37.0 120-124 35.581399999999995 37.0 37.0 37.0 37.0 37.0 125-129 35.559000000000005 37.0 37.0 37.0 37.0 37.0 130-134 35.41610000000001 37.0 37.0 37.0 37.0 37.0 135-139 35.31510000000001 37.0 37.0 37.0 34.6 37.0 140-144 35.3035 37.0 37.0 37.0 34.6 37.0 145-149 35.0281 37.0 37.0 37.0 25.0 37.0 150 35.0405 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 3.0 23 2.0 24 2.0 25 8.0 26 14.0 27 23.0 28 18.0 29 45.0 30 51.0 31 72.0 32 87.0 33 162.0 34 189.0 35 367.0 36 2563.0 37 393.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.7 16.75 13.825000000000001 31.724999999999998 2 20.9 22.125 34.225 22.75 3 24.0 22.175 28.999999999999996 24.825 4 25.424999999999997 28.025 22.325 24.224999999999998 5 26.275 31.2 23.0 19.525000000000002 6 21.6 35.75 24.5 18.15 7 20.424999999999997 21.6 40.25 17.724999999999998 8 19.975 25.275 28.625 26.125 9 23.275000000000002 23.275000000000002 29.625 23.825 10-14 22.145 30.12 26.39 21.345 15-19 21.834999999999997 28.88 27.01 22.275 20-24 22.345000000000002 28.79 26.36 22.505 25-29 22.12 28.939999999999998 26.275 22.665 30-34 22.25 28.26 26.950000000000003 22.54 35-39 22.765 28.799999999999997 26.33 22.105 40-44 21.845 28.475 26.889999999999997 22.79 45-49 22.275 28.34 26.924999999999997 22.46 50-54 22.8 27.36 27.315 22.525000000000002 55-59 21.740000000000002 27.33 27.96 22.97 60-64 22.314999999999998 27.775 27.525 22.384999999999998 65-69 22.16 28.78 26.445 22.615 70-74 23.185 27.98 26.875 21.959999999999997 75-79 23.52 27.46 26.584999999999997 22.435 80-84 23.765 27.944999999999997 26.83 21.46 85-89 23.380000000000003 26.905 27.76 21.955 90-94 23.54 27.595 26.974999999999998 21.89 95-99 23.22 27.134999999999998 27.58 22.065 100-104 23.875 27.794999999999998 26.900000000000002 21.43 105-109 23.855 26.75 27.3 22.095000000000002 110-114 23.775 27.889999999999997 26.284999999999997 22.05 115-119 23.47 27.060000000000002 27.005000000000003 22.465 120-124 23.93 28.125 26.055 21.89 125-129 23.635 27.944999999999997 26.029999999999998 22.39 130-134 24.005000000000003 27.36 26.455000000000002 22.18 135-139 23.955000000000002 27.224999999999998 26.450000000000003 22.37 140-144 23.645 27.775 26.279999999999998 22.3 145-149 23.845 27.6 25.505 23.05 150 23.825 28.050000000000004 26.25 21.875 >>END_MODULE >>Per sequence GC content warn #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 1.0 9 1.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 1.0 17 2.0 18 2.0 19 1.0 20 0.5 21 1.0 22 1.0 23 0.5 24 0.0 25 3.5 26 4.5 27 5.0 28 7.0 29 9.5 30 15.0 31 19.5 32 22.5 33 34.5 34 49.0 35 58.0 36 67.0 37 83.0 38 111.5 39 149.0 40 186.5 41 197.5 42 217.5 43 253.0 44 270.0 45 257.5 46 251.0 47 260.0 48 241.0 49 208.5 50 187.0 51 160.0 52 126.0 53 102.0 54 74.5 55 63.0 56 62.0 57 48.5 58 34.0 59 23.5 60 17.0 61 13.0 62 10.5 63 7.5 64 5.5 65 6.5 66 11.5 67 15.0 68 13.5 69 11.0 70 6.0 71 3.0 72 2.0 73 1.0 74 2.0 75 1.5 76 0.5 77 0.5 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 0.0 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 91.07499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 91.68267911062311 83.5 2 7.658523195168816 13.950000000000001 3 0.5489980785067252 1.5 4 0.02744990392533626 0.1 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.02744990392533626 0.22499999999999998 >10 0.05489980785067252 0.7250000000000001 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGCAGGAAATCTCGTAT 16 0.4 TruSeq Adapter, Index 1 (97% over 37bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGCAGGAAATCTCGTTT 13 0.325 TruSeq Adapter, Index 1 (97% over 37bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGCAGGAAATCGCGTAT 9 0.22499999999999998 TruSeq Adapter, Index 1 (97% over 37bp) >>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 0.0 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 0.025 0.0 0.0 0.0 0.0 54-55 0.075 0.0 0.0 0.0 0.0 56-57 0.125 0.0 0.0 0.0 0.0 58-59 0.15 0.0 0.0 0.0 0.0 60-61 0.15 0.0 0.0 0.0 0.0 62-63 0.15 0.0 0.0 0.0 0.0 64-65 0.15 0.0 0.0 0.0 0.0 66-67 0.1875 0.0 0.0 0.0 0.0 68-69 0.2 0.0 0.0 0.0 0.0 70-71 0.25 0.0 0.0 0.0 0.0 72-73 0.30000000000000004 0.0 0.0 0.0 0.0 74-75 0.35 0.0 0.0 0.0 0.0 76-77 0.3625 0.0 0.0 0.0 0.0 78-79 0.425 0.0 0.0 0.0 0.0 80-81 0.45 0.0 0.0 0.0 0.0 82-83 0.5 0.0 0.0 0.0 0.0 84-85 0.5375000000000001 0.0 0.0 0.0 0.0 86-87 0.5625 0.0 0.0 0.0 0.0 88-89 0.6125 0.0 0.0 0.0 0.0 90-91 0.7875000000000001 0.0 0.0 0.0 0.0 92-93 0.8625 0.0 0.0 0.0 0.0 94-95 0.975 0.0 0.0 0.0 0.0 96-97 1.075 0.0 0.0 0.0 0.0 98-99 1.225 0.0 0.0 0.0 0.0 100-101 1.4375 0.0 0.0 0.0 0.0 102-103 1.7625000000000002 0.0 0.0 0.0 0.0 104-105 1.9625 0.0 0.0 0.0 0.0 106-107 2.125 0.0 0.0 0.0 0.0 108-109 2.2875 0.0 0.0 0.0 0.0 110-111 2.4124999999999996 0.0 0.0 0.0 0.0 112-113 2.6 0.0 0.0 0.0 0.0 114-115 2.75 0.0 0.0 0.0 0.0 116-117 2.8875 0.0 0.0 0.0 0.0 118-119 3.0375 0.0 0.0 0.0 0.0 120-121 3.35 0.0 0.0 0.0 0.0 122-123 3.6500000000000004 0.0 0.0 0.0 0.0 124-125 3.875 0.0 0.0 0.0 0.0 126-127 4.1625 0.0 0.0 0.0 0.0 128-129 4.2875 0.0 0.0 0.0 0.0 130-131 4.475 0.0 0.0 0.0 0.0 132-133 4.9375 0.0 0.0 0.0 0.0 134-135 5.35 0.0 0.0 0.0 0.0 136-137 5.65 0.0 0.0 0.0 0.0 138 5.825 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGCAACT 10 0.006973645 144.0 7 TCGGAAG 35 3.1411873E-5 82.28571 3 ATCGGAA 35 3.1411873E-5 82.28571 2 GATCGGA 40 6.0911432E-5 72.0 1 GAGCACA 40 6.0911432E-5 72.0 9 CGGAAGA 40 6.0911432E-5 72.0 4 AGAGCAC 40 6.0911432E-5 72.0 8 AAGAGCA 45 1.0917089E-4 64.0 7 GAAGAGC 50 1.838823E-4 57.6 6 GGAAGAG 50 1.838823E-4 57.6 5 GTCTGAA 40 0.007966741 18.0 15-19 >>END_MODULE SRR14040102 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR14040102_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.671 37.0 37.0 37.0 37.0 37.0 2 35.4405 37.0 37.0 37.0 37.0 37.0 3 35.4205 37.0 37.0 37.0 37.0 37.0 4 35.689 37.0 37.0 37.0 37.0 37.0 5 35.718 37.0 37.0 37.0 37.0 37.0 6 35.513 37.0 37.0 37.0 37.0 37.0 7 35.5905 37.0 37.0 37.0 37.0 37.0 8 35.5825 37.0 37.0 37.0 37.0 37.0 9 35.7255 37.0 37.0 37.0 37.0 37.0 10-14 35.7034 37.0 37.0 37.0 37.0 37.0 15-19 35.7332 37.0 37.0 37.0 37.0 37.0 20-24 35.6543 37.0 37.0 37.0 37.0 37.0 25-29 35.5128 37.0 37.0 37.0 37.0 37.0 30-34 35.4387 37.0 37.0 37.0 37.0 37.0 35-39 35.38770000000001 37.0 37.0 37.0 37.0 37.0 40-44 35.400600000000004 37.0 37.0 37.0 37.0 37.0 45-49 35.3373 37.0 37.0 37.0 37.0 37.0 50-54 35.351099999999995 37.0 37.0 37.0 37.0 37.0 55-59 35.2904 37.0 37.0 37.0 37.0 37.0 60-64 35.3241 37.0 37.0 37.0 34.6 37.0 65-69 35.279999999999994 37.0 37.0 37.0 37.0 37.0 70-74 35.175 37.0 37.0 37.0 32.2 37.0 75-79 35.1198 37.0 37.0 37.0 29.8 37.0 80-84 35.128499999999995 37.0 37.0 37.0 29.8 37.0 85-89 35.1023 37.0 37.0 37.0 29.8 37.0 90-94 35.0673 37.0 37.0 37.0 29.8 37.0 95-99 35.0864 37.0 37.0 37.0 27.4 37.0 100-104 35.183400000000006 37.0 37.0 37.0 32.2 37.0 105-109 34.9847 37.0 37.0 37.0 25.0 37.0 110-114 35.083999999999996 37.0 37.0 37.0 25.0 37.0 115-119 35.065999999999995 37.0 37.0 37.0 27.4 37.0 120-124 34.973 37.0 37.0 37.0 25.0 37.0 125-129 34.88549999999999 37.0 37.0 37.0 25.0 37.0 130-134 34.764300000000006 37.0 37.0 37.0 25.0 37.0 135-139 34.816100000000006 37.0 37.0 37.0 25.0 37.0 140-144 34.5182 37.0 37.0 37.0 25.0 37.0 145-149 34.557100000000005 37.0 37.0 37.0 25.0 37.0 150 34.414 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 5.0 14 6.0 15 3.0 16 3.0 17 4.0 18 5.0 19 7.0 20 5.0 21 13.0 22 16.0 23 20.0 24 22.0 25 12.0 26 32.0 27 38.0 28 36.0 29 38.0 30 52.0 31 67.0 32 88.0 33 179.0 34 224.0 35 553.0 36 2364.0 37 208.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.525 15.5 13.825000000000001 33.15 2 23.849999999999998 21.425 31.175000000000004 23.549999999999997 3 26.75 22.900000000000002 26.6 23.75 4 29.95 26.424999999999997 19.5 24.125 5 27.6 32.074999999999996 22.075 18.25 6 22.8 35.15 23.549999999999997 18.5 7 20.8 21.099999999999998 39.65 18.45 8 21.575 23.849999999999998 29.849999999999998 24.725 9 24.175 23.075000000000003 31.075000000000003 21.675 10-14 23.36 29.185 25.85 21.605 15-19 23.549999999999997 27.965 26.540000000000003 21.945 20-24 23.34 28.560000000000002 26.224999999999998 21.875 25-29 23.625 28.205000000000002 26.605 21.565 30-34 23.465 27.965 27.02 21.55 35-39 23.195 28.34 26.729999999999997 21.735 40-44 23.635 28.345 26.32 21.7 45-49 23.265 28.355000000000004 26.47 21.91 50-54 23.68 28.675 26.155 21.490000000000002 55-59 24.025 27.49 26.96 21.525 60-64 23.31 28.665000000000003 26.52 21.505 65-69 24.075 27.87 26.555 21.5 70-74 23.315 28.405 26.085 22.195 75-79 23.28 27.939999999999998 26.810000000000002 21.97 80-84 23.794999999999998 28.645 26.265 21.295 85-89 23.47 28.294999999999998 26.229999999999997 22.005 90-94 24.005000000000003 28.465 26.035000000000004 21.495 95-99 23.61 28.689999999999998 26.290000000000003 21.41 100-104 23.849999999999998 28.439999999999998 26.334999999999997 21.375 105-109 24.205 27.955000000000002 26.029999999999998 21.81 110-114 24.15 27.900000000000002 25.874999999999996 22.075 115-119 24.279999999999998 27.655 27.089999999999996 20.974999999999998 120-124 24.585 28.26 26.229999999999997 20.925 125-129 24.065 28.37 25.900000000000002 21.665 130-134 24.992499249924993 28.212821282128214 26.107610761076106 20.687068706870686 135-139 25.41 27.845 25.724999999999998 21.02 140-144 25.545 27.889999999999997 25.61 20.955 145-149 25.369999999999997 27.625 25.53 21.475 150 25.474999999999998 27.800000000000004 25.6 21.125 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 1.0 3 1.0 4 0.0 5 0.0 6 2.0 7 3.5 8 2.5 9 2.5 10 2.5 11 2.5 12 2.5 13 2.5 14 3.0 15 3.5 16 2.5 17 2.5 18 2.5 19 2.0 20 3.0 21 2.0 22 3.5 23 4.5 24 4.0 25 6.0 26 6.5 27 5.0 28 6.5 29 11.0 30 15.5 31 20.5 32 27.0 33 37.0 34 46.0 35 58.0 36 71.0 37 87.0 38 118.5 39 154.0 40 167.0 41 183.5 42 229.0 43 242.5 44 245.0 45 257.5 46 276.0 47 259.0 48 215.5 49 203.5 50 179.5 51 145.0 52 117.0 53 92.5 54 79.5 55 68.5 56 44.0 57 35.0 58 32.5 59 26.0 60 18.5 61 8.0 62 5.0 63 8.5 64 8.5 65 6.5 66 6.0 67 4.5 68 3.0 69 0.5 70 0.0 71 2.0 72 5.0 73 5.0 74 2.0 75 1.0 76 1.5 77 1.5 78 1.0 79 0.5 80 1.0 81 2.0 82 1.5 83 0.0 84 0.5 85 0.5 86 0.5 87 1.5 88 1.5 89 1.5 90 2.0 91 1.0 92 1.0 93 3.0 94 3.5 95 2.0 96 1.5 97 1.5 98 3.5 99 10.0 100 28.0 >>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 0.01 135-139 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 91.2 #Duplication Level Percentage of deduplicated Percentage of total 1 92.35197368421053 84.22500000000001 2 7.209429824561403 13.15 3 0.3837719298245614 1.05 4 0.027412280701754384 0.1 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 0.027412280701754384 1.4749999999999999 >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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 59 1.4749999999999999 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 0.0 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 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.15 0.0 0.0 0.0 0.0 58-59 0.175 0.0 0.0 0.0 0.0 60-61 0.175 0.0 0.0 0.0 0.0 62-63 0.175 0.0 0.0 0.0 0.0 64-65 0.175 0.0 0.0 0.0 0.0 66-67 0.21250000000000002 0.0 0.0 0.0 0.0 68-69 0.225 0.0 0.0 0.0 0.0 70-71 0.275 0.0 0.0 0.0 0.0 72-73 0.32499999999999996 0.0 0.0 0.0 0.0 74-75 0.375 0.0 0.0 0.0 0.0 76-77 0.3875 0.0 0.0 0.0 0.0 78-79 0.45 0.0 0.0 0.0 0.0 80-81 0.475 0.0 0.0 0.0 0.0 82-83 0.525 0.0 0.0 0.0 0.0 84-85 0.5625 0.0 0.0 0.0 0.0 86-87 0.5874999999999999 0.0 0.0 0.0 0.0 88-89 0.6375 0.0 0.0 0.0 0.0 90-91 0.7875000000000001 0.0 0.0 0.0 0.0 92-93 0.8625 0.0 0.0 0.0 0.0 94-95 0.975 0.0 0.0 0.0 0.0 96-97 1.075 0.0 0.0 0.0 0.0 98-99 1.225 0.0 0.0 0.0 0.0 100-101 1.45 0.0 0.0 0.0 0.0 102-103 1.7875 0.0 0.0 0.0 0.0 104-105 1.9874999999999998 0.0 0.0 0.0 0.0 106-107 2.1375 0.0 0.0 0.0 0.0 108-109 2.2875 0.0 0.0 0.0 0.0 110-111 2.4124999999999996 0.0 0.0 0.0 0.0 112-113 2.6 0.0 0.0 0.0 0.0 114-115 2.75 0.0 0.0 0.0 0.0 116-117 2.9000000000000004 0.0 0.0 0.0 0.0 118-119 3.1125 0.0 0.0 0.0 0.0 120-121 3.4124999999999996 0.0 0.0 0.0 0.0 122-123 3.675 0.0 0.0 0.0 0.0 124-125 3.9125 0.0 0.0 0.0 0.0 126-127 4.2125 0.0 0.0 0.0 0.0 128-129 4.3375 0.0 0.0 0.0 0.0 130-131 4.475 0.0 0.0 0.0 0.0 132-133 4.9375 0.0 0.0 0.0 0.0 134-135 5.35 0.0 0.0 0.0 0.0 136-137 5.6625 0.0 0.0 0.0 0.0 138 5.85 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1170687 spots for SRR14040102.sra Written 1170687 spots for SRR14040102.sra Read 1170687 spots for SRR14040102.sra Written 1170687 spots for SRR14040102.sra Read 1170687 spots for SRR14040102.sra Written 1170687 spots for SRR14040102.sra Read 1170687 spots for SRR14040102.sra Written 1170687 spots for SRR14040102.sra Read 1170687 spots for SRR14040102.sra Written 1170687 spots for SRR14040102.sra Read 1170687 spots for SRR14040102.sra Written 1170687 spots for SRR14040102.sra Read 1170687 spots for SRR14040102.sra Written 1170687 spots for SRR14040102.sra Read 1170687 spots for SRR14040102.sra Written 1170687 spots for SRR14040102.sra Read 1170687 spots for SRR14040102.sra Written 1170687 spots for SRR14040102.sra Read 1170687 spots for SRR14040102.sra Written 1170687 spots for SRR14040102.sra Read 1170687 spots for SRR14040102.sra Written 1170687 spots for SRR14040102.sra Read 1170687 spots for SRR14040102.sra Written 1170687 spots for SRR14040102.sra Read 1170687 spots for SRR14040102.sra Written 1170687 spots for SRR14040102.sra Read 1170687 spots for SRR14040102.sra Written 1170687 spots for SRR14040102.sra Read 1170687 spots for SRR14040102.sra Written 1170687 spots for SRR14040102.sra Read 1170687 spots for SRR14040102.sra Written 1170687 spots for SRR14040102.sra Read 1170705 spots for SRR14040102.sra Written 1170705 spots for SRR14040102.sra Read 1170687 spots for SRR14040102.sra Written 1170687 spots for SRR14040102.sra Read 1170687 spots for SRR14040102.sra Written 1170687 spots for SRR14040102.sra Read 1170687 spots for SRR14040102.sra Written 1170687 spots for SRR14040102.sra SRR ids: ['SRR14040102.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_lk2jrg1i SRR14040102.sra spots: 23413758 blocks: [[1, 1170687], [1170688, 2341374], [2341375, 3512061], [3512062, 4682748], [4682749, 5853435], [5853436, 7024122], [7024123, 8194809], [8194810, 9365496], [9365497, 10536183], [10536184, 11706870], [11706871, 12877557], [12877558, 14048244], [14048245, 15218931], [15218932, 16389618], [16389619, 17560305], [17560306, 18730992], [18730993, 19901679], [19901680, 21072366], [21072367, 22243053], [22243054, 23413758]] SRR14040102 file size 7889588 SRR14040102 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 SRR14040102 SRR14040102_1.fastq SRR14040102_2.fastq Input file: SRR14040102_1.fastq Paired file: SRR14040102_2.fastq trimmed: SRR14040102-trimmed-pair1.fastq, SRR14040102-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 06:27:29 2025 >> started Wed Feb 12 06:27:54 2025 >> done (25.048s) 23413758 read pairs processed; of these: 178 ( 0.00%) short read pairs filtered out after trimming by size control 252025 ( 1.08%) empty read pairs filtered out after trimming by size control 23161555 (98.92%) read pairs available; of these: 1660271 ( 7.17%) trimmed read pairs available after processing 21501284 (92.83%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 6 0.00% 19 16 0.00% 20 17 0.00% 21 12 0.00% 22 17 0.00% 23 18 0.00% 24 26 0.00% 25 33 0.00% 26 19 0.00% 27 46 0.00% 28 67 0.00% 29 214 0.00% 30 94 0.00% 31 92 0.00% 32 83 0.00% 33 109 0.00% 34 141 0.00% 35 152 0.00% 36 200 0.00% 37 185 0.00% 38 248 0.00% 39 305 0.00% 40 324 0.00% 41 375 0.00% 42 398 0.00% 43 417 0.00% 44 439 0.00% 45 480 0.00% 46 531 0.00% 47 621 0.00% 48 751 0.00% 49 863 0.00% 50 885 0.00% 51 1028 0.00% 52 1086 0.00% 53 1130 0.00% 54 1200 0.01% 55 1286 0.01% 56 1354 0.01% 57 1516 0.01% 58 1733 0.01% 59 1912 0.01% 60 2127 0.01% 61 2216 0.01% 62 2377 0.01% 63 2429 0.01% 64 2471 0.01% 65 2729 0.01% 66 2911 0.01% 67 3104 0.01% 68 3168 0.01% 69 3595 0.02% 70 3853 0.02% 71 4209 0.02% 72 4546 0.02% 73 4565 0.02% 74 4810 0.02% 75 4994 0.02% 76 5292 0.02% 77 5585 0.02% 78 5697 0.02% 79 5982 0.03% 80 6327 0.03% 81 7015 0.03% 82 7093 0.03% 83 7373 0.03% 84 7742 0.03% 85 8075 0.03% 86 8112 0.04% 87 8334 0.04% 88 8839 0.04% 89 9092 0.04% 90 9512 0.04% 91 9927 0.04% 92 10606 0.05% 93 11063 0.05% 94 10981 0.05% 95 11688 0.05% 96 11928 0.05% 97 12164 0.05% 98 12665 0.05% 99 13091 0.06% 100 13543 0.06% 101 14062 0.06% 102 14697 0.06% 103 15242 0.07% 104 15613 0.07% 105 15804 0.07% 106 16245 0.07% 107 16564 0.07% 108 16950 0.07% 109 17609 0.08% 110 18286 0.08% 111 18651 0.08% 112 19590 0.08% 113 19788 0.09% 114 20536 0.09% 115 21193 0.09% 116 21698 0.09% 117 21964 0.09% 118 22187 0.10% 119 22791 0.10% 120 23366 0.10% 121 24124 0.10% 122 24841 0.11% 123 25498 0.11% 124 26675 0.12% 125 27052 0.12% 126 27563 0.12% 127 27833 0.12% 128 28929 0.12% 129 29439 0.13% 130 29467 0.13% 131 30261 0.13% 132 31440 0.14% 133 32363 0.14% 134 33182 0.14% 135 33931 0.15% 136 34310 0.15% 137 35238 0.15% 138 35563 0.15% 139 36308 0.16% 140 36671 0.16% 141 37991 0.16% 142 39159 0.17% 143 39546 0.17% 144 40659 0.18% 145 42019 0.18% 146 42673 0.18% 147 43099 0.19% 148 43953 0.19% 149 45389 0.20% 150 21501284 92.83% 23161555 reads passed initial QC criterion=sequence-density sequence-density=0.11 sequence-density-rank=1 fanout-score=4.26 fanout-score-rank=24 prefix-density=0.16 prefix-fanout=3.0 sequence=TCCTTGTCCTGGATCTTGGCCTTCAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=42 fanout-score=152.98 fanout-score-rank=1 prefix-density=0.17 prefix-fanout=8.2 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAAC criterion=sequence-density sequence-density=0.10 sequence-density-rank=1 fanout-score=3.98 fanout-score-rank=25 prefix-density=0.14 prefix-fanout=3.0 sequence=TCCTTGTCCTGGATCTTGGCCTTCAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=42 fanout-score=109.66 fanout-score-rank=1 prefix-density=0.14 prefix-fanout=5.9 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCAC SRR14040102 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 12 06:28:46 Started mapping on | Feb 12 06:28:46 Finished on | Feb 12 06:30:47 Mapping speed, Million of reads per hour | 689.10 Number of input reads | 23161555 Average input read length | 295 UNIQUE READS: Uniquely mapped reads number | 21128143 Uniquely mapped reads % | 91.22% Average mapped length | 294.01 Number of splices: Total | 18566854 Number of splices: Annotated (sjdb) | 18279525 Number of splices: GT/AG | 18299381 Number of splices: GC/AG | 214182 Number of splices: AT/AC | 16620 Number of splices: Non-canonical | 36671 Mismatch rate per base, % | 0.27% Deletion rate per base | 0.02% Deletion average length | 2.65 Insertion rate per base | 0.01% Insertion average length | 1.98 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 448427 % of reads mapped to multiple loci | 1.94% Number of reads mapped to too many loci | 458521 % of reads mapped to too many loci | 1.98% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.02% % of reads unmapped: other | 0.85% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1584985 1584985 1584985 N_multimapping 448427 448427 448427 N_noFeature 500243 10744222 10695334 N_ambiguous 273916 42597 42945 UnstrandedReadsAssigned:20353984 PositiveStrandReadsAssigned:10341324 NegativeStrandReadsAssigned:10389864 Dataset is classified unstranded MeadianReadLen=150 20thPercentileLength=150 echo kmer=145 SRR14040102 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: SRR14040102-trimmed-pair1.fastq SRR14040102-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 23,161,555 reads, 21,454,686 reads pseudoaligned [quant] estimated average fragment length: 239.261 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,244 rounds 52401 SRR14040102.ke.tsv 34699 SRR14040102.se.tsv 87100 total ==> SRR14040102.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1779.74 586 15.9968 Potri.005G024800.1.v4.1 1035 796.739 45 2.74402 Potri.004G059700.1.v4.1 961 722.739 26 1.74777 Potri.007G009000.2.v4.1 1416 1177.74 0 0 Potri.003G141000.2.v4.1 2943 2704.74 306 5.49651 Potri.016G087400.1.v4.1 270 76.5355 1630.53 1035.04 Potri.015G069301.1.v4.1 564 326.438 0 0 Potri.010G195200.1.v4.1 1773 1534.74 84 2.65911 Potri.012G127500.1.v4.1 977 738.739 6007 395.055 ==> SRR14040102.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 2780 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 417 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 36 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 6 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR14040102 completed mapping pipeline successfully