Starting /dee2/code/volunteer_pipeline.sh SRR18694424 current disk space = 1526045790208 free memory = 1556698056 SRR18694424 SRAfilesize 6038acd90f5b3bd7ffea0a8cd75b2c9d SRR18694424.sra SRR18694424.sra file validated SRR18694424 is paired end SRR18694424 is conventional basespace SRR18694424 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR18694424_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 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.105 37.0 37.0 37.0 37.0 37.0 2 36.067 37.0 37.0 37.0 37.0 37.0 3 36.4135 37.0 37.0 37.0 37.0 37.0 4 36.5175 37.0 37.0 37.0 37.0 37.0 5 36.5605 37.0 37.0 37.0 37.0 37.0 6 36.4895 37.0 37.0 37.0 37.0 37.0 7 36.5065 37.0 37.0 37.0 37.0 37.0 8 36.492 37.0 37.0 37.0 37.0 37.0 9 36.68 37.0 37.0 37.0 37.0 37.0 10-14 36.6372 37.0 37.0 37.0 37.0 37.0 15-19 36.616699999999994 37.0 37.0 37.0 37.0 37.0 20-24 36.6366 37.0 37.0 37.0 37.0 37.0 25-29 36.571600000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.528200000000005 37.0 37.0 37.0 37.0 37.0 35-39 36.6572 37.0 37.0 37.0 37.0 37.0 40-44 36.618700000000004 37.0 37.0 37.0 37.0 37.0 45-49 36.4233 37.0 37.0 37.0 37.0 37.0 50-54 36.5078 37.0 37.0 37.0 37.0 37.0 55-59 36.5395 37.0 37.0 37.0 37.0 37.0 60-64 36.51049999999999 37.0 37.0 37.0 37.0 37.0 65-69 36.2701 37.0 37.0 37.0 37.0 37.0 70-74 36.4204 37.0 37.0 37.0 37.0 37.0 75-79 36.481500000000004 37.0 37.0 37.0 37.0 37.0 80-84 36.4227 37.0 37.0 37.0 37.0 37.0 85-89 36.169 37.0 37.0 37.0 37.0 37.0 90-94 35.402499999999996 37.0 37.0 37.0 29.8 37.0 95-99 36.0696 37.0 37.0 37.0 37.0 37.0 100-104 36.12480000000001 37.0 37.0 37.0 37.0 37.0 105-109 36.1469 37.0 37.0 37.0 37.0 37.0 110-114 36.1502 37.0 37.0 37.0 37.0 37.0 115-119 36.451299999999996 37.0 37.0 37.0 37.0 37.0 120-124 36.522200000000005 37.0 37.0 37.0 37.0 37.0 125-129 36.505900000000004 37.0 37.0 37.0 37.0 37.0 130-134 36.4669 37.0 37.0 37.0 37.0 37.0 135-139 36.356899999999996 37.0 37.0 37.0 37.0 37.0 140-144 36.1763 37.0 37.0 37.0 37.0 37.0 145-149 36.1519 37.0 37.0 37.0 37.0 37.0 150-151 33.72825 37.0 31.0 37.0 24.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 1.0 24 0.0 25 2.0 26 1.0 27 1.0 28 5.0 29 5.0 30 9.0 31 10.0 32 37.0 33 54.0 34 133.0 35 351.0 36 3203.0 37 188.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 46.949999999999996 11.475 5.2749999999999995 36.3 2 21.339017051153462 9.704112337011033 36.133400200601805 32.8234704112337 3 18.475 14.45 26.35 40.725 4 24.275 19.875 23.1 32.75 5 25.525 28.775000000000002 21.675 24.025 6 21.775 31.424999999999997 22.975 23.825 7 18.125 24.725 39.425 17.724999999999998 8 19.025 22.325 32.95 25.7 9 18.825 21.45 34.425 25.3 10-14 21.86 27.0 26.31 24.83 15-19 22.445 25.385 26.41 25.759999999999998 20-24 22.115000000000002 25.924999999999997 26.71 25.25 25-29 22.39 25.629999999999995 26.3 25.679999999999996 30-34 22.43 25.669999999999998 26.525 25.374999999999996 35-39 22.31 25.430000000000003 26.58 25.679999999999996 40-44 22.384999999999998 24.86 27.05 25.705 45-49 22.345000000000002 24.86 26.705000000000002 26.090000000000003 50-54 21.990000000000002 25.419999999999998 27.02 25.569999999999997 55-59 22.42 25.945 25.955000000000002 25.679999999999996 60-64 22.41 25.31 26.61 25.669999999999998 65-69 21.955 25.295 26.735 26.015 70-74 22.46 25.985000000000003 26.029999999999998 25.525 75-79 22.46 24.965 26.669999999999998 25.905 80-84 21.955 25.924999999999997 26.619999999999997 25.5 85-89 22.545 25.629999999999995 26.055 25.77 90-94 22.25 26.015 25.715 26.02 95-99 22.54 25.8 26.040000000000003 25.619999999999997 100-104 22.15 26.26 26.08 25.509999999999998 105-109 22.81 25.4 26.07 25.72 110-114 22.915 25.95 26.075 25.06 115-119 22.75 25.615 26.25 25.385 120-124 22.634999999999998 25.855 26.14 25.369999999999997 125-129 22.400000000000002 25.105 26.465 26.029999999999998 130-134 23.305 25.509999999999998 25.555 25.629999999999995 135-139 22.425 26.090000000000003 25.88 25.605 140-144 23.41 25.45 25.745 25.395 145-149 23.32 26.21 25.06 25.41 150-151 22.3625 25.5 25.624999999999996 26.5125 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 2.0 1 1.0 2 0.0 3 0.5 4 0.5 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.5 19 0.5 20 0.0 21 1.0 22 1.0 23 0.0 24 0.5 25 0.5 26 2.0 27 3.0 28 3.5 29 8.0 30 10.5 31 14.0 32 18.5 33 22.5 34 34.5 35 44.5 36 47.5 37 72.5 38 93.5 39 104.0 40 131.5 41 141.0 42 152.5 43 165.0 44 166.5 45 185.0 46 192.5 47 190.5 48 196.5 49 197.5 50 196.0 51 171.0 52 149.5 53 149.0 54 145.5 55 144.0 56 140.0 57 115.5 58 95.5 59 87.5 60 66.0 61 53.5 62 43.0 63 47.0 64 41.5 65 25.0 66 23.5 67 27.0 68 24.0 69 13.0 70 12.0 71 10.5 72 7.0 73 3.5 74 1.5 75 1.0 76 2.0 77 1.5 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 0.3 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 81.325 #Duplication Level Percentage of deduplicated Percentage of total 1 82.44697202582232 67.05 2 13.802643713495236 22.45 3 2.7974177682139563 6.825 4 0.5840762373193975 1.9 5 0.1537042729787888 0.625 6 0.1537042729787888 0.75 7 0.03074085459575776 0.17500000000000002 8 0.0 0.0 9 0.03074085459575776 0.22499999999999998 >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 GCCTAAAATACCACTCACGCTCCGTCATGGGTAATCCTCTCCCTCTCCAT 9 0.22499999999999998 No Hit GTGGGCTTACTACTTATATGCTTTCAGCAGTTATCCTCTCCGCACTTGGC 7 0.17500000000000002 No Hit CCTAGATGTCCAGTCAACTGCTGCGCCTCAACGCATTTCGGGGAGAACCA 6 0.15 No Hit GCAACAATTAGCTCCCATGTTTATTGTCTAGAAGAAATCAATTCGCCTTA 6 0.15 No Hit GCACCATCATCAGTATCTTTATCACATTCAACTGTCACGAGCGGGGTGGT 6 0.15 No Hit GGCCACCTTCTCGATGCCGTCTTCATCTTCAGAGTCCACCTCTCGTTTCT 6 0.15 No Hit GGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTA 6 0.15 No Hit ATAGCCCCAATGCTGGCTCTCGACTCGCTTAGCTGGCTGGTTTCGCACAC 5 0.125 No Hit GTTCGAGCTTTTCCTGGGAGTATGGCATCGGTTACATACTTCAGTGCCGT 5 0.125 No Hit CCTTAACCAAGCCACTGCCTATGAGTCGCCGGCTCATTCTTCAACAGGCA 5 0.125 No Hit CCACAGCTTCGGCAGATCGCTTAGCCCCGTTCATCTTCAGCGCAAGGGCG 5 0.125 No Hit CACGACTTAGTCGCAACTTACATTTATAGATGGAAGCTAAACTTGAGCTA 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 0.0 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 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.0625 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.0875 0.0 0.0 0.0 0.0 78-79 0.1125 0.0 0.0 0.0 0.0 80-81 0.15 0.0 0.0 0.0 0.0 82-83 0.16249999999999998 0.0 0.0 0.0 0.0 84-85 0.2 0.0 0.0 0.0 0.0 86-87 0.25 0.0 0.0 0.0 0.0 88-89 0.35 0.0 0.0 0.0 0.0 90-91 0.375 0.0 0.0 0.0 0.0 92-93 0.475 0.0 0.0 0.0 0.0 94-95 0.625 0.0 0.0 0.0 0.0 96-97 0.6875 0.0 0.0 0.0 0.0 98-99 0.8500000000000001 0.0 0.0 0.0 0.0 100-101 0.9875 0.0 0.0 0.0 0.0 102-103 1.1749999999999998 0.0 0.0 0.0 0.0 104-105 1.4375 0.0 0.0 0.0 0.0 106-107 1.65 0.0 0.0 0.0 0.0 108-109 1.875 0.0 0.0 0.0 0.0 110-111 2.1625 0.0 0.0 0.0 0.0 112-113 2.375 0.0 0.0 0.0 0.0 114-115 2.675 0.0 0.0 0.0 0.0 116-117 2.925 0.0 0.0 0.0 0.0 118-119 3.15 0.0 0.0 0.0 0.0 120-121 3.4000000000000004 0.0 0.0 0.0 0.0 122-123 3.625 0.0 0.0 0.0 0.0 124-125 3.95 0.0 0.0 0.0 0.0 126-127 4.45 0.0 0.0 0.0 0.0 128-129 4.8 0.0 0.0 0.0 0.0 130-131 5.175 0.0 0.0 0.0 0.0 132-133 5.5375 0.0 0.0 0.0 0.0 134-135 5.85 0.0 0.0 0.0 0.0 136-137 6.2875 0.0 0.0 0.0 0.0 138-139 6.875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTCACAT 10 0.006830828 145.0 5 >>END_MODULE SRR18694424 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR18694424_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 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 34.02 37.0 37.0 37.0 25.0 37.0 2 34.937 37.0 37.0 37.0 25.0 37.0 3 34.9875 37.0 37.0 37.0 25.0 37.0 4 34.968 37.0 37.0 37.0 25.0 37.0 5 34.933 37.0 37.0 37.0 25.0 37.0 6 35.057 37.0 37.0 37.0 25.0 37.0 7 35.03 37.0 37.0 37.0 25.0 37.0 8 35.222 37.0 37.0 37.0 25.0 37.0 9 35.494 37.0 37.0 37.0 37.0 37.0 10-14 35.371399999999994 37.0 37.0 37.0 34.6 37.0 15-19 35.5103 37.0 37.0 37.0 37.0 37.0 20-24 35.2512 37.0 37.0 37.0 32.2 37.0 25-29 35.436600000000006 37.0 37.0 37.0 32.2 37.0 30-34 35.714800000000004 37.0 37.0 37.0 37.0 37.0 35-39 35.5128 37.0 37.0 37.0 34.6 37.0 40-44 35.1253 37.0 37.0 37.0 29.8 37.0 45-49 35.4163 37.0 37.0 37.0 37.0 37.0 50-54 34.8489 37.0 37.0 37.0 29.8 37.0 55-59 34.173 37.0 37.0 37.0 25.0 37.0 60-64 35.011300000000006 37.0 37.0 37.0 27.4 37.0 65-69 34.0553 37.0 34.6 37.0 27.4 37.0 70-74 33.0293 37.0 29.8 37.0 22.2 37.0 75-79 33.4918 37.0 34.6 37.0 22.2 37.0 80-84 34.507999999999996 37.0 37.0 37.0 25.0 37.0 85-89 32.564499999999995 37.0 32.2 37.0 19.4 37.0 90-94 33.9521 37.0 37.0 37.0 25.0 37.0 95-99 33.81340000000001 37.0 37.0 37.0 25.0 37.0 100-104 33.333600000000004 37.0 37.0 37.0 25.0 37.0 105-109 34.000600000000006 37.0 37.0 37.0 25.0 37.0 110-114 34.50170000000001 37.0 37.0 37.0 25.0 37.0 115-119 34.389500000000005 37.0 37.0 37.0 25.0 37.0 120-124 33.9664 37.0 37.0 37.0 25.0 37.0 125-129 33.7737 37.0 37.0 37.0 25.0 37.0 130-134 33.5269 37.0 34.6 37.0 25.0 37.0 135-139 32.0855 37.0 25.0 37.0 13.8 37.0 140-144 31.350599999999996 37.0 25.0 37.0 11.0 37.0 145-149 30.898400000000002 37.0 25.0 37.0 11.0 37.0 150-151 30.55325 37.0 25.0 37.0 11.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 16 2.0 17 2.0 18 2.0 19 2.0 20 7.0 21 5.0 22 1.0 23 3.0 24 6.0 25 5.0 26 7.0 27 22.0 28 35.0 29 57.0 30 98.0 31 172.0 32 294.0 33 610.0 34 1175.0 35 1333.0 36 162.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 43.525000000000006 22.825 7.575 26.075 2 31.55 22.725 27.150000000000002 18.575 3 21.525 24.775 30.775000000000002 22.925 4 25.95 30.825000000000003 21.05 22.175 5 27.950000000000003 34.300000000000004 19.05 18.7 6 23.225 36.95 19.45 20.375 7 22.125 21.675 35.099999999999994 21.099999999999998 8 22.275 22.8 25.874999999999996 29.049999999999997 9 25.424999999999997 22.0 27.975 24.6 10-14 26.284999999999997 26.525 23.995 23.195 15-19 26.384999999999998 25.080000000000002 24.865000000000002 23.669999999999998 20-24 25.47 26.450000000000003 24.990000000000002 23.09 25-29 25.82 25.874999999999996 24.535 23.77 30-34 25.674999999999997 26.745 24.675 22.905 35-39 25.77 26.875 24.145 23.21 40-44 26.279999999999998 26.965 24.15 22.605 45-49 25.785000000000004 26.82 24.345 23.05 50-54 24.945 26.46 25.685000000000002 22.91 55-59 25.380000000000003 26.700000000000003 25.045 22.875 60-64 26.435 26.115 24.44 23.01 65-69 26.665 26.21 24.335 22.79 70-74 25.645 26.584999999999997 25.055 22.715 75-79 26.825 25.215 25.474999999999998 22.485 80-84 24.959999999999997 26.14 25.679999999999996 23.22 85-89 23.525 28.860000000000003 24.595 23.02 90-94 26.125 26.13 24.98 22.765 95-99 25.974999999999998 26.765 25.055 22.205 100-104 26.035000000000004 26.58 25.069999999999997 22.314999999999998 105-109 26.31 26.369999999999997 25.7 21.62 110-114 26.25 26.68 24.83 22.24 115-119 26.63 26.169999999999998 24.79 22.41 120-124 26.455000000000002 26.58 24.725 22.24 125-129 26.064999999999998 26.345000000000002 25.15 22.439999999999998 130-134 26.889999999999997 26.729999999999997 25.264999999999997 21.115000000000002 135-139 26.345000000000002 26.474999999999998 25.545 21.634999999999998 140-144 27.005000000000003 25.86 25.19 21.945 145-149 27.1 26.57 24.46 21.87 150-151 25.0125 26.375 27.3625 21.25 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.0 4 0.5 5 0.5 6 0.0 7 0.0 8 0.0 9 0.0 10 0.5 11 0.5 12 0.0 13 0.0 14 0.5 15 0.5 16 0.0 17 0.0 18 0.5 19 0.5 20 1.0 21 1.5 22 1.5 23 1.0 24 0.0 25 0.5 26 3.5 27 4.5 28 6.5 29 9.5 30 16.0 31 18.0 32 16.5 33 26.5 34 36.5 35 39.5 36 53.5 37 72.0 38 80.5 39 99.5 40 129.0 41 139.0 42 139.0 43 155.5 44 170.5 45 188.5 46 188.5 47 174.0 48 171.5 49 168.5 50 174.0 51 160.5 52 136.5 53 144.5 54 154.0 55 154.5 56 142.5 57 113.0 58 93.5 59 83.5 60 73.5 61 64.5 62 67.5 63 60.0 64 46.5 65 43.5 66 43.5 67 35.5 68 22.5 69 14.5 70 13.5 71 12.0 72 7.0 73 7.0 74 4.5 75 2.5 76 1.0 77 2.0 78 1.5 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.5 87 0.5 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 0.5 99 1.0 100 1.0 >>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 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 83.8 #Duplication Level Percentage of deduplicated Percentage of total 1 85.17303102625299 71.375 2 11.78400954653938 19.75 3 2.267303102625298 5.7 4 0.5071599045346062 1.7000000000000002 5 0.11933174224343676 0.5 6 0.08949880668257756 0.44999999999999996 7 0.0 0.0 8 0.0 0.0 9 0.02983293556085919 0.22499999999999998 >10 0.02983293556085919 0.3 >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 GGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAG 12 0.3 No Hit ATCATCATGAGTACTGGTTCTGAACTAGAGATTGCTGTCAAGGCTGCCGA 9 0.22499999999999998 No Hit GTATGACTTCCAGTATTTCATCATATGGATGAGTCCTGAAGATTTGTTTA 6 0.15 No Hit GTAATGATATTCATGTTGCAAAACCCTGTGATGAGCACATTAATGCATGT 6 0.15 No Hit GTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTTAACACATGCAA 6 0.15 No Hit TTTAAAAGCTAAAAGTAGTTGCAATACTTGTATATATTTTCTGAATAATT 5 0.125 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 5 0.125 No Hit GAGGAGACTGGTGATTTGGAGCAAGACTCCAACTCTTCCTCCGACAATGT 5 0.125 No Hit CCATCATTGTTCGTCCTGTTGACACTGAACAGCAGCCAATTAAAGAAATC 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 0.0 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 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.0625 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.0875 0.0 0.0 0.0 0.0 78-79 0.1125 0.0 0.0 0.0 0.0 80-81 0.125 0.0 0.0 0.0 0.0 82-83 0.1375 0.0 0.0 0.0 0.0 84-85 0.175 0.0 0.0 0.0 0.0 86-87 0.225 0.0 0.0 0.0 0.0 88-89 0.32499999999999996 0.0 0.0 0.0 0.0 90-91 0.35 0.0 0.0 0.0 0.0 92-93 0.4375 0.0 0.0 0.0 0.0 94-95 0.575 0.0 0.0 0.0 0.0 96-97 0.6375 0.0 0.0 0.0 0.0 98-99 0.8 0.0 0.0 0.0 0.0 100-101 0.9375 0.0 0.0 0.0 0.0 102-103 1.125 0.0 0.0 0.0 0.0 104-105 1.3875000000000002 0.0 0.0 0.0 0.0 106-107 1.6 0.0 0.0 0.0 0.0 108-109 1.7875 0.0 0.0 0.0 0.0 110-111 2.0625 0.0 0.0 0.0 0.0 112-113 2.2750000000000004 0.0 0.0 0.0 0.0 114-115 2.575 0.0 0.0 0.0 0.0 116-117 2.8 0.0 0.0 0.0 0.0 118-119 3.05 0.0 0.0 0.0 0.0 120-121 3.3 0.0 0.0 0.0 0.0 122-123 3.5250000000000004 0.0 0.0 0.0 0.0 124-125 3.8 0.0 0.0 0.0 0.0 126-127 4.3 0.0 0.0 0.0 0.0 128-129 4.6625 0.0 0.0 0.0 0.0 130-131 5.05 0.0 0.0 0.0 0.0 132-133 5.4125 0.0 0.0 0.0 0.0 134-135 5.725 0.0 0.0 0.0 0.0 136-137 6.1625 0.0 0.0 0.0 0.0 138-139 6.75 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGAAGG 10 0.006830828 145.0 5 AAAAAAA 60 0.004491891 14.500001 95-99 >>END_MODULE Read 751837 spots for SRR18694424.sra Written 751837 spots for SRR18694424.sra Read 751837 spots for SRR18694424.sra Written 751837 spots for SRR18694424.sra Read 751837 spots for SRR18694424.sra Written 751837 spots for SRR18694424.sra Read 751837 spots for SRR18694424.sra Written 751837 spots for SRR18694424.sra Read 751837 spots for SRR18694424.sra Written 751837 spots for SRR18694424.sra Read 751837 spots for SRR18694424.sra Written 751837 spots for SRR18694424.sra Read 751837 spots for SRR18694424.sra Written 751837 spots for SRR18694424.sra Read 751837 spots for SRR18694424.sra Written 751837 spots for SRR18694424.sra Read 751837 spots for SRR18694424.sra Written 751837 spots for SRR18694424.sra Read 751837 spots for SRR18694424.sra Written 751837 spots for SRR18694424.sra Read 751837 spots for SRR18694424.sra Written 751837 spots for SRR18694424.sra Read 751837 spots for SRR18694424.sra Written 751837 spots for SRR18694424.sra Read 751837 spots for SRR18694424.sra Written 751837 spots for SRR18694424.sra Read 751837 spots for SRR18694424.sra Written 751837 spots for SRR18694424.sra Read 751837 spots for SRR18694424.sra Written 751837 spots for SRR18694424.sra Read 751837 spots for SRR18694424.sra Written 751837 spots for SRR18694424.sra Read 751849 spots for SRR18694424.sra Written 751849 spots for SRR18694424.sra Read 751837 spots for SRR18694424.sra Written 751837 spots for SRR18694424.sra Read 751837 spots for SRR18694424.sra Written 751837 spots for SRR18694424.sra Read 751837 spots for SRR18694424.sra Written 751837 spots for SRR18694424.sra SRR ids: ['SRR18694424.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_yz7e38q9 SRR18694424.sra spots: 15036752 blocks: [[1, 751837], [751838, 1503674], [1503675, 2255511], [2255512, 3007348], [3007349, 3759185], [3759186, 4511022], [4511023, 5262859], [5262860, 6014696], [6014697, 6766533], [6766534, 7518370], [7518371, 8270207], [8270208, 9022044], [9022045, 9773881], [9773882, 10525718], [10525719, 11277555], [11277556, 12029392], [12029393, 12781229], [12781230, 13533066], [13533067, 14284903], [14284904, 15036752]] SRR18694424 file size 5088445 SRR18694424 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 SRR18694424 SRR18694424_1.fastq SRR18694424_2.fastq Input file: SRR18694424_1.fastq Paired file: SRR18694424_2.fastq trimmed: SRR18694424-trimmed-pair1.fastq, SRR18694424-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 Tue Dec 10 06:32:13 2024 >> started Tue Dec 10 06:32:39 2024 >> done (25.888s) 15036752 read pairs processed; of these: 99 ( 0.00%) short read pairs filtered out after trimming by size control 4054 ( 0.03%) empty read pairs filtered out after trimming by size control 15032599 (99.97%) read pairs available; of these: 1709583 (11.37%) trimmed read pairs available after processing 13323016 (88.63%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 6 0.00% 19 12 0.00% 20 13 0.00% 21 18 0.00% 22 13 0.00% 23 21 0.00% 24 12 0.00% 25 21 0.00% 26 25 0.00% 27 24 0.00% 28 23 0.00% 29 27 0.00% 30 29 0.00% 31 25 0.00% 32 24 0.00% 33 13 0.00% 34 31 0.00% 35 26 0.00% 36 34 0.00% 37 27 0.00% 38 35 0.00% 39 28 0.00% 40 35 0.00% 41 42 0.00% 42 42 0.00% 43 39 0.00% 44 48 0.00% 45 47 0.00% 46 45 0.00% 47 43 0.00% 48 70 0.00% 49 76 0.00% 50 72 0.00% 51 131 0.00% 52 112 0.00% 53 90 0.00% 54 116 0.00% 55 120 0.00% 56 150 0.00% 57 178 0.00% 58 197 0.00% 59 219 0.00% 60 282 0.00% 61 273 0.00% 62 325 0.00% 63 394 0.00% 64 437 0.00% 65 447 0.00% 66 566 0.00% 67 547 0.00% 68 676 0.00% 69 796 0.01% 70 939 0.01% 71 982 0.01% 72 1177 0.01% 73 1379 0.01% 74 1536 0.01% 75 1538 0.01% 76 1805 0.01% 77 2081 0.01% 78 2153 0.01% 79 2495 0.02% 80 2596 0.02% 81 3161 0.02% 82 3442 0.02% 83 3919 0.03% 84 4027 0.03% 85 4589 0.03% 86 4868 0.03% 87 5178 0.03% 88 5728 0.04% 89 6086 0.04% 90 6426 0.04% 91 7040 0.05% 92 7710 0.05% 93 8225 0.05% 94 8813 0.06% 95 9314 0.06% 96 9758 0.06% 97 10501 0.07% 98 10800 0.07% 99 11414 0.08% 100 11928 0.08% 101 12282 0.08% 102 13373 0.09% 103 13731 0.09% 104 14871 0.10% 105 14946 0.10% 106 15909 0.11% 107 16354 0.11% 108 17287 0.11% 109 17847 0.12% 110 18348 0.12% 111 19073 0.13% 112 20228 0.13% 113 20319 0.14% 114 21347 0.14% 115 22117 0.15% 116 23553 0.16% 117 23784 0.16% 118 23767 0.16% 119 24645 0.16% 120 26404 0.18% 121 26446 0.18% 122 27237 0.18% 123 29608 0.20% 124 30357 0.20% 125 30553 0.20% 126 31594 0.21% 127 31733 0.21% 128 33091 0.22% 129 33862 0.23% 130 33723 0.22% 131 34534 0.23% 132 35790 0.24% 133 36298 0.24% 134 37006 0.25% 135 38447 0.26% 136 39417 0.26% 137 39788 0.26% 138 40291 0.27% 139 41676 0.28% 140 41975 0.28% 141 42059 0.28% 142 43696 0.29% 143 44485 0.30% 144 45461 0.30% 145 46810 0.31% 146 47511 0.32% 147 48468 0.32% 148 48883 0.33% 149 49776 0.33% 150 50113 0.33% 151 13323016 88.63% 15032599 reads passed initial QC criterion=sequence-density sequence-density=0.75 sequence-density-rank=1 fanout-score=1.98 fanout-score-rank=37 prefix-density=0.67 prefix-fanout=2.0 sequence=CCGTCAATTCCTTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=37 fanout-score=21.65 fanout-score-rank=1 prefix-density=0.15 prefix-fanout=1.8 sequence=ATCGCCGGCCCCCATCCGCTTCCCTCCCGGCAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTTCCCTCGCGGTACTTGTTCGCTATCGG criterion=sequence-density sequence-density=0.34 sequence-density-rank=1 fanout-score=5.70 fanout-score-rank=10 prefix-density=1.00 prefix-fanout=2.0 sequence=TGGTGCATGGCTGTCGTCAGCTCGTGCCGTAAGGTGTTGGGTTAAGTCTCGCAACGAGCGCAACCCTCGTGTTTAGTTGCCACTATGAGTTTGGAACCCTGAACAGACCGCCGGTGTTAAGCCGGAGGAAGGAGAGGATGAGGCCAAGTCATCATGCCCCTTATGCCCTGGGCGACACACGTGCTACAATGGGCGGGACAAAGGGTCGCGATCTCGCGAGGGTGAGCTAACTCCAAAAACCCGTCCTCAGTTCGGATTGCAGGCTGCAACTCGCCTGCATGAAGCAGGAATCGCTAGTAATCGCCGGTCAGCCATACGGCGGTGAATCCGTTCCCGGGCCTTGTACACACC criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=82.88 fanout-score-rank=1 prefix-density=0.42 prefix-fanout=1.9 sequence=AAGGAAGCTATAAGTAATGCAACTATGAATCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTTAACACATGCAAGTCGAACGGGAAGTGGTGTTTCCAGTGGCGAACGGGTGAGTAACGCGTAAGAACCTGCCCTTGGGAGGGGAACAACAACTGGAAACGGTTGCTAATACCCCGTAGGCTGAGGAGCAAAAGGAGAAATCCGCCCAAGGAGGGGCTCGCGTCTGATTAGCTAGTTGGTGAGGCAATAGCTTACCAAGGCGATGATCAGTAGCTGGTCCGAGAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATGCCGCGTGGAGGTGGAAGGCCTACGGGTCGTCAACTTCTTTTCTCGGAGAAGAAACAATGACGGTATCTGAGGAATAAGCATCGGCTAACTCTGTGCCAGCAGC SRR18694424 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 10 06:33:27 Started mapping on | Dec 10 06:33:27 Finished on | Dec 10 06:35:50 Mapping speed, Million of reads per hour | 378.44 Number of input reads | 15032599 Average input read length | 296 UNIQUE READS: Uniquely mapped reads number | 12110158 Uniquely mapped reads % | 80.56% Average mapped length | 295.03 Number of splices: Total | 11954522 Number of splices: Annotated (sjdb) | 11247701 Number of splices: GT/AG | 11789195 Number of splices: GC/AG | 134596 Number of splices: AT/AC | 7525 Number of splices: Non-canonical | 23206 Mismatch rate per base, % | 0.45% Deletion rate per base | 0.01% Deletion average length | 2.39 Insertion rate per base | 0.01% Insertion average length | 2.20 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1255131 % of reads mapped to multiple loci | 8.35% Number of reads mapped to too many loci | 102574 % of reads mapped to too many loci | 0.68% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.08% % of reads unmapped: other | 6.33% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1667310 1667310 1667310 N_multimapping 1255131 1255131 1255131 N_noFeature 1300407 11759378 1407852 N_ambiguous 356078 2618 124317 UnstrandedReadsAssigned:10453673 PositiveStrandReadsAssigned:348162 NegativeStrandReadsAssigned:10577989 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR18694424 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: SRR18694424-trimmed-pair1.fastq SRR18694424-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 15,032,599 reads, 11,506,761 reads pseudoaligned [quant] estimated average fragment length: 257.258 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,116 rounds 52973 SRR18694424.ke.tsv 35125 SRR18694424.se.tsv 88098 total ==> SRR18694424.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 680.108 0 0 PNS24247 1044 787.742 48.7863 7.89796 PNS24249 1928 1671.74 23.1434 1.76546 PNS24246 1044 787.742 48.7863 7.89796 PNS24248 1044 787.742 48.7863 7.89796 PNS24244 1471 1214.74 100.498 10.5505 PNS24243 293 97.1406 0 0 KQK14069 1603 1346.74 1010.24 95.6627 KQK14071 474 240.328 21.0118 11.1496 ==> SRR18694424.se.tsv <== BRADI_1g14170v3 1125 BRADI_1g53295v3 42 BRADI_1g59795v3 400 BRADI_1g07683v3 0 BRADI_1g00485v3 13 BRADI_1g20270v3 1431 BRADI_1g74790v3 33 BRADI_1g09890v3 9 BRADI_1g77505v3 175 BRADI_1g48960v3 0 SRR18694424 completed mapping pipeline successfully