Starting /dee2/code/volunteer_pipeline.sh SRR8096909 current disk space = 1524580773888 free memory = 1465589144 SRR8096909 SRAfilesize 0738933c915ab946983594b45fed17b6 SRR8096909.sra SRR8096909.sra file validated SRR8096909 is paired end SRR8096909 is conventional basespace SRR8096909 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8096909_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 48 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.42975 34.0 33.0 34.0 32.0 34.0 2 33.07025 34.0 33.0 34.0 32.0 34.0 3 33.024 34.0 33.0 34.0 32.0 34.0 4 33.22375 34.0 33.0 34.0 32.0 34.0 5 33.2695 34.0 33.0 34.0 33.0 34.0 6 36.8835 38.0 37.0 38.0 35.0 38.0 7 37.31875 38.0 38.0 38.0 37.0 38.0 8 37.4485 38.0 38.0 38.0 37.0 38.0 9 37.35425 38.0 38.0 38.0 37.0 38.0 10-14 37.37665 38.0 38.0 38.0 37.0 38.0 15-19 37.4529 38.0 38.0 38.0 37.0 38.0 20-24 37.42245 38.0 38.0 38.0 37.2 38.0 25-29 37.357549999999996 38.0 38.0 38.0 37.0 38.0 30-34 37.35295 38.0 38.0 38.0 37.0 38.0 35-39 37.317099999999996 38.0 38.0 38.0 37.0 38.0 40-44 37.22605 38.0 38.0 38.0 37.0 38.0 45-49 37.2644 38.0 38.0 38.0 37.0 38.0 50-54 37.23325 38.0 38.0 38.0 36.6 38.0 55-59 37.083600000000004 38.0 38.0 38.0 36.0 38.0 60-64 37.040049999999994 38.0 38.0 38.0 36.2 38.0 65-69 36.8681 38.0 38.0 38.0 35.8 38.0 70-74 36.679500000000004 38.0 38.0 38.0 35.0 38.0 75-79 36.501 38.0 38.0 38.0 35.0 38.0 80-84 36.4053 38.0 38.0 38.0 34.8 38.0 85-89 35.7312 38.0 37.4 38.0 31.6 38.0 90-94 36.24775 38.0 38.0 38.0 34.0 38.0 95-99 36.2416 38.0 38.0 38.0 34.4 38.0 100-104 36.09565 38.0 38.0 38.0 33.8 38.0 105-109 35.943149999999996 38.0 38.0 38.0 33.6 38.0 110-114 35.7689 38.0 37.8 38.0 32.8 38.0 115-119 35.38265 38.0 37.0 38.0 31.0 38.0 120-124 35.4717 38.0 37.4 38.0 31.2 38.0 125-129 35.253550000000004 38.0 36.6 38.0 31.0 38.0 130-134 34.653200000000005 38.0 35.6 38.0 27.2 38.0 135-139 34.5385 38.0 36.0 38.0 27.2 38.0 140-144 34.00895 38.0 35.6 38.0 23.6 38.0 145-149 32.7928 38.0 33.8 38.0 11.4 38.0 150 23.178 28.0 2.0 36.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 5 1.0 6 0.0 7 2.0 8 3.0 9 0.0 10 1.0 11 1.0 12 2.0 13 1.0 14 0.0 15 3.0 16 3.0 17 5.0 18 16.0 19 21.0 20 6.0 21 5.0 22 11.0 23 6.0 24 8.0 25 8.0 26 23.0 27 20.0 28 30.0 29 40.0 30 49.0 31 64.0 32 75.0 33 121.0 34 150.0 35 238.0 36 538.0 37 2549.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.01875160544567 10.300539429745697 8.271256100693552 42.409452864115075 2 22.95 16.0 36.7 24.349999999999998 3 22.675 18.75 25.1 33.475 4 26.775 27.0 20.4 25.825 5 26.275 30.025000000000002 23.674999999999997 20.025000000000002 6 21.4 32.7 24.25 21.65 7 16.85 23.125 40.25 19.775000000000002 8 19.375 24.75 30.325000000000003 25.55 9 21.5 19.225 32.525 26.75 10-14 22.775000000000002 26.685 24.92 25.619999999999997 15-19 22.31 25.545 26.235000000000003 25.91 20-24 22.96 25.89 26.075 25.074999999999996 25-29 23.225 25.55 26.05 25.174999999999997 30-34 22.384999999999998 25.665 26.105 25.845000000000002 35-39 22.884999999999998 24.81 26.52 25.785000000000004 40-44 22.715 25.64 25.88 25.765 45-49 23.025000000000002 24.995 26.38 25.6 50-54 22.585 24.825 25.995 26.595000000000002 55-59 23.21 24.7 26.76 25.330000000000002 60-64 23.46 25.224999999999998 25.615 25.7 65-69 22.54 26.96 25.81 24.69 70-74 23.125 26.55 24.535 25.790000000000003 75-79 23.125 25.585 25.335 25.955000000000002 80-84 23.115 25.205 26.21 25.47 85-89 23.32 25.124999999999996 25.430000000000003 26.125 90-94 23.3 24.745 25.83 26.125 95-99 23.919999999999998 25.27 25.785000000000004 25.025 100-104 23.025000000000002 25.15 25.624999999999996 26.200000000000003 105-109 23.46 25.924999999999997 25.025 25.590000000000003 110-114 23.39 25.900000000000002 25.46 25.25 115-119 23.794999999999998 25.41 25.814999999999998 24.98 120-124 23.44 25.380000000000003 25.169999999999998 26.009999999999998 125-129 23.775 25.230000000000004 25.465 25.53 130-134 23.705000000000002 26.384999999999998 24.795 25.115 135-139 23.575 26.045 24.755 25.624999999999996 140-144 23.400000000000002 25.305 25.314999999999998 25.979999999999997 145-149 23.815 25.53 25.39 25.264999999999997 150 23.35 25.424999999999997 25.074999999999996 26.150000000000002 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 2.0 1 1.5 2 0.5 3 1.0 4 2.0 5 1.0 6 0.5 7 0.5 8 0.5 9 0.5 10 0.0 11 0.5 12 1.0 13 0.5 14 0.0 15 0.0 16 0.5 17 0.5 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 1.5 25 3.0 26 2.5 27 2.0 28 3.0 29 7.5 30 8.5 31 9.5 32 15.0 33 23.0 34 32.5 35 38.5 36 49.0 37 68.5 38 87.0 39 97.0 40 113.0 41 138.0 42 169.0 43 187.0 44 199.5 45 199.0 46 197.5 47 202.5 48 189.0 49 176.0 50 151.0 51 144.0 52 148.5 53 123.5 54 111.5 55 106.0 56 111.0 57 110.0 58 81.0 59 87.5 60 88.5 61 68.0 62 58.5 63 60.0 64 57.0 65 54.5 66 55.0 67 41.5 68 33.0 69 26.5 70 17.5 71 13.0 72 9.5 73 4.0 74 3.0 75 3.0 76 1.5 77 0.5 78 0.0 79 0.0 80 0.0 81 0.0 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 pass #Base N-Count 1 2.675 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 96.3 #Duplication Level Percentage of deduplicated Percentage of total 1 98.0269989615784 94.39999999999999 2 1.6614745586708204 3.2 3 0.181723779854621 0.525 4 0.05192107995846314 0.2 5 0.02596053997923157 0.125 6 0.02596053997923157 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.02596053997923157 1.4000000000000001 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTTCCATCTCGTATGC 56 1.4000000000000001 TruSeq Adapter, Index 14 (98% over 50bp) TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 6 0.15 No Hit AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTTCCATCTCGTATG 5 0.125 TruSeq Adapter, Index 14 (97% over 49bp) >>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 0.125 0.0 0.0 0.0 0.0 2 0.125 0.0 0.0 0.0 0.0 3 0.125 0.0 0.0 0.0 0.0 4 0.125 0.0 0.0 0.0 0.0 5 0.125 0.0 0.0 0.0 0.0 6 0.125 0.0 0.0 0.0 0.0 7 0.125 0.0 0.0 0.0 0.0 8 0.125 0.0 0.0 0.0 0.0 9 0.125 0.0 0.0 0.0 0.0 10-11 0.125 0.0 0.0 0.0 0.0 12-13 0.125 0.0 0.0 0.0 0.0 14-15 0.125 0.0 0.0 0.0 0.0 16-17 0.125 0.0 0.0 0.0 0.0 18-19 0.125 0.0 0.0 0.0 0.0 20-21 0.125 0.0 0.0 0.0 0.0 22-23 0.125 0.0 0.0 0.0 0.0 24-25 0.125 0.0 0.0 0.0 0.0 26-27 0.125 0.0 0.0 0.0 0.0 28-29 0.125 0.0 0.0 0.0 0.0 30-31 0.125 0.0 0.0 0.0 0.0 32-33 0.125 0.0 0.0 0.0 0.0 34-35 0.125 0.0 0.0 0.0 0.0 36-37 0.125 0.0 0.0 0.0 0.0 38-39 0.125 0.0 0.0 0.0 0.0 40-41 0.125 0.0 0.0 0.0 0.0 42-43 0.125 0.0 0.0 0.0 0.0 44-45 0.15 0.0 0.0 0.0 0.0 46-47 0.15 0.0 0.0 0.0 0.0 48-49 0.15 0.0 0.0 0.0 0.0 50-51 0.15 0.0 0.0 0.0 0.0 52-53 0.15 0.0 0.0 0.0 0.0 54-55 0.15 0.0 0.0 0.0 0.0 56-57 0.15 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 0.15 0.0 0.0 0.0 0.0 68-69 0.15 0.0 0.0 0.0 0.0 70-71 0.15 0.0 0.0 0.0 0.0 72-73 0.15 0.0 0.0 0.0 0.0 74-75 0.15 0.0 0.0 0.0 0.0 76-77 0.15 0.0 0.0 0.0 0.0 78-79 0.15 0.0 0.0 0.0 0.0 80-81 0.15 0.0 0.0 0.0 0.0 82-83 0.175 0.0 0.0 0.0 0.0 84-85 0.21250000000000002 0.0 0.0 0.0 0.0 86-87 0.225 0.0 0.0 0.0 0.0 88-89 0.25 0.0 0.0 0.0 0.0 90-91 0.25 0.0 0.0 0.0 0.0 92-93 0.275 0.0 0.0 0.0 0.0 94-95 0.3 0.0 0.0 0.0 0.0 96-97 0.32499999999999996 0.0 0.0 0.0 0.0 98-99 0.35 0.0 0.0 0.0 0.0 100-101 0.4 0.0 0.0 0.0 0.0 102-103 0.425 0.0 0.0 0.0 0.0 104-105 0.475 0.0 0.0 0.0 0.0 106-107 0.525 0.0 0.0 0.0 0.0 108-109 0.65 0.0 0.0 0.0 0.0 110-111 0.7375 0.0 0.0 0.0 0.0 112-113 0.8 0.0 0.0 0.0 0.0 114-115 0.9125000000000001 0.0 0.0 0.0 0.0 116-117 1.0125 0.0 0.0 0.0 0.0 118-119 1.1 0.0 0.0 0.0 0.0 120-121 1.2000000000000002 0.0 0.0 0.0 0.0 122-123 1.3125 0.0 0.0 0.0 0.0 124-125 1.4625 0.0 0.0 0.0 0.0 126-127 1.6625 0.0 0.0 0.0 0.0 128-129 1.8624999999999998 0.0 0.0 0.0 0.0 130-131 2.0 0.0 0.0 0.0 0.0 132-133 2.15 0.0 0.0 0.0 0.0 134-135 2.3375000000000004 0.0 0.0 0.0 0.0 136-137 2.575 0.0 0.0 0.0 0.0 138 2.775 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CGACACA 10 0.0069790767 143.96251 3 CACAAGC 10 0.0069790767 143.96251 6 GACACAA 10 0.0069790767 143.96251 4 ACACAAG 10 0.0069790767 143.96251 5 CGGAAGA 40 0.005783394 53.98594 4 AAAAAAA 240 0.0030118325 6.5982814 65-69 >>END_MODULE SRR8096909 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8096909_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 49 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.15975 33.0 32.0 33.0 27.0 34.0 2 31.23225 33.0 32.0 34.0 27.0 34.0 3 31.03925 33.0 31.0 34.0 27.0 34.0 4 31.2375 33.0 32.0 34.0 27.0 34.0 5 30.9815 33.0 31.0 34.0 27.0 34.0 6 34.90575 38.0 36.0 38.0 28.0 38.0 7 34.995 38.0 37.0 38.0 28.0 38.0 8 34.8355 38.0 37.0 38.0 27.0 38.0 9 34.78 38.0 37.0 38.0 26.0 38.0 10-14 34.806650000000005 38.0 36.6 38.0 27.0 38.0 15-19 34.57165 38.0 36.0 38.0 26.0 38.0 20-24 34.4172 38.0 36.0 38.0 25.0 38.0 25-29 34.247699999999995 38.0 36.0 38.0 22.8 38.0 30-34 33.9972 38.0 35.2 38.0 16.0 38.0 35-39 33.8131 38.0 35.0 38.0 16.0 38.0 40-44 33.71065 38.0 34.4 38.0 16.0 38.0 45-49 33.5496 38.0 34.2 38.0 16.0 38.0 50-54 33.41345 38.0 34.0 38.0 16.0 38.0 55-59 33.1386 38.0 33.8 38.0 16.0 38.0 60-64 32.92035 38.0 33.2 38.0 16.0 38.0 65-69 32.4768 38.0 32.4 38.0 15.6 38.0 70-74 31.987599999999997 37.4 30.6 38.0 15.0 38.0 75-79 31.55065 37.0 29.0 38.0 15.0 38.0 80-84 31.2431 37.0 28.8 38.0 15.0 38.0 85-89 30.6724 36.6 28.0 38.0 14.0 38.0 90-94 30.16375 36.4 26.4 38.0 13.2 38.0 95-99 29.500550000000004 35.4 24.4 38.0 10.8 38.0 100-104 28.673899999999996 34.8 19.8 38.0 2.0 38.0 105-109 28.03435 34.6 19.0 38.0 2.0 38.0 110-114 27.149700000000003 34.0 15.0 38.0 2.0 38.0 115-119 26.039599999999997 33.8 15.0 38.0 2.0 38.0 120-124 25.26345 32.6 14.0 37.8 2.0 38.0 125-129 24.2636 31.4 13.2 37.2 2.0 38.0 130-134 22.959899999999998 28.4 6.4 36.0 2.0 38.0 135-139 21.34865 25.0 2.0 35.0 2.0 38.0 140-144 19.5409 21.8 2.0 33.8 2.0 38.0 145-149 16.546349999999997 9.0 2.0 33.0 2.0 38.0 150 10.95075 2.0 2.0 24.0 2.0 35.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 86.0 3 18.0 4 7.0 5 8.0 6 7.0 7 10.0 8 11.0 9 11.0 10 8.0 11 17.0 12 20.0 13 37.0 14 26.0 15 35.0 16 49.0 17 35.0 18 60.0 19 48.0 20 71.0 21 59.0 22 59.0 23 71.0 24 75.0 25 91.0 26 80.0 27 124.0 28 131.0 29 156.0 30 189.0 31 241.0 32 290.0 33 305.0 34 400.0 35 476.0 36 493.0 37 196.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 36.60443995963673 16.9021190716448 9.20787083753784 37.28557013118062 2 26.307808946171342 25.473843821076574 31.53904473085671 16.67930250189538 3 21.85999494566591 24.842052059641144 28.96133434420015 24.3366186504928 4 27.982810920121338 30.51061678463094 18.048533872598586 23.458038422649143 5 29.033889731917046 32.220536165907944 19.878603945371776 18.866970156803237 6 23.614274867122248 35.054416603391545 20.50113895216401 20.830169577322195 7 22.129489124936775 19.625695498229643 34.57258472432979 23.672230652503792 8 22.073324905183313 23.438685208596713 27.079646017699115 27.408343868520856 9 24.911482043500254 21.269600404653517 28.022255943348505 25.796661608497722 10-14 26.564159627737595 25.709372312983664 22.477365838854887 25.249102220423854 15-19 26.266511463130726 25.446631914570577 24.211751606862695 24.075105015436005 20-24 26.239627605747824 26.29022465088039 24.084193483100588 23.3859542602712 25-29 25.541059870550164 26.466423948220065 23.604368932038835 24.38814724919094 30-34 26.717557251908396 25.741873514989134 24.063495273242 23.477073959860473 35-39 25.648283880099076 25.78981954203104 24.54632765505737 24.015568922812516 40-44 26.793025018953752 25.595147839272176 23.760424564063683 23.851402577710388 45-49 25.76860841423948 25.59668284789644 23.912823624595468 24.72188511326861 50-54 25.828149496788548 25.80791989076013 24.19966621150053 24.164264400950792 55-59 25.590451625954586 25.80286248925302 24.568856521519244 24.03782936327315 60-64 24.929192797896015 27.432733158001216 23.6698361319037 23.96823791219907 65-69 25.039210726030863 27.154060207437393 23.809764735643814 23.99696433088793 70-74 25.475612224246102 26.649463671321595 23.977939688322202 23.896984416110097 75-79 25.242865816636307 26.295284355393644 24.306820481683868 24.155029346286177 80-84 26.033706159218582 26.843463738043422 23.052786072169646 24.07004403056835 85-89 25.297423176226395 26.461803270389307 23.996354984053056 24.24441856933124 90-94 24.983550134129676 26.96765703295035 23.859897757756745 24.188895075163234 95-99 25.058180714357984 26.49499139937266 24.607912577152685 23.838915309116665 100-104 25.669315248747402 26.210840629586517 23.923275469406345 24.196568652259728 105-109 25.569274364942817 26.6015585467058 23.899402894443885 23.9297641939075 110-114 25.640246988561593 27.08776191922259 23.691669197287172 23.580321894928634 115-119 25.68695916198573 27.119072921410858 23.374323161783312 23.8196447548201 120-124 24.902566179075773 27.311838841929443 23.66249936731285 24.123095611681936 125-129 24.951918210345177 27.99372406113979 23.30195363903229 23.75240408948274 130-134 25.07968631419175 27.179357450037944 23.728813559322035 24.012142676448267 135-139 24.87101669195751 27.663125948406673 23.338391502276178 24.12746585735964 140-144 24.854584998229733 28.071417733043347 23.064083759041022 24.009913509685905 145-149 24.64760166311733 29.134976168745563 22.700537470844743 23.516884697292365 150 22.5594334850784 34.59787556904401 20.333839150227618 22.508851795649974 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 38.0 1 21.5 2 2.5 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.5 9 0.5 10 0.0 11 0.5 12 0.5 13 0.0 14 0.5 15 0.5 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.5 22 1.5 23 2.5 24 1.5 25 2.5 26 2.5 27 3.0 28 7.5 29 8.5 30 7.5 31 10.0 32 15.0 33 18.5 34 28.5 35 41.5 36 50.5 37 60.0 38 76.0 39 95.5 40 109.0 41 125.5 42 138.5 43 142.5 44 163.0 45 185.0 46 188.5 47 171.0 48 153.0 49 173.0 50 180.0 51 162.0 52 144.0 53 124.5 54 127.5 55 117.5 56 96.0 57 82.0 58 97.0 59 114.5 60 94.0 61 81.5 62 83.5 63 76.0 64 61.0 65 60.5 66 58.0 67 51.0 68 47.0 69 34.0 70 20.5 71 15.5 72 15.5 73 12.5 74 6.5 75 4.5 76 3.5 77 1.5 78 0.5 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 0.8999999999999999 2 1.075 3 1.075 4 1.0999999999999999 5 1.15 6 1.225 7 1.15 8 1.125 9 1.15 10-14 1.145 15-19 1.205 20-24 1.18 25-29 1.1199999999999999 30-34 1.095 35-39 1.085 40-44 1.075 45-49 1.1199999999999999 50-54 1.135 55-59 1.135 60-64 1.1400000000000001 65-69 1.175 70-74 1.18 75-79 1.18 80-84 1.205 85-89 1.2349999999999999 90-94 1.2149999999999999 95-99 1.17 100-104 1.205 105-109 1.1900000000000002 110-114 1.21 115-119 1.195 120-124 1.2149999999999999 125-129 1.21 130-134 1.175 135-139 1.15 140-144 1.145 145-149 1.39 150 1.15 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 96.925 #Duplication Level Percentage of deduplicated Percentage of total 1 98.89089502192417 95.85000000000001 2 0.6964147536755223 1.35 3 0.20634511220015478 0.6 4 0.07737941707505804 0.3 5 0.051586278050038695 0.25 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.025793139025019347 0.22499999999999998 >10 0.051586278050038695 1.425 >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 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 36 0.8999999999999999 No Hit GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 21 0.525 Illumina Single End PCR Primer 1 (100% over 50bp) CCTCTTGTTAGCTATCTACGTACGTGTACGATGGCTCCCACAGTGATGTC 9 0.22499999999999998 No Hit CTGCAATTGCAAGCTTGTGTCAAAGAAGAGGGTAGCACCTGATCCTCTTG 5 0.125 No Hit CTTGATCATCTGAAAAATCTTAATCCAGATCAGACCAAGCAGAGCAGAGA 5 0.125 No Hit >>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 0.1 0.0 0.0 0.0 0.0 2 0.1 0.0 0.0 0.0 0.0 3 0.1 0.0 0.0 0.0 0.0 4 0.1 0.0 0.0 0.0 0.0 5 0.1 0.0 0.0 0.0 0.0 6 0.1 0.0 0.0 0.0 0.0 7 0.1 0.0 0.0 0.0 0.0 8 0.1 0.0 0.0 0.0 0.0 9 0.125 0.0 0.0 0.0 0.0 10-11 0.125 0.0 0.0 0.0 0.0 12-13 0.125 0.0 0.0 0.0 0.0 14-15 0.125 0.0 0.0 0.0 0.0 16-17 0.125 0.0 0.0 0.0 0.0 18-19 0.125 0.0 0.0 0.0 0.0 20-21 0.125 0.0 0.0 0.0 0.0 22-23 0.125 0.0 0.0 0.0 0.0 24-25 0.125 0.0 0.0 0.0 0.0 26-27 0.125 0.0 0.0 0.0 0.0 28-29 0.125 0.0 0.0 0.0 0.0 30-31 0.125 0.0 0.0 0.0 0.0 32-33 0.125 0.0 0.0 0.0 0.0 34-35 0.125 0.0 0.0 0.0 0.0 36-37 0.125 0.0 0.0 0.0 0.0 38-39 0.125 0.0 0.0 0.0 0.0 40-41 0.125 0.0 0.0 0.0 0.0 42-43 0.125 0.0 0.0 0.0 0.0 44-45 0.175 0.0 0.0 0.0 0.0 46-47 0.175 0.0 0.0 0.0 0.0 48-49 0.175 0.0 0.0 0.0 0.0 50-51 0.175 0.0 0.0 0.0 0.0 52-53 0.175 0.0 0.0 0.0 0.0 54-55 0.175 0.0 0.0 0.0 0.0 56-57 0.175 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 0.2 0.0 0.0 0.0 0.0 64-65 0.2 0.0 0.0 0.0 0.0 66-67 0.2 0.0 0.0 0.0 0.0 68-69 0.2 0.0 0.0 0.0 0.0 70-71 0.2 0.0 0.0 0.0 0.0 72-73 0.2 0.0 0.0 0.0 0.0 74-75 0.2 0.0 0.0 0.0 0.0 76-77 0.2 0.0 0.0 0.0 0.0 78-79 0.2 0.0 0.0 0.0 0.0 80-81 0.2 0.0 0.0 0.0 0.0 82-83 0.225 0.0 0.0 0.0 0.0 84-85 0.2625 0.0 0.0 0.0 0.0 86-87 0.275 0.0 0.0 0.0 0.0 88-89 0.275 0.0 0.0 0.0 0.0 90-91 0.275 0.0 0.0 0.0 0.0 92-93 0.3 0.0 0.0 0.0 0.0 94-95 0.325 0.0 0.0 0.0 0.0 96-97 0.3375 0.0 0.0 0.0 0.0 98-99 0.35 0.0 0.0 0.0 0.0 100-101 0.35 0.0 0.0 0.0 0.0 102-103 0.35 0.0 0.0 0.0 0.0 104-105 0.375 0.0 0.0 0.0 0.0 106-107 0.42500000000000004 0.0 0.0 0.0 0.0 108-109 0.55 0.0 0.0 0.0 0.0 110-111 0.6125 0.0 0.0 0.0 0.0 112-113 0.6375 0.0 0.0 0.0 0.0 114-115 0.6875 0.0 0.0 0.0 0.0 116-117 0.7625 0.0 0.0 0.0 0.0 118-119 0.85 0.0 0.0 0.0 0.0 120-121 0.9125000000000001 0.0 0.0 0.0 0.0 122-123 0.9624999999999999 0.0 0.0 0.0 0.0 124-125 1.0 0.0 0.0 0.0 0.0 126-127 1.1124999999999998 0.0 0.0 0.0 0.0 128-129 1.2 0.0 0.0 0.0 0.0 130-131 1.2625000000000002 0.0 0.0 0.0 0.0 132-133 1.35 0.0 0.0 0.0 0.0 134-135 1.45 0.0 0.0 0.0 0.0 136-137 1.5750000000000002 0.0 0.0 0.0 0.0 138 1.675 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1996316 spots for SRR8096909.sra Written 1996316 spots for SRR8096909.sra Read 1996316 spots for SRR8096909.sra Written 1996316 spots for SRR8096909.sra Read 1996316 spots for SRR8096909.sra Written 1996316 spots for SRR8096909.sra Read 1996327 spots for SRR8096909.sra Written 1996327 spots for SRR8096909.sra Read 1996316 spots for SRR8096909.sra Written 1996316 spots for SRR8096909.sra Read 1996316 spots for SRR8096909.sra Written 1996316 spots for SRR8096909.sra Read 1996316 spots for SRR8096909.sra Written 1996316 spots for SRR8096909.sra Read 1996316 spots for SRR8096909.sra Written 1996316 spots for SRR8096909.sra Read 1996316 spots for SRR8096909.sra Written 1996316 spots for SRR8096909.sra Read 1996316 spots for SRR8096909.sra Written 1996316 spots for SRR8096909.sra Read 1996316 spots for SRR8096909.sra Written 1996316 spots for SRR8096909.sra Read 1996316 spots for SRR8096909.sra Written 1996316 spots for SRR8096909.sra Read 1996316 spots for SRR8096909.sra Written 1996316 spots for SRR8096909.sra Read 1996316 spots for SRR8096909.sra Written 1996316 spots for SRR8096909.sra Read 1996316 spots for SRR8096909.sra Written 1996316 spots for SRR8096909.sra Read 1996316 spots for SRR8096909.sra Written 1996316 spots for SRR8096909.sra Read 1996316 spots for SRR8096909.sra Written 1996316 spots for SRR8096909.sra Read 1996316 spots for SRR8096909.sra Written 1996316 spots for SRR8096909.sra Read 1996316 spots for SRR8096909.sra Written 1996316 spots for SRR8096909.sra Read 1996316 spots for SRR8096909.sra Written 1996316 spots for SRR8096909.sra SRR ids: ['SRR8096909.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_dxql2uug SRR8096909.sra spots: 39926331 blocks: [[1, 1996316], [1996317, 3992632], [3992633, 5988948], [5988949, 7985264], [7985265, 9981580], [9981581, 11977896], [11977897, 13974212], [13974213, 15970528], [15970529, 17966844], [17966845, 19963160], [19963161, 21959476], [21959477, 23955792], [23955793, 25952108], [25952109, 27948424], [27948425, 29944740], [29944741, 31941056], [31941057, 33937372], [33937373, 35933688], [35933689, 37930004], [37930005, 39926331]] SRR8096909 file size 13430042 SRR8096909 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 SRR8096909 SRR8096909_1.fastq SRR8096909_2.fastq Input file: SRR8096909_1.fastq Paired file: SRR8096909_2.fastq trimmed: SRR8096909-trimmed-pair1.fastq, SRR8096909-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 Sun Dec 8 03:50:42 2024 >> started Sun Dec 8 03:55:50 2024 >> done (307.135s) 39926331 read pairs processed; of these: 163830 ( 0.41%) short read pairs filtered out after trimming by size control 1348203 ( 3.38%) empty read pairs filtered out after trimming by size control 38414298 (96.21%) read pairs available; of these: 21561378 (56.13%) trimmed read pairs available after processing 16852920 (43.87%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 82 0.00% 19 170 0.00% 20 74 0.00% 21 88 0.00% 22 94 0.00% 23 113 0.00% 24 105 0.00% 25 107 0.00% 26 125 0.00% 27 136 0.00% 28 227 0.00% 29 195 0.00% 30 237 0.00% 31 155 0.00% 32 181 0.00% 33 142 0.00% 34 256 0.00% 35 316 0.00% 36 211 0.00% 37 199 0.00% 38 208 0.00% 39 342 0.00% 40 410 0.00% 41 471 0.00% 42 359 0.00% 43 432 0.00% 44 444 0.00% 45 628 0.00% 46 796 0.00% 47 719 0.00% 48 737 0.00% 49 820 0.00% 50 842 0.00% 51 824 0.00% 52 763 0.00% 53 850 0.00% 54 977 0.00% 55 1085 0.00% 56 1261 0.00% 57 1151 0.00% 58 1732 0.00% 59 2324 0.01% 60 1855 0.00% 61 6460 0.02% 62 2506 0.01% 63 1291 0.00% 64 1468 0.00% 65 1807 0.00% 66 1640 0.00% 67 1652 0.00% 68 1981 0.01% 69 2869 0.01% 70 2671 0.01% 71 2336 0.01% 72 2478 0.01% 73 3173 0.01% 74 2796 0.01% 75 3145 0.01% 76 3318 0.01% 77 3736 0.01% 78 4148 0.01% 79 4716 0.01% 80 5298 0.01% 81 6019 0.02% 82 7048 0.02% 83 9664 0.03% 84 18422 0.05% 85 19407 0.05% 86 20683 0.05% 87 21941 0.06% 88 22120 0.06% 89 22503 0.06% 90 22457 0.06% 91 22222 0.06% 92 22855 0.06% 93 23709 0.06% 94 25160 0.07% 95 26000 0.07% 96 28450 0.07% 97 31224 0.08% 98 32873 0.09% 99 34549 0.09% 100 35042 0.09% 101 36856 0.10% 102 38988 0.10% 103 41518 0.11% 104 44846 0.12% 105 47238 0.12% 106 49910 0.13% 107 52627 0.14% 108 54960 0.14% 109 55286 0.14% 110 56316 0.15% 111 58786 0.15% 112 61486 0.16% 113 64550 0.17% 114 67456 0.18% 115 70349 0.18% 116 75083 0.20% 117 78583 0.20% 118 81879 0.21% 119 86092 0.22% 120 90399 0.24% 121 95616 0.25% 122 100027 0.26% 123 106799 0.28% 124 111654 0.29% 125 119068 0.31% 126 124771 0.32% 127 133034 0.35% 128 143539 0.37% 129 150057 0.39% 130 157788 0.41% 131 167438 0.44% 132 178161 0.46% 133 188255 0.49% 134 199835 0.52% 135 211056 0.55% 136 227355 0.59% 137 248342 0.65% 138 261498 0.68% 139 284323 0.74% 140 315806 0.82% 141 343998 0.90% 142 394803 1.03% 143 449950 1.17% 144 536334 1.40% 145 660374 1.72% 146 879988 2.29% 147 1251135 3.26% 148 2333072 6.07% 149 9439014 24.57% 150 16852920 43.87% 38414298 reads passed initial QC criterion=sequence-density sequence-density=0.98 sequence-density-rank=1 fanout-score=2.06 fanout-score-rank=32 prefix-density=1.00 prefix-fanout=2.0 sequence=AACATGGAGAACATGGCGAGGCGGCCGTTCTTGATCTCCTTCACCTTGAGCTCAGCGAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=35 fanout-score=23.53 fanout-score-rank=1 prefix-density=0.03 prefix-fanout=4.8 sequence=CACCAAATGAATATACTCAATATCTTTATATATGAACAAAAACTTTTCATGCCCAGCAATTGCTTGGATGCAATGCGGTACTTAGGTACAAAGAGTGAAACATCAGAATAATTAAAGTGGCATGCTTAAAAGGTGTAAAGGCAGCTGCCGTCGTCACTCCTTGCTGTTGGGTCGTAGTTCTCGGCATTCCGGTCAGTGCAACCTTCTGGGACGGGCAAATTACCTTGTTGTGCTCCTTTACCTCCTCCTATGCAGCTAGAGATGGTGTGTGTATGAAGAGTGTTCTAACCGTAGAAGGAACCAGTCTTCATGGCATCTGAGTTAGCATCTCCCAGAGCAGCCTCGCTCATGTACTTGTCAGCAAGCTGCACACGCTTGACATTGTCCTGCTCTTGGACGAGCATGTGGCCGTACTCCAGGAGCTTCTCGATTGTCATCTTTGGCTGCTCAAAGGACACCGGTCCATCCTTCGAGTTCACCAGCTTCTTGCCGATGTTCTCTATTCCGGTTG criterion=sequence-density sequence-density=0.50 sequence-density-rank=1 fanout-score=2.13 fanout-score-rank=34 prefix-density=0.51 prefix-fanout=2.1 sequence=TTCGCTGAGCTCAAGGTGAAGGAGATCAAGAACGGCCGCCTCGCCATGTTCTCCATGTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=70.62 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=7.4 sequence=TGCTCATCATCTTGTTTAATACCAAAGCTCTTCATATTCTCCTCCTTGATTTCATCAGCTTGAGGTTAGAGAGATTTGGAAGATGTCTTGCAGCTGTGGATCAAGCTGCAACTGTGGCTCAAACTGCACTTGCGGGAAGATGTACCCAGACCTGGCAGAGCAGGCCAGCACCACCAGCAGCACCCAGGCCCAGGTGGTGGTTCTCGGCATGGCGCCGGAGA SRR8096909 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 08 04:00:54 Started mapping on | Dec 08 04:00:55 Finished on | Dec 08 04:45:50 Mapping speed, Million of reads per hour | 51.31 Number of input reads | 38414298 Average input read length | 291 UNIQUE READS: Uniquely mapped reads number | 36862219 Uniquely mapped reads % | 95.96% Average mapped length | 290.61 Number of splices: Total | 39343730 Number of splices: Annotated (sjdb) | 37127291 Number of splices: GT/AG | 38826910 Number of splices: GC/AG | 454389 Number of splices: AT/AC | 12179 Number of splices: Non-canonical | 50252 Mismatch rate per base, % | 0.30% Deletion rate per base | 0.01% Deletion average length | 2.10 Insertion rate per base | 0.01% Insertion average length | 1.88 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 463123 % of reads mapped to multiple loci | 1.21% Number of reads mapped to too many loci | 11887 % of reads mapped to too many loci | 0.03% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.57% % of reads unmapped: other | 0.24% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1232644 1232644 1232644 N_multimapping 463123 463123 463123 N_noFeature 1410047 35736447 1683652 N_ambiguous 1013592 4552 164677 UnstrandedReadsAssigned:34438580 PositiveStrandReadsAssigned:1121220 NegativeStrandReadsAssigned:35013890 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=149 echo kmer=145 SRR8096909 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: SRR8096909-trimmed-pair1.fastq SRR8096909-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 38,414,298 reads, 35,090,212 reads pseudoaligned [quant] estimated average fragment length: 287.45 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,125 rounds 52973 SRR8096909.ke.tsv 35125 SRR8096909.se.tsv 88098 total ==> SRR8096909.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 650.224 0 0 PNS24247 1044 757.55 112.728 5.95128 PNS24249 1928 1641.55 64.2087 1.56434 PNS24246 1044 757.55 112.728 5.95128 PNS24248 1044 757.55 112.728 5.95128 PNS24244 1471 1184.55 214.609 7.24578 PNS24243 293 78.3387 0 0 KQK14069 1603 1316.55 8712.67 264.67 KQK14071 474 211.019 115.581 21.9057 ==> SRR8096909.se.tsv <== BRADI_1g14170v3 10177 BRADI_1g53295v3 40 BRADI_1g59795v3 1534 BRADI_1g07683v3 0 BRADI_1g00485v3 6 BRADI_1g20270v3 274 BRADI_1g74790v3 92 BRADI_1g09890v3 0 BRADI_1g77505v3 450 BRADI_1g48960v3 0 SRR8096909 completed mapping pipeline successfully