Starting /dee2/code/volunteer_pipeline.sh SRR13165350 current disk space = 1542248984576 free memory = 1603239588 SRR13165350 SRAfilesize cd35fa56783010512da9221b84aeee87 SRR13165350.sra SRR13165350.sra file validated SRR13165350 is paired end SRR13165350 is conventional basespace SRR13165350 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13165350_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.591 37.0 37.0 37.0 37.0 37.0 2 36.099 37.0 37.0 37.0 37.0 37.0 3 36.4665 37.0 37.0 37.0 37.0 37.0 4 36.5895 37.0 37.0 37.0 37.0 37.0 5 36.5975 37.0 37.0 37.0 37.0 37.0 6 36.5455 37.0 37.0 37.0 37.0 37.0 7 36.4455 37.0 37.0 37.0 37.0 37.0 8 36.5125 37.0 37.0 37.0 37.0 37.0 9 36.5485 37.0 37.0 37.0 37.0 37.0 10-14 36.5591 37.0 37.0 37.0 37.0 37.0 15-19 36.5412 37.0 37.0 37.0 37.0 37.0 20-24 36.5403 37.0 37.0 37.0 37.0 37.0 25-29 36.475100000000005 37.0 37.0 37.0 37.0 37.0 30-34 36.47869999999999 37.0 37.0 37.0 37.0 37.0 35-39 36.4171 37.0 37.0 37.0 37.0 37.0 40-44 36.4269 37.0 37.0 37.0 37.0 37.0 45-49 36.299899999999994 37.0 37.0 37.0 37.0 37.0 50-54 36.354600000000005 37.0 37.0 37.0 37.0 37.0 55-59 36.357899999999994 37.0 37.0 37.0 37.0 37.0 60-64 36.3351 37.0 37.0 37.0 37.0 37.0 65-69 36.2755 37.0 37.0 37.0 37.0 37.0 70-74 36.2145 37.0 37.0 37.0 37.0 37.0 75-79 36.2248 37.0 37.0 37.0 37.0 37.0 80-84 36.2535 37.0 37.0 37.0 37.0 37.0 85-89 36.263 37.0 37.0 37.0 37.0 37.0 90-94 36.170899999999996 37.0 37.0 37.0 37.0 37.0 95-99 36.104 37.0 37.0 37.0 37.0 37.0 100-104 36.1147 37.0 37.0 37.0 37.0 37.0 105-109 36.12519999999999 37.0 37.0 37.0 37.0 37.0 110-114 36.08 37.0 37.0 37.0 37.0 37.0 115-119 36.0559 37.0 37.0 37.0 37.0 37.0 120-124 35.9386 37.0 37.0 37.0 37.0 37.0 125-129 35.889500000000005 37.0 37.0 37.0 37.0 37.0 130-134 35.865899999999996 37.0 37.0 37.0 37.0 37.0 135-139 35.7637 37.0 37.0 37.0 37.0 37.0 140-144 35.682 37.0 37.0 37.0 37.0 37.0 145-149 35.425200000000004 37.0 37.0 37.0 37.0 37.0 150-151 35.255250000000004 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 2.0 23 0.0 24 2.0 25 1.0 26 8.0 27 6.0 28 14.0 29 29.0 30 22.0 31 35.0 32 55.0 33 95.0 34 149.0 35 337.0 36 2819.0 37 425.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 50.875 10.85 6.525 31.75 2 24.308002013085055 10.493205837946654 33.03975842979366 32.15903371917464 3 19.625 15.35 25.924999999999997 39.1 4 27.775 20.7 23.325000000000003 28.199999999999996 5 29.025000000000002 25.0 23.225 22.75 6 25.324999999999996 29.675 21.425 23.575 7 18.825 25.324999999999996 37.25 18.6 8 21.15 24.65 28.299999999999997 25.900000000000002 9 22.05 20.0 32.1 25.85 10-14 24.515 25.765 24.89 24.83 15-19 23.555 25.14 25.145 26.16 20-24 24.39 25.009999999999998 24.02 26.58 25-29 24.83 25.240000000000002 24.165 25.765 30-34 24.975 24.529999999999998 24.315 26.179999999999996 35-39 25.16 24.565 24.43 25.845000000000002 40-44 25.44 23.79 25.005 25.765 45-49 24.48 24.425 24.87 26.224999999999998 50-54 24.63 24.695 24.265 26.41 55-59 24.6 24.66 23.965 26.775 60-64 24.55 24.63 24.46 26.36 65-69 25.025 24.2 24.36 26.415 70-74 25.369999999999997 25.074999999999996 24.0 25.555 75-79 25.085 24.525 24.145 26.245 80-84 24.57 23.775 24.795 26.86 85-89 24.92 24.14 23.935000000000002 27.005000000000003 90-94 25.419999999999998 23.880000000000003 24.104999999999997 26.595000000000002 95-99 25.53 24.025 24.005000000000003 26.44 100-104 25.645 25.3 23.615 25.44 105-109 26.345000000000002 24.03 23.29 26.334999999999997 110-114 25.685000000000002 24.01 23.87 26.435 115-119 26.224999999999998 24.965 23.095 25.715 120-124 25.52 24.685000000000002 23.205000000000002 26.590000000000003 125-129 25.55 23.865 23.435 27.150000000000002 130-134 24.91 24.675 23.69 26.724999999999998 135-139 25.724999999999998 23.875 23.72 26.68 140-144 25.945 23.45 24.104999999999997 26.5 145-149 26.424999999999997 22.89 24.305 26.38 150-151 25.162499999999998 23.525 24.087500000000002 27.224999999999998 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.5 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 0.5 21 1.0 22 0.5 23 0.0 24 0.5 25 1.5 26 1.0 27 0.5 28 2.0 29 3.0 30 4.0 31 5.5 32 9.0 33 14.5 34 20.5 35 25.5 36 43.0 37 52.5 38 67.0 39 96.0 40 116.0 41 136.0 42 146.5 43 152.0 44 169.5 45 182.0 46 189.0 47 190.0 48 158.0 49 139.0 50 145.5 51 151.0 52 149.5 53 122.5 54 102.0 55 95.0 56 91.0 57 91.5 58 85.5 59 70.5 60 64.5 61 74.5 62 78.5 63 73.0 64 78.5 65 74.0 66 71.5 67 74.0 68 62.5 69 47.0 70 48.0 71 51.0 72 36.0 73 29.0 74 23.5 75 18.5 76 16.5 77 16.0 78 12.0 79 8.5 80 5.0 81 2.5 82 1.0 83 0.5 84 0.0 85 0.0 86 0.0 87 0.0 88 0.5 89 0.5 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 0.65 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 72.175 #Duplication Level Percentage of deduplicated Percentage of total 1 73.67509525458954 53.175 2 18.35815725666782 26.5 3 5.2649809490820925 11.4 4 1.8704537582265326 5.4 5 0.48493245583650846 1.7500000000000002 6 0.10391409767925182 0.44999999999999996 7 0.13855213023900242 0.7000000000000001 8 0.06927606511950121 0.4 9 0.034638032559750606 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 GCAACCTTCAAGACCATGACTATCAGTTCCACCATATGGTGATCTACTAC 9 0.22499999999999998 No Hit ATTTAATTCATCAAACAGGTCACACACTACATTAGGAAAACGAGCAGGAG 8 0.2 No Hit GTCCTCATCATCCTCTGATTCAGAGAGACAGAGAGAGAGATGGGTTTATG 8 0.2 No Hit GCCCAGTGTTTGGGGAATACCGAAGCTGCAGCCGGAAGGGAGGAGAAGAA 7 0.17500000000000002 No Hit GTCTTCATGTTCTCCTCGAGGTGGCGAAGGTCAATGGCCTGGCACAGAGC 7 0.17500000000000002 No Hit CCTGCCATCTCATTCATAGCACTCTTCTCTGATGTGTGCATATGCATATA 7 0.17500000000000002 No Hit AGAGAAACTGGTGAGCGTGCCGAACGAGACGTACACCACGGAGTTGGCGT 7 0.17500000000000002 No Hit CCCGTTCTCCTCCTCTCCTCTCCTTCCAACTTTCTAGTCTCTCCCTGCGC 6 0.15 No Hit TTCTAGGCAAGGCAGAGATTTCAGCAGCAGCTGGAGGAGCCCGGTCCTGA 6 0.15 No Hit GATCTGTCCACCTTTTCCAGGTCCTTCTCCAACCATCTGTACTGCTCCCC 6 0.15 No Hit AGGTGCATTGCCGTAGAAACGGCCGCCATGACTTTCGTGAGGGGGCGTGT 5 0.125 No Hit GTTCGGCAGATCCTGGAACAACATCAATTTTGGCTTCAGCCCCTAAAGCT 5 0.125 No Hit GGAGGGAGTCGGCCATATCGTCGAGCTGCTGGTGCTGGTGGAACCAGTAG 5 0.125 No Hit CCCATTGCCCCCAGACCAGCTGAAGATAGCCACTGCCGTGGACGCTTGTA 5 0.125 No Hit ATTTCTATGATGTATAAATATTGTGGACTAGAGGGAAGAGATTGTCTCAA 5 0.125 No Hit CGCTGCTACGCCAAAACTCGGCGCAAAGAACCAACCGGATTGCCCCAGTG 5 0.125 No Hit GTCGGCGGGAACAGCTTCCGGAACTGCGCCGGCGCGCCCGCGGGGAGCAT 5 0.125 No Hit TCAGTGAACTCCATCTCGTCCATGCCCTCCCCAGTGTACCAGTGCAAGAA 5 0.125 No Hit GCCTGAACAGGGGATCCCTCTGCCCCGCAGAACCGGCGGACCCCGCGCCG 5 0.125 No Hit GGGGAATTGAACTGAACCGGTCGCATCAGCAGCACCCATGCCGGACTGGC 5 0.125 No Hit GGGTCATTGTCATCATACCCAGCAATCAACAGTGATACACCGAATGGTCT 5 0.125 No Hit GGGAAGGGGATCAACAAACTTGGCCGGTGACGAATTGATCCCAATCCCGA 5 0.125 No Hit GCAGTGAAAGAACCACATCCCTGGGTTGTTGGCGACGAAGCGGATGACGG 5 0.125 No Hit GGCATCTGTCGGTCAGACTGTCACACACAGAAAACGGTATTAACAGGTAA 5 0.125 No Hit >>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 0.0 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 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 60-61 0.1125 0.0 0.0 0.0 0.0 62-63 0.125 0.0 0.0 0.0 0.0 64-65 0.125 0.0 0.0 0.0 0.0 66-67 0.15 0.0 0.0 0.0 0.0 68-69 0.225 0.0 0.0 0.0 0.0 70-71 0.3 0.0 0.0 0.0 0.0 72-73 0.4 0.0 0.0 0.0 0.0 74-75 0.48750000000000004 0.0 0.0 0.0 0.0 76-77 0.6 0.0 0.0 0.0 0.0 78-79 0.7875000000000001 0.0 0.0 0.0 0.0 80-81 0.9 0.0 0.0 0.0 0.0 82-83 0.975 0.0 0.0 0.0 0.0 84-85 1.05 0.0 0.0 0.0 0.0 86-87 1.2875 0.0 0.0 0.0 0.0 88-89 1.6625 0.0 0.0 0.0 0.0 90-91 1.9375 0.0 0.0 0.0 0.0 92-93 2.175 0.0 0.0 0.0 0.0 94-95 2.5875000000000004 0.0 0.0 0.0 0.0 96-97 2.9375 0.0 0.0 0.0 0.0 98-99 3.4749999999999996 0.0 0.0 0.0 0.0 100-101 4.1625 0.0 0.0 0.0 0.0 102-103 4.6875 0.0 0.0 0.0 0.0 104-105 5.075 0.0 0.0 0.0 0.0 106-107 5.7125 0.0 0.0 0.0 0.0 108-109 6.375 0.0 0.0 0.0 0.0 110-111 6.887499999999999 0.0 0.0 0.0 0.0 112-113 7.6 0.0 0.0 0.0 0.0 114-115 8.0875 0.0 0.0 0.0 0.0 116-117 8.6125 0.0 0.0 0.0 0.0 118-119 9.1875 0.0 0.0 0.0 0.0 120-121 9.5375 0.0 0.0 0.0 0.0 122-123 10.3 0.0 0.0 0.0 0.0 124-125 10.962499999999999 0.0 0.0 0.0 0.0 126-127 11.7 0.0 0.0 0.0 0.0 128-129 12.5 0.0 0.0 0.0 0.0 130-131 13.45 0.0 0.0 0.0 0.0 132-133 14.175 0.0 0.0 0.0 0.0 134-135 14.9375 0.0 0.0 0.0 0.0 136-137 15.875 0.0 0.0 0.0 0.0 138-139 16.6375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR13165350 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13165350_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 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.19425 37.0 37.0 37.0 37.0 37.0 2 36.1865 37.0 37.0 37.0 37.0 37.0 3 36.142 37.0 37.0 37.0 37.0 37.0 4 36.243 37.0 37.0 37.0 37.0 37.0 5 36.3795 37.0 37.0 37.0 37.0 37.0 6 36.3325 37.0 37.0 37.0 37.0 37.0 7 36.3205 37.0 37.0 37.0 37.0 37.0 8 36.3065 37.0 37.0 37.0 37.0 37.0 9 36.167 37.0 37.0 37.0 37.0 37.0 10-14 36.297200000000004 37.0 37.0 37.0 37.0 37.0 15-19 36.211 37.0 37.0 37.0 37.0 37.0 20-24 36.180400000000006 37.0 37.0 37.0 37.0 37.0 25-29 36.1524 37.0 37.0 37.0 37.0 37.0 30-34 36.1092 37.0 37.0 37.0 37.0 37.0 35-39 36.1078 37.0 37.0 37.0 37.0 37.0 40-44 36.117599999999996 37.0 37.0 37.0 37.0 37.0 45-49 36.06445 37.0 37.0 37.0 37.0 37.0 50-54 35.9562 37.0 37.0 37.0 37.0 37.0 55-59 36.047999999999995 37.0 37.0 37.0 37.0 37.0 60-64 35.9833 37.0 37.0 37.0 37.0 37.0 65-69 35.99355 37.0 37.0 37.0 37.0 37.0 70-74 35.8832 37.0 37.0 37.0 37.0 37.0 75-79 35.8649 37.0 37.0 37.0 37.0 37.0 80-84 35.915949999999995 37.0 37.0 37.0 37.0 37.0 85-89 35.829950000000004 37.0 37.0 37.0 37.0 37.0 90-94 35.821 37.0 37.0 37.0 37.0 37.0 95-99 35.854699999999994 37.0 37.0 37.0 37.0 37.0 100-104 35.820100000000004 37.0 37.0 37.0 37.0 37.0 105-109 35.7414 37.0 37.0 37.0 37.0 37.0 110-114 35.6528 37.0 37.0 37.0 37.0 37.0 115-119 35.5714 37.0 37.0 37.0 37.0 37.0 120-124 35.4967 37.0 37.0 37.0 37.0 37.0 125-129 35.44175 37.0 37.0 37.0 37.0 37.0 130-134 35.2786 37.0 37.0 37.0 34.6 37.0 135-139 35.14365 37.0 37.0 37.0 27.4 37.0 140-144 34.9049 37.0 37.0 37.0 25.0 37.0 145-149 34.6783 37.0 37.0 37.0 25.0 37.0 150-151 34.355875 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 5 1.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 1.0 13 4.0 14 3.0 15 1.0 16 3.0 17 3.0 18 0.0 19 4.0 20 2.0 21 6.0 22 4.0 23 7.0 24 4.0 25 5.0 26 11.0 27 16.0 28 20.0 29 16.0 30 22.0 31 49.0 32 75.0 33 99.0 34 206.0 35 555.0 36 2611.0 37 272.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 45.221971407072985 18.811136192626034 8.878856282919488 27.088036117381492 2 32.425 22.025 24.2 21.349999999999998 3 24.875 23.775 27.6 23.75 4 27.075 30.3 18.5 24.125 5 28.4 32.25 18.725 20.625 6 24.349999999999998 35.475 18.475 21.7 7 23.525 19.675 31.95 24.85 8 25.575 21.65 23.400000000000002 29.375 9 24.2 21.625 25.05 29.125 10-14 26.38 25.21 22.02 26.39 15-19 25.55 24.455 23.75 26.245 20-24 25.977793338001398 24.647394218265482 23.16695008502551 26.20786235870761 25-29 26.778389194597295 23.921960980490244 23.676838419209606 25.62281140570285 30-34 26.395558223289317 24.65986394557823 22.99919967987195 25.945378151260506 35-39 26.087826347904368 25.277583274982497 22.636791037311195 25.99779933980194 40-44 26.28051220488195 23.79951980792317 23.95958383353341 25.960384153661465 45-49 26.524283499224726 24.21347471615065 23.763317161006352 25.49892462361827 50-54 26.342902870861256 24.5223567070121 23.572071621486444 25.562668800640193 55-59 26.60830415207604 24.482241120560282 23.34167083541771 25.56778389194597 60-64 27.63829148744623 23.477043112933877 23.652095628688606 25.232569770931278 65-69 26.894034105115765 25.258788818322746 22.268340251037657 25.578836825523826 70-74 27.378689344672335 24.73736868434217 22.701350675337668 25.18259129564782 75-79 26.680672268907564 24.399759903961584 23.10924369747899 25.810324129651864 80-84 27.056764191047762 24.33108277069267 23.23080770192548 25.381345336334082 85-89 27.882547146215796 23.645640538242212 23.230453704166877 25.24135861137512 90-94 26.96809042712814 24.52735820746224 22.846854056216863 25.657697309192756 95-99 27.59327798339502 24.62738821646494 22.506752025607682 25.27258177453236 100-104 28.124062031015505 23.38169084542271 23.58679339669835 24.907453726863434 105-109 28.21910955477739 24.682341170585293 22.61630815407704 24.482241120560282 110-114 28.16845053516055 24.392317695308595 23.211963589076724 24.227268180454136 115-119 28.544272136068034 24.977488744372188 22.28614307153577 24.192096048024013 120-124 28.54927463731866 25.012506253126567 22.61630815407704 23.821910955477737 125-129 28.988044620079034 24.250912910809863 23.100395177830023 23.660647291281077 130-134 29.057434460676408 24.244546728036823 23.138883329998 23.559135481288774 135-139 29.541247686227422 23.472910100555307 23.918154985241884 23.067687227975387 140-144 30.299089726918076 23.477043112933877 23.622086625987794 22.60178053416025 145-149 29.63481740870435 23.751875937968983 23.321660830415208 23.291645822911455 150-151 30.7567229518449 23.42714196372733 23.364602876798 22.451532207629768 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.5 14 0.5 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 1.5 23 2.0 24 0.5 25 0.0 26 0.5 27 1.0 28 1.5 29 2.0 30 6.0 31 11.5 32 9.5 33 9.0 34 23.0 35 30.0 36 44.0 37 58.0 38 54.5 39 63.0 40 79.5 41 107.5 42 126.5 43 155.0 44 166.0 45 154.0 46 168.5 47 169.0 48 157.5 49 163.0 50 161.0 51 147.0 52 126.0 53 112.5 54 112.0 55 104.0 56 92.5 57 84.0 58 79.5 59 85.5 60 89.5 61 88.0 62 89.5 63 89.0 64 89.5 65 77.0 66 73.5 67 76.5 68 69.5 69 67.0 70 58.0 71 54.0 72 51.5 73 36.5 74 27.5 75 20.5 76 13.0 77 11.0 78 13.5 79 7.5 80 4.0 81 4.5 82 1.5 83 1.0 84 0.5 85 0.5 86 0.0 87 0.0 88 0.0 89 0.0 90 0.5 91 0.5 92 0.5 93 1.5 94 2.0 95 1.5 96 2.5 97 3.5 98 1.5 99 0.0 100 1.5 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.325 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 0.03 25-29 0.05 30-34 0.04 35-39 0.03 40-44 0.04 45-49 0.034999999999999996 50-54 0.03 55-59 0.05 60-64 0.03 65-69 0.015 70-74 0.05 75-79 0.04 80-84 0.025 85-89 0.045 90-94 0.03 95-99 0.03 100-104 0.05 105-109 0.05 110-114 0.03 115-119 0.05 120-124 0.05 125-129 0.045 130-134 0.06 135-139 0.055 140-144 0.03 145-149 0.05 150-151 0.0625 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 72.175 #Duplication Level Percentage of deduplicated Percentage of total 1 73.9175614825078 53.349999999999994 2 18.115691028749566 26.150000000000002 3 5.230342916522342 11.325000000000001 4 1.6972635954277795 4.9 5 0.6581226186352616 2.375 6 0.17319016279875304 0.75 7 0.10391409767925182 0.525 8 0.06927606511950121 0.4 9 0.034638032559750606 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 GTTACTGCTGCAATATCAATATTTGGTAAAAGATTCTCGCTCCAATTTTC 9 0.22499999999999998 No Hit CTTCCACTAGTATTCTTCAGGGAGGGAAGCTAAGAACTCTCTCTGGAAAT 8 0.2 No Hit TGAGAACAAGCGCGAGTACAACCGCAAAGTTCGTGAGATCGTTGAGCAAA 8 0.2 No Hit GTACCATGTAACAAGGATCATCAACCTTCAAAAAATTATATGCATATGCA 7 0.17500000000000002 No Hit CCGCAACCCGAGCTTGGACTACGGCTTCAAGGGCGCAGAGATCGCCATGG 7 0.17500000000000002 No Hit GGTGCGTGCGCATGGTGAACAACATCTACCTCAACTTCGACGCGCTCAAC 7 0.17500000000000002 No Hit GCACAATGTCGACCGCCGCGGCCAACTGGTGCTACGCAACCGTCGCGCCC 6 0.15 No Hit GCGGCCTATGCTGACTACAGTAAATCAGGGGAGCAGTACAGATGGTTGGA 6 0.15 No Hit CAACGCCGCGGACCAGAGGAGCTTCGGCGAGCTGTTCAACAGCTTCCACG 6 0.15 No Hit TCGGCTTGGTGGGGGGGGAGGCAAGGAGGCGGTGGGGCTCCGGCTTGGTG 6 0.15 No Hit TTAAAATGCTCGCCTTTGACAATTCTGATCATAGGACCTATGTTGACCTT 6 0.15 No Hit GCAATCTCATTCTCTGGTCCAATCGCTGTTTTTGTTTCTGTATTCCTTAT 5 0.125 No Hit ATGTAAAGTATATTTATGCCGAAGTGAGAGAGCGGCTACTCTGTTTCGAG 5 0.125 No Hit GGAATTAGTTCCCAATTCTAGTAAAGTTTATTATTATCAAGAATGTCTCA 5 0.125 No Hit GAAGAAATTGCCCTCTATTTTAGTGGATGAAACATCTGTGCAAAAGATTC 5 0.125 No Hit GGACCGCCGGTTCGACGTCGCCCGGTACAACGCTCTCAAGCACGGCGCGG 5 0.125 No Hit GGTCTACACCGCCGATTTCCCCGACGGGCCCCCGGGGAGCGGCATGGCGA 5 0.125 No Hit ATGTTCCGCCCTGCTGATGGCAAGGAGACTGCTGGGGCATACAAAGTCGC 5 0.125 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 5 0.125 No Hit GAGCGCATCGACATCTGCCAGCTCGCCGTCGCCGATGGCGTCACCATCTG 5 0.125 No Hit CCAGGAGGAAATCATGAGCGCCATGGTCGCGTCGTCGCTGAACCCGGAGG 5 0.125 No Hit GTGGAAGCTTCCCATGTTCGGGTGCACCGACGCCACGCAGGTGCTAAAGG 5 0.125 No Hit GGAAGATGGTGGACTCCTCTGCCGAGTCACAGGCAACTCCTCCTGATATA 5 0.125 No Hit GTTGTTAGGCTTGCTGAATTGGGCTGATTTTCACAGGCTATCTCAATGTG 5 0.125 No Hit CAGCAGAAGAGAGAGTTCCCACTGGCATACAAGACTTTTGGTGAAGCGAT 5 0.125 No Hit ATGAACTTCATGCACCGGGATGAGGAGGTCGACTACTACCCGTCCCGCCA 5 0.125 No Hit GCCTGACAATGTCGTCCACCTTCATCGGCAACTCGACCTCAATCCAGGAG 5 0.125 No Hit CCCAGGACTTCAAGACCGACCTCCGGTTCCAGAGCCACGCCGTGCTGGCG 5 0.125 No Hit GTTGTTCATCTGGAAAGTGGCACTGTTATTGAATATGATTGGCTCGTTTT 5 0.125 No Hit AAAGACGGGCCCCTGGAGCGCGCATTCATGGGGCTCTTCGCCCGGAAGAT 5 0.125 No Hit >>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 0.0 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 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 60-61 0.1125 0.0 0.0 0.0 0.0 62-63 0.125 0.0 0.0 0.0 0.0 64-65 0.125 0.0 0.0 0.0 0.0 66-67 0.15 0.0 0.0 0.0 0.0 68-69 0.225 0.0 0.0 0.0 0.0 70-71 0.3 0.0 0.0 0.0 0.0 72-73 0.4 0.0 0.0 0.0 0.0 74-75 0.48750000000000004 0.0 0.0 0.0 0.0 76-77 0.6 0.0 0.0 0.0 0.0 78-79 0.8125 0.0 0.0 0.0 0.0 80-81 0.925 0.0 0.0 0.0 0.0 82-83 1.0 0.0 0.0 0.0 0.0 84-85 1.075 0.0 0.0 0.0 0.0 86-87 1.3125 0.0 0.0 0.0 0.0 88-89 1.725 0.0 0.0 0.0 0.0 90-91 2.0375 0.0 0.0 0.0 0.0 92-93 2.275 0.0 0.0 0.0 0.0 94-95 2.6875 0.0 0.0 0.0 0.0 96-97 3.0374999999999996 0.0 0.0 0.0 0.0 98-99 3.5999999999999996 0.0 0.0 0.0 0.0 100-101 4.35 0.0 0.0 0.0 0.0 102-103 4.9125 0.0 0.0 0.0 0.0 104-105 5.3125 0.0 0.0 0.0 0.0 106-107 5.95 0.0 0.0 0.0 0.0 108-109 6.6 0.0 0.0 0.0 0.0 110-111 7.112500000000001 0.0 0.0 0.0 0.0 112-113 7.8125 0.0 0.0 0.0 0.0 114-115 8.3125 0.0 0.0 0.0 0.0 116-117 8.837499999999999 0.0 0.0 0.0 0.0 118-119 9.4375 0.0 0.0 0.0 0.0 120-121 9.7625 0.0 0.0 0.0 0.0 122-123 10.525 0.0 0.0 0.0 0.0 124-125 11.1875 0.0 0.0 0.0 0.0 126-127 11.95 0.0 0.0 0.0 0.0 128-129 12.725000000000001 0.0 0.0 0.0 0.0 130-131 13.6875 0.0 0.0 0.0 0.0 132-133 14.4375 0.0 0.0 0.0 0.0 134-135 15.1875 0.0 0.0 0.0 0.0 136-137 16.1 0.0 0.0 0.0 0.0 138-139 16.85 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTTCAGA 10 0.006830828 145.0 8 >>END_MODULE Read 1610565 spots for SRR13165350.sra Written 1610565 spots for SRR13165350.sra Read 1610565 spots for SRR13165350.sra Written 1610565 spots for SRR13165350.sra Read 1610565 spots for SRR13165350.sra Written 1610565 spots for SRR13165350.sra Read 1610565 spots for SRR13165350.sra Written 1610565 spots for SRR13165350.sra Read 1610565 spots for SRR13165350.sra Written 1610565 spots for SRR13165350.sra Read 1610565 spots for SRR13165350.sra Written 1610565 spots for SRR13165350.sra Read 1610580 spots for SRR13165350.sra Written 1610580 spots for SRR13165350.sra Read 1610565 spots for SRR13165350.sra Written 1610565 spots for SRR13165350.sra Read 1610565 spots for SRR13165350.sra Written 1610565 spots for SRR13165350.sra Read 1610565 spots for SRR13165350.sra Written 1610565 spots for SRR13165350.sra Read 1610565 spots for SRR13165350.sra Written 1610565 spots for SRR13165350.sra Read 1610565 spots for SRR13165350.sra Written 1610565 spots for SRR13165350.sra Read 1610565 spots for SRR13165350.sra Written 1610565 spots for SRR13165350.sra Read 1610565 spots for SRR13165350.sra Written 1610565 spots for SRR13165350.sra Read 1610565 spots for SRR13165350.sra Written 1610565 spots for SRR13165350.sra Read 1610565 spots for SRR13165350.sra Written 1610565 spots for SRR13165350.sra Read 1610565 spots for SRR13165350.sra Written 1610565 spots for SRR13165350.sra Read 1610565 spots for SRR13165350.sra Written 1610565 spots for SRR13165350.sra Read 1610565 spots for SRR13165350.sra Written 1610565 spots for SRR13165350.sra Read 1610565 spots for SRR13165350.sra Written 1610565 spots for SRR13165350.sra SRR ids: ['SRR13165350.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_woo5kkm1 SRR13165350.sra spots: 32211315 blocks: [[1, 1610565], [1610566, 3221130], [3221131, 4831695], [4831696, 6442260], [6442261, 8052825], [8052826, 9663390], [9663391, 11273955], [11273956, 12884520], [12884521, 14495085], [14495086, 16105650], [16105651, 17716215], [17716216, 19326780], [19326781, 20937345], [20937346, 22547910], [22547911, 24158475], [24158476, 25769040], [25769041, 27379605], [27379606, 28990170], [28990171, 30600735], [30600736, 32211315]] SRR13165350 file size 10925113 SRR13165350 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 SRR13165350 SRR13165350_1.fastq SRR13165350_2.fastq Input file: SRR13165350_1.fastq Paired file: SRR13165350_2.fastq trimmed: SRR13165350-trimmed-pair1.fastq, SRR13165350-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 Sat Dec 7 15:46:00 2024 >> started Sat Dec 7 15:46:33 2024 >> done (32.896s) 32211315 read pairs processed; of these: 763 ( 0.00%) short read pairs filtered out after trimming by size control 56367 ( 0.17%) empty read pairs filtered out after trimming by size control 32154185 (99.82%) read pairs available; of these: 6396972 (19.89%) trimmed read pairs available after processing 25757213 (80.11%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 57 0.00% 19 53 0.00% 20 65 0.00% 21 75 0.00% 22 64 0.00% 23 95 0.00% 24 131 0.00% 25 147 0.00% 26 145 0.00% 27 174 0.00% 28 168 0.00% 29 160 0.00% 30 222 0.00% 31 211 0.00% 32 217 0.00% 33 276 0.00% 34 247 0.00% 35 247 0.00% 36 284 0.00% 37 300 0.00% 38 324 0.00% 39 316 0.00% 40 392 0.00% 41 416 0.00% 42 446 0.00% 43 444 0.00% 44 433 0.00% 45 604 0.00% 46 526 0.00% 47 629 0.00% 48 704 0.00% 49 739 0.00% 50 939 0.00% 51 1060 0.00% 52 1110 0.00% 53 1189 0.00% 54 1266 0.00% 55 1417 0.00% 56 1537 0.00% 57 1774 0.01% 58 1987 0.01% 59 2237 0.01% 60 2627 0.01% 61 3049 0.01% 62 3391 0.01% 63 3669 0.01% 64 4246 0.01% 65 4522 0.01% 66 4685 0.01% 67 5468 0.02% 68 6050 0.02% 69 6708 0.02% 70 7630 0.02% 71 8654 0.03% 72 9972 0.03% 73 10894 0.03% 74 12225 0.04% 75 13317 0.04% 76 14407 0.04% 77 15518 0.05% 78 16981 0.05% 79 18779 0.06% 80 20419 0.06% 81 23109 0.07% 82 25410 0.08% 83 27765 0.09% 84 30679 0.10% 85 32552 0.10% 86 34189 0.11% 87 35561 0.11% 88 37464 0.12% 89 39677 0.12% 90 41827 0.13% 91 45565 0.14% 92 48163 0.15% 93 51695 0.16% 94 55173 0.17% 95 57633 0.18% 96 58871 0.18% 97 61103 0.19% 98 62100 0.19% 99 63885 0.20% 100 66155 0.21% 101 68466 0.21% 102 70817 0.22% 103 74165 0.23% 104 76654 0.24% 105 78582 0.24% 106 80543 0.25% 107 81591 0.25% 108 83002 0.26% 109 83953 0.26% 110 85280 0.27% 111 88148 0.27% 112 90595 0.28% 113 92148 0.29% 114 95143 0.30% 115 96388 0.30% 116 97975 0.30% 117 100025 0.31% 118 99545 0.31% 119 100111 0.31% 120 102327 0.32% 121 103152 0.32% 122 104310 0.32% 123 106267 0.33% 124 108731 0.34% 125 110740 0.34% 126 111665 0.35% 127 111806 0.35% 128 110233 0.34% 129 113105 0.35% 130 111875 0.35% 131 113021 0.35% 132 115691 0.36% 133 117417 0.37% 134 117696 0.37% 135 119722 0.37% 136 120087 0.37% 137 118197 0.37% 138 119484 0.37% 139 121065 0.38% 140 121802 0.38% 141 121324 0.38% 142 122393 0.38% 143 122974 0.38% 144 125320 0.39% 145 127682 0.40% 146 127799 0.40% 147 130368 0.41% 148 127481 0.40% 149 128149 0.40% 150 126344 0.39% 151 25757213 80.11% 32154185 reads passed initial QC criterion=sequence-density sequence-density=0.47 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=30 prefix-density=0.48 prefix-fanout=2.0 sequence=TAGGCGTCCGGGTACTCCTTCTTGACCTCCTCCAGCTCCTTGAGCACCTG criterion=fanout-score sequence-density=0.03 sequence-density-rank=27 fanout-score=327.21 fanout-score-rank=1 prefix-density=0.63 prefix-fanout=17.0 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.36 sequence-density-rank=1 fanout-score=3.07 fanout-score-rank=23 prefix-density=0.40 prefix-fanout=2.8 sequence=GAGTTCAGCAAGGTCGGCTT criterion=fanout-score sequence-density=0.02 sequence-density-rank=32 fanout-score=101.34 fanout-score-rank=1 prefix-density=0.19 prefix-fanout=8.9 sequence=GCAGCAGCCATTACTTGATCATCTGAAAAATCTTAATCCAGATCAGACCAAGCAGAGCAGAGATGTCTGCTACCTTCTCGTCCACCGTCGGAGCTCCGGCTTCTACGCCAACCAGCTTCCTTGGGAAGAAGCTCAAGAAGCAGGTGACCTCGGCCGTGAACTACCATGGCAAGAGCACCAAGGCCAACAGATTCACAGTCATGGCCAAGGAGGTGGACGAGTCAAAGCAGACTGACCAGGACAGGTGGAAGGGCCTCGCCTACGATATCTCCGACGACCAGCAGGACATCACCAGGGGGAAGGGTATCGTCGACTCGCTCTTCCAGGCGCCCATGGGCGACGGTACCCACGTGGCCGTCCTCAGCTCCCAAGAGTACATCAGCCAGGGCCTAAGGAAGTACGACTTCGACAACA SRR13165350 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 15:47:12 Started mapping on | Dec 07 15:47:12 Finished on | Dec 07 15:49:54 Mapping speed, Million of reads per hour | 714.54 Number of input reads | 32154185 Average input read length | 290 UNIQUE READS: Uniquely mapped reads number | 30468066 Uniquely mapped reads % | 94.76% Average mapped length | 288.83 Number of splices: Total | 28370474 Number of splices: Annotated (sjdb) | 26531691 Number of splices: GT/AG | 28003643 Number of splices: GC/AG | 306441 Number of splices: AT/AC | 12890 Number of splices: Non-canonical | 47500 Mismatch rate per base, % | 0.23% Deletion rate per base | 0.01% Deletion average length | 2.99 Insertion rate per base | 0.01% Insertion average length | 2.44 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 361313 % of reads mapped to multiple loci | 1.12% Number of reads mapped to too many loci | 74716 % of reads mapped to too many loci | 0.23% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.87% % of reads unmapped: other | 1.02% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1325187 1325187 1325187 N_multimapping 361313 361313 361313 N_noFeature 1073257 29621361 1395399 N_ambiguous 636683 4462 112577 UnstrandedReadsAssigned:28758126 PositiveStrandReadsAssigned:842243 NegativeStrandReadsAssigned:28960090 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=150 echo kmer=145 SRR13165350 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: SRR13165350-trimmed-pair1.fastq SRR13165350-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 32,154,185 reads, 29,349,995 reads pseudoaligned [quant] estimated average fragment length: 243.4 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,215 rounds 52973 SRR13165350.ke.tsv 35125 SRR13165350.se.tsv 88098 total ==> SRR13165350.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 694.361 0 0 PNS24247 1044 801.6 83.9537 5.26748 PNS24249 1928 1685.6 232.633 6.94125 PNS24246 1044 801.6 83.9537 5.26748 PNS24248 1044 801.6 83.9537 5.26748 PNS24244 1471 1228.6 105.506 4.31902 PNS24243 293 112.23 0 0 KQK14069 1603 1360.6 608.333 22.487 KQK14071 474 253.171 5.71039 1.13441 ==> SRR13165350.se.tsv <== BRADI_1g14170v3 646 BRADI_1g53295v3 226 BRADI_1g59795v3 622 BRADI_1g07683v3 0 BRADI_1g00485v3 19 BRADI_1g20270v3 683 BRADI_1g74790v3 601 BRADI_1g09890v3 0 BRADI_1g77505v3 442 BRADI_1g48960v3 0 SRR13165350 completed mapping pipeline successfully