Starting /dee2/code/volunteer_pipeline.sh SRR13165389 current disk space = 1541305143296 free memory = 1602379396 SRR13165389 SRAfilesize ffcee0de24ee1546e6a584061c13ff8b SRR13165389.sra SRR13165389.sra file validated SRR13165389 is paired end SRR13165389 is conventional basespace SRR13165389 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13165389_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.5545 37.0 37.0 37.0 37.0 37.0 2 36.11375 37.0 37.0 37.0 37.0 37.0 3 36.51 37.0 37.0 37.0 37.0 37.0 4 36.5465 37.0 37.0 37.0 37.0 37.0 5 36.5175 37.0 37.0 37.0 37.0 37.0 6 36.526 37.0 37.0 37.0 37.0 37.0 7 36.482 37.0 37.0 37.0 37.0 37.0 8 36.61 37.0 37.0 37.0 37.0 37.0 9 36.513 37.0 37.0 37.0 37.0 37.0 10-14 36.5428 37.0 37.0 37.0 37.0 37.0 15-19 36.518299999999996 37.0 37.0 37.0 37.0 37.0 20-24 36.4956 37.0 37.0 37.0 37.0 37.0 25-29 36.4458 37.0 37.0 37.0 37.0 37.0 30-34 36.4292 37.0 37.0 37.0 37.0 37.0 35-39 36.3857 37.0 37.0 37.0 37.0 37.0 40-44 36.353899999999996 37.0 37.0 37.0 37.0 37.0 45-49 36.3431 37.0 37.0 37.0 37.0 37.0 50-54 36.3548 37.0 37.0 37.0 37.0 37.0 55-59 36.335699999999996 37.0 37.0 37.0 37.0 37.0 60-64 36.281 37.0 37.0 37.0 37.0 37.0 65-69 36.2566 37.0 37.0 37.0 37.0 37.0 70-74 36.244899999999994 37.0 37.0 37.0 37.0 37.0 75-79 36.2549 37.0 37.0 37.0 37.0 37.0 80-84 36.182 37.0 37.0 37.0 37.0 37.0 85-89 36.1649 37.0 37.0 37.0 37.0 37.0 90-94 36.095 37.0 37.0 37.0 37.0 37.0 95-99 36.112700000000004 37.0 37.0 37.0 37.0 37.0 100-104 36.0762 37.0 37.0 37.0 37.0 37.0 105-109 36.0438 37.0 37.0 37.0 37.0 37.0 110-114 36.0269 37.0 37.0 37.0 37.0 37.0 115-119 35.9622 37.0 37.0 37.0 37.0 37.0 120-124 35.950900000000004 37.0 37.0 37.0 37.0 37.0 125-129 35.960699999999996 37.0 37.0 37.0 37.0 37.0 130-134 35.87349999999999 37.0 37.0 37.0 37.0 37.0 135-139 35.7142 37.0 37.0 37.0 37.0 37.0 140-144 35.6596 37.0 37.0 37.0 37.0 37.0 145-149 35.3519 37.0 37.0 37.0 37.0 37.0 150-151 35.16 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 0.0 24 3.0 25 3.0 26 7.0 27 9.0 28 15.0 29 25.0 30 30.0 31 32.0 32 57.0 33 95.0 34 158.0 35 343.0 36 2838.0 37 384.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 55.925000000000004 9.0 5.1499999999999995 29.925 2 21.833291362377235 11.130697557290354 32.183329136237724 34.85268194409469 3 19.275000000000002 14.95 26.825 38.95 4 26.075 22.375 22.2 29.349999999999998 5 29.325000000000003 26.674999999999997 21.55 22.45 6 23.549999999999997 31.0 20.849999999999998 24.6 7 19.45 25.85 35.6 19.1 8 20.3 25.874999999999996 29.375 24.45 9 19.900000000000002 21.099999999999998 34.125 24.875 10-14 23.085 26.715 25.77 24.43 15-19 23.885 24.745 26.14 25.230000000000004 20-24 23.23 25.474999999999998 24.97 26.325 25-29 23.064999999999998 25.435000000000002 25.650000000000002 25.85 30-34 23.165 25.95 25.485000000000003 25.4 35-39 23.3 25.405 25.47 25.825 40-44 23.025000000000002 25.919999999999998 25.119999999999997 25.935000000000002 45-49 22.785 25.45 25.545 26.22 50-54 23.885 26.22 24.725 25.169999999999998 55-59 23.150000000000002 25.979999999999997 25.275 25.595000000000002 60-64 23.275000000000002 25.974999999999998 25.05 25.7 65-69 24.474999999999998 25.415 24.18 25.929999999999996 70-74 23.52 26.479999999999997 24.125 25.874999999999996 75-79 23.43 24.875 25.419999999999998 26.275 80-84 24.044999999999998 25.105 24.865000000000002 25.985000000000003 85-89 24.68 24.445 25.064999999999998 25.81 90-94 23.705000000000002 26.015 24.75 25.53 95-99 24.099999999999998 25.695 24.925 25.28 100-104 24.04 26.009999999999998 24.965 24.985 105-109 24.705 25.779999999999998 24.545 24.97 110-114 24.175 25.650000000000002 24.51 25.665 115-119 23.745 25.545 25.14 25.569999999999997 120-124 23.45 25.31 25.055 26.185000000000002 125-129 24.115000000000002 26.08 23.98 25.825 130-134 24.265 25.86 24.285 25.590000000000003 135-139 23.665 26.165 23.95 26.22 140-144 24.335 24.884999999999998 24.545 26.235000000000003 145-149 24.295 25.105 24.175 26.424999999999997 150-151 24.7375 25.4875 22.95 26.825 >>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 0.5 6 0.5 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 0.5 23 0.5 24 0.0 25 0.5 26 3.0 27 4.0 28 2.0 29 8.0 30 15.0 31 11.5 32 13.0 33 17.5 34 22.5 35 37.5 36 60.0 37 68.0 38 71.5 39 95.0 40 129.0 41 144.5 42 136.5 43 161.5 44 212.5 45 202.0 46 178.0 47 208.5 48 203.5 49 171.5 50 162.5 51 146.5 52 130.5 53 118.0 54 118.5 55 105.0 56 95.0 57 95.5 58 73.0 59 63.0 60 72.0 61 62.5 62 51.5 63 62.0 64 58.5 65 51.0 66 53.0 67 52.0 68 44.5 69 36.0 70 31.5 71 28.0 72 20.5 73 21.0 74 22.5 75 19.0 76 12.5 77 3.0 78 3.5 79 3.5 80 1.0 81 1.0 82 1.5 83 1.5 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 0.0 2 0.7250000000000001 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 71.05 #Duplication Level Percentage of deduplicated Percentage of total 1 72.97677691766363 51.849999999999994 2 18.1210415200563 25.75 3 6.01688951442646 12.825000000000001 4 1.688951442646024 4.8 5 0.7389162561576355 2.625 6 0.211118930330753 0.8999999999999999 7 0.211118930330753 1.05 8 0.03518648838845883 0.2 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source CTCGGCGACTGTGTCGACGAAGACGCGGACACGGTTAGGGATGAAATCGG 8 0.2 No Hit GCACGACACATGGACCATACGAACAATAAAGTGTGGCAAGCCACAAGTAT 7 0.17500000000000002 No Hit CCACGTATGGACTATGGAGCGGGAGATCAGCTGGATTTTGATGAAATTGA 7 0.17500000000000002 No Hit GGTAGCTTTTCATAAATCCAGCAACAAGATTGCGGAAGTTTAAACATCCA 7 0.17500000000000002 No Hit GAGTACAGCAAATGAATGATCATGGTTCTTATTCATTCAGTACATCTACA 7 0.17500000000000002 No Hit ACCGAATATCTGCGCGAGTTTAATCGCCTTGCTATGCCCCAAAAGATGTA 7 0.17500000000000002 No Hit GCTAGGAATCCCTTGAAGTACTTACTATTCATCTGAACGGTACCACGTGA 7 0.17500000000000002 No Hit ACCAGGCTGCTTTAGAGAGACGCGGAAGGTAAGCTTCCCACAGAACTCGG 6 0.15 No Hit CGTCAACGCGGAACCTGCACATAAATAAACGGGCGTTTGGCACAAATCAT 6 0.15 No Hit CTCGGGAGAGGCGAAGAGGAAGCAGTCGGCGGCGAGGACCTTGGCGCGGA 6 0.15 No Hit ACCAGAGTGCAGTTTATTGTTCAATCCGAGATCTGATATCGGGATGAGCA 6 0.15 No Hit ATGTACAAGTTAGAAGTTCTTTGTTTCAGAAAGAAAACAACTCAGAAATT 6 0.15 No Hit GGCTTCCAGCAGCGGCAGAGCAGGAGGCCGTTGCAGCAGTCCAAGATATC 6 0.15 No Hit GCCATCTACAAGTTCTTGACACAAGCGAAATGTCTCCTCCCCTACAACTT 5 0.125 No Hit GCATGCTACTTTCATGGCCAAGGACATGACCTATCCTTTTTCCACTCTCA 5 0.125 No Hit GTCATCTGTCTGCTGCTTGACCTGCCTGATCTTCTTGGCCAGATTGTTTC 5 0.125 No Hit GTTCGTTAAAATTCTTGTGACCCCGTTTTTCCCGATCTTCTCCTCGTCCG 5 0.125 No Hit CTCACGGAAAAAACGCTTACAGAACAATGTCTTCTCTGGATCAAGCCTGT 5 0.125 No Hit GTAAAAAATATACCGAAGCACCAAAAGGGTAAATTGTCAAACCGACTCAA 5 0.125 No Hit GGACAGATCATGGCTAGCTAGCTTCATTCATGGTTTCCCCCATCCATGCA 5 0.125 No Hit GATCAGTATATAAAGCCACAACAGAACAACACACTTTGTCTCCATTTCTC 5 0.125 No Hit CCGGTTAATGTAGTATTCCTGCCGCATGACCTTTAAATCGTAATCCCCTT 5 0.125 No Hit AGCAATGCCAGAGCAAACATGCAGGCAACACCTTGGCTCGCCATTTGGAC 5 0.125 No Hit GTCAGTGGTGGGCCGGGTTACTGATGAGGTGGTTGCGGATCGGCACTTCG 5 0.125 No Hit GGGTCATCGGCTTCCGCCTGGGGCTGCTGCTGCTGCTGCGTCTGGCGCTG 5 0.125 No Hit GTACAATAGGTGCTGGTGCAGCAGCTGCTGGAGGTGCTGGCACCACCGGT 5 0.125 No Hit GGTTGCCATCGACCAGACAAACTCTGACCCAGAGATCCAGAGTGGCAAAA 5 0.125 No Hit GATACTTTTCATGATCTGAGATAACTTCGACAATTTGTTGTATGGAATGG 5 0.125 No Hit CAGAGATTGATAAACTGGATGACTTTCGCTAATTGCTGATTCGCAAGGTT 5 0.125 No Hit GCCATCTGGATCGTCAGCCCGCGCGCCGGCAGGCCCATCCCGCCGCCTAC 5 0.125 No Hit CTCTGATCTCGCATCTACCATCGAATTATCCTGATCTTCATCACCTAAAC 5 0.125 No Hit GTTGGTTAGCTGGTCCTAGAAGAGAGGCTTGGAGATGAGGCACTGGGTGC 5 0.125 No Hit CACAACAAAATAAGAGCAAGGACAACAATCCCTTGAGGAGCACCAGTTGC 5 0.125 No Hit CACTCCCTTCCGTCCAACCTTGCTCATAGCCTCTGCTATCATGTTACCGA 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 0.0 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.0875 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.125 0.0 0.0 0.0 0.0 60-61 0.15 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 0.225 0.0 0.0 0.0 0.0 68-69 0.3125 0.0 0.0 0.0 0.0 70-71 0.375 0.0 0.0 0.0 0.0 72-73 0.4 0.0 0.0 0.0 0.0 74-75 0.475 0.0 0.0 0.0 0.0 76-77 0.5125 0.0 0.0 0.0 0.0 78-79 0.55 0.0 0.0 0.0 0.0 80-81 0.6875 0.0 0.0 0.0 0.0 82-83 0.775 0.0 0.0 0.0 0.0 84-85 1.0125 0.0 0.0 0.0 0.0 86-87 1.1875 0.0 0.0 0.0 0.0 88-89 1.6 0.0 0.0 0.0 0.0 90-91 1.95 0.0 0.0 0.0 0.0 92-93 2.1624999999999996 0.0 0.0 0.0 0.0 94-95 2.475 0.0 0.0 0.0 0.0 96-97 3.0125 0.0 0.0 0.0 0.0 98-99 3.2875 0.0 0.0 0.0 0.0 100-101 3.6500000000000004 0.0 0.0 0.0 0.0 102-103 4.2125 0.0 0.0 0.0 0.0 104-105 4.824999999999999 0.0 0.0 0.0 0.0 106-107 5.6 0.0 0.0 0.0 0.0 108-109 6.0375 0.0 0.0 0.0 0.0 110-111 6.4625 0.0 0.0 0.0 0.0 112-113 6.825 0.0 0.0 0.0 0.0 114-115 7.175 0.0 0.0 0.0 0.0 116-117 7.9 0.0 0.0 0.0 0.0 118-119 8.6375 0.0 0.0 0.0 0.0 120-121 9.3 0.0 0.0 0.0 0.0 122-123 9.8625 0.0 0.0 0.0 0.0 124-125 10.475 0.0 0.0 0.0 0.0 126-127 11.2 0.0 0.0 0.0 0.0 128-129 11.9375 0.0 0.0 0.0 0.0 130-131 12.65 0.0 0.0 0.0 0.0 132-133 13.1875 0.0 0.0 0.0 0.0 134-135 13.962499999999999 0.0 0.0 0.0 0.0 136-137 14.524999999999999 0.0 0.0 0.0 0.0 138-139 15.05 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CATGAAT 10 0.006830828 145.0 3 TAAGTGC 10 0.006830828 145.0 5 CATTTGT 10 0.006830828 145.0 145 AGTGCCA 10 0.006830828 145.0 7 TGCCAGT 10 0.006830828 145.0 9 GTAAGTG 10 0.006830828 145.0 4 GGTAAGT 10 0.006830828 145.0 3 CCGAAAG 10 0.006830828 145.0 3 GTGCCAG 10 0.006830828 145.0 8 >>END_MODULE SRR13165389 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13165389_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.064 37.0 37.0 37.0 37.0 37.0 2 36.119 37.0 37.0 37.0 37.0 37.0 3 36.0675 37.0 37.0 37.0 37.0 37.0 4 36.143 37.0 37.0 37.0 37.0 37.0 5 36.2135 37.0 37.0 37.0 37.0 37.0 6 36.147 37.0 37.0 37.0 37.0 37.0 7 36.175 37.0 37.0 37.0 37.0 37.0 8 36.225 37.0 37.0 37.0 37.0 37.0 9 36.141 37.0 37.0 37.0 37.0 37.0 10-14 36.129599999999996 37.0 37.0 37.0 37.0 37.0 15-19 36.047799999999995 37.0 37.0 37.0 37.0 37.0 20-24 36.0252 37.0 37.0 37.0 37.0 37.0 25-29 35.917 37.0 37.0 37.0 37.0 37.0 30-34 35.8818 37.0 37.0 37.0 37.0 37.0 35-39 35.862300000000005 37.0 37.0 37.0 37.0 37.0 40-44 35.937599999999996 37.0 37.0 37.0 37.0 37.0 45-49 35.83669999999999 37.0 37.0 37.0 37.0 37.0 50-54 35.8322 37.0 37.0 37.0 37.0 37.0 55-59 35.819 37.0 37.0 37.0 37.0 37.0 60-64 35.7941 37.0 37.0 37.0 37.0 37.0 65-69 35.7342 37.0 37.0 37.0 37.0 37.0 70-74 35.7039 37.0 37.0 37.0 37.0 37.0 75-79 35.7676 37.0 37.0 37.0 37.0 37.0 80-84 35.7141 37.0 37.0 37.0 37.0 37.0 85-89 35.64 37.0 37.0 37.0 37.0 37.0 90-94 35.5966 37.0 37.0 37.0 37.0 37.0 95-99 35.550599999999996 37.0 37.0 37.0 37.0 37.0 100-104 35.552800000000005 37.0 37.0 37.0 37.0 37.0 105-109 35.5807 37.0 37.0 37.0 37.0 37.0 110-114 35.50170000000001 37.0 37.0 37.0 37.0 37.0 115-119 35.4292 37.0 37.0 37.0 37.0 37.0 120-124 35.288 37.0 37.0 37.0 37.0 37.0 125-129 35.29690000000001 37.0 37.0 37.0 37.0 37.0 130-134 35.0878 37.0 37.0 37.0 29.8 37.0 135-139 34.8779 37.0 37.0 37.0 25.0 37.0 140-144 34.7884 37.0 37.0 37.0 25.0 37.0 145-149 34.632 37.0 37.0 37.0 25.0 37.0 150-151 34.195750000000004 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 8.0 14 13.0 15 8.0 16 5.0 17 4.0 18 1.0 19 3.0 20 5.0 21 5.0 22 6.0 23 5.0 24 6.0 25 4.0 26 8.0 27 9.0 28 12.0 29 17.0 30 24.0 31 43.0 32 74.0 33 138.0 34 238.0 35 656.0 36 2513.0 37 194.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 50.05017561465128 18.740592072252884 7.551430005017562 23.657802308078274 2 29.599999999999998 23.275000000000002 25.724999999999998 21.4 3 23.45 24.95 28.9 22.7 4 25.924999999999997 29.049999999999997 21.875 23.150000000000002 5 28.15 31.6 20.175 20.075000000000003 6 22.45 35.825 19.3 22.425 7 23.525 18.875 34.375 23.225 8 24.85 23.474999999999998 24.825 26.85 9 23.150000000000002 21.275 28.225 27.35 10-14 26.275 25.61 23.45 24.665 15-19 25.285000000000004 24.64 24.58 25.495 20-24 25.36 25.490000000000002 24.12 25.03 25-29 26.36 24.560000000000002 24.5 24.58 30-34 25.119999999999997 25.75 24.685000000000002 24.445 35-39 25.55 25.34 24.41 24.7 40-44 26.19 24.8 24.14 24.87 45-49 25.55 25.905 24.654999999999998 23.89 50-54 25.685000000000002 24.84 24.955 24.52 55-59 26.790000000000003 25.945 23.95 23.315 60-64 25.480000000000004 24.495 25.555 24.47 65-69 25.795 26.009999999999998 24.0 24.195 70-74 27.089999999999996 25.124999999999996 24.415 23.369999999999997 75-79 26.13 26.06 23.86 23.95 80-84 26.3 25.14 24.555 24.005000000000003 85-89 25.929999999999996 25.490000000000002 24.965 23.615 90-94 26.555 24.855 24.654999999999998 23.935000000000002 95-99 26.474999999999998 24.985 24.635 23.905 100-104 26.419999999999998 24.845 24.48 24.255 105-109 26.495 25.8 23.955000000000002 23.75 110-114 27.365000000000002 25.95 23.93 22.755 115-119 28.04 26.040000000000003 22.884999999999998 23.035 120-124 27.66 25.295 24.235 22.81 125-129 28.21 26.119999999999997 23.23 22.439999999999998 130-134 29.5 25.1 23.66 21.740000000000002 135-139 29.7 24.834999999999997 23.785 21.68 140-144 29.775000000000002 25.435000000000002 23.200000000000003 21.59 145-149 31.46 25.174999999999997 22.765 20.599999999999998 150-151 31.8625 24.675 22.325 21.1375 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.5 3 1.0 4 0.5 5 0.5 6 1.0 7 0.5 8 0.0 9 0.0 10 0.5 11 1.0 12 2.0 13 2.0 14 1.0 15 0.5 16 0.5 17 0.5 18 0.5 19 0.5 20 0.0 21 0.0 22 1.5 23 3.0 24 1.5 25 0.0 26 1.0 27 2.5 28 4.5 29 5.5 30 4.0 31 7.5 32 15.5 33 23.0 34 25.0 35 29.0 36 39.5 37 52.0 38 67.0 39 93.0 40 124.5 41 142.0 42 146.0 43 143.0 44 156.5 45 194.0 46 219.5 47 227.0 48 207.0 49 166.0 50 147.0 51 141.0 52 132.0 53 118.5 54 110.5 55 95.0 56 98.5 57 98.0 58 82.0 59 80.0 60 62.5 61 52.0 62 62.0 63 64.5 64 51.0 65 47.5 66 48.0 67 47.5 68 58.0 69 59.5 70 43.5 71 39.0 72 34.5 73 20.0 74 15.0 75 19.5 76 18.0 77 8.5 78 7.0 79 4.5 80 0.0 81 1.0 82 1.0 83 0.5 84 1.0 85 0.5 86 0.0 87 1.0 88 1.0 89 0.5 90 0.5 91 1.5 92 2.0 93 0.5 94 0.0 95 0.0 96 0.5 97 1.5 98 1.5 99 1.5 100 3.5 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.35000000000000003 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 71.825 #Duplication Level Percentage of deduplicated Percentage of total 1 74.13853115210581 53.25 2 17.298990602158025 24.85 3 5.708318830490776 12.3 4 1.6359206404455273 4.7 5 0.7657500870170553 2.75 6 0.20884093282283328 0.8999999999999999 7 0.20884093282283328 1.05 8 0.034806822137138885 0.2 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source CTACCACACGCAACACACCACGCCCTAAATTAGCAGCTGATATTCCATTA 8 0.2 No Hit CTTGACCCCAGTGTGCACTCTTTTCATTAATCTGCTTATACTCGAATAAG 7 0.17500000000000002 No Hit GGAAGACTCAACGTGGTGCCTAAGAATAGAATCCTAACTTTCCTAACGAG 7 0.17500000000000002 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 7 0.17500000000000002 No Hit AACGACTGTTACCAACGACATCATTGGCGACACCTCAGGATACTACAAGG 7 0.17500000000000002 No Hit GGGTGGCAAACCGAATTTTGCCCAGGCTGGTGGTCGGCAGCCGGAGAACC 7 0.17500000000000002 No Hit GCAAGATGGATTTCATGATGTCAGCAGCTCCCTCGATTTATCGTTCGATG 7 0.17500000000000002 No Hit GGCTCGCTATTTCATCAACGTCTCGGGCGAAGGCGACCCGCTTATCGATG 6 0.15 No Hit ATCGAAGAGATGGAAGGGTCGACGGCGGCGAAGCGGACGACGTTAAGAGT 6 0.15 No Hit AATAAAGAAAAAATGTTCTTACCATTACATTGACTTATCCTCAGGGCTTG 6 0.15 No Hit GTTGGCTTCTCCTCCCCCTCACTAGTCCTCGGTTCCGGTTCCGGTTCGTT 6 0.15 No Hit GTTTGGCAAATTAAAGACTCCTGTATTCAATGAGTGGGTTTCGTTTATTG 6 0.15 No Hit CACAAATTCCTCTCCTCCACCCTTTCCCCGTGAACACGCCGCGTCCACCC 6 0.15 No Hit TCCTGACATTATCGCTGGACAAGGAACTGTTGGCATGGAAATTGTTCGCC 5 0.125 No Hit AGCTGCTGCAGGCCAATGGGGCCAGACTCGCACTCACTGATTGCAATAAC 5 0.125 No Hit GTGTGAACGGGAGCATCTCAGGCAGCCATAATGGAAGCAATGTACAGAAT 5 0.125 No Hit ACCTTACTGAGACTATGGGTCATACTGGTGAATCAGTTCCAGGACCTGGA 5 0.125 No Hit CGGAGAACAAATTGGAAATAATTAAAAGAAGGAAACAACATGGAATGTGT 5 0.125 No Hit AGAGGCCACATCTCCACATTTTCCTCCAAAAGATGGCTGAGATGTTTGAC 5 0.125 No Hit ATCATCTACACTCTGGTCACAGTGTGTGGGTATAAAAGTGTCATCAAGTT 5 0.125 No Hit GGAAAAAAGGAGGATCAGAAGGGGATGGAAATGGTGAGGAGGAGGATGTC 5 0.125 No Hit GTTTTTGATTGTGTAAACAATTGCATAGTATTGCCAACAGAATATTATGT 5 0.125 No Hit ATACGCTGGAGTAGCGCCCGAAAGGTGGATCGAAGGAGTCATGAGAAGCT 5 0.125 No Hit AATCTTACGAGGTATTAAAAGTAGCGATTGCCTAATCATCGGTCCAAACT 5 0.125 No Hit GTCTTTTACTCGGTGCAAGCGGCAGGCCGGCCGGCGTTCCCGGTCTCGAC 5 0.125 No Hit CCCAAAGCCGCCGAAATGTCGTCGGAGCCGCCTCCACCTGCATCCGCCCC 5 0.125 No Hit CATAGAACTATTTTTCTCCGGTTGAGCAGCTCATAATGGATGCTCATATT 5 0.125 No Hit GCAAAGTTCTTGAAAACAACTTCCTTGTGATAATGCTTAGACAGAATAAG 5 0.125 No Hit AAGAACTAGAAGCACATGTATCTATGGTGGAGCACCTAAGGGACCACAGA 5 0.125 No Hit GCATTCCCCAAGTAGACCGGACAAGGCGCGGCAGCTTTGCGCGGAAATCT 5 0.125 No Hit CCTGCCTTCTCCACGCGACAGCAATGGCGTCCTTCACGCTGGTGGGGGCC 5 0.125 No Hit CAACCTACAGTTTCTTGGAGGAAAACAAAATGCTTATCGGCTAAGAGTAG 5 0.125 No Hit GCCAAGGAGAGCTTCACAAAGACTTTGGTCTTACACACACACACCCCATA 5 0.125 No Hit GGTCGTTGCTGAGGATCTAGCTAGCTCCAATTGAGACCGATATTAGTTGG 5 0.125 No Hit GTGATCAAGACCTGTGGGACTACCATGCTCCTGCTCACCATTCCAAGGAT 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 0.0 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.0875 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.125 0.0 0.0 0.0 0.0 60-61 0.15 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 0.225 0.0 0.0 0.0 0.0 68-69 0.3125 0.0 0.0 0.0 0.0 70-71 0.375 0.0 0.0 0.0 0.0 72-73 0.4 0.0 0.0 0.0 0.0 74-75 0.475 0.0 0.0 0.0 0.0 76-77 0.4875 0.0 0.0 0.0 0.0 78-79 0.525 0.0 0.0 0.0 0.0 80-81 0.6499999999999999 0.0 0.0 0.0 0.0 82-83 0.725 0.0 0.0 0.0 0.0 84-85 0.9625 0.0 0.0 0.0 0.0 86-87 1.1375000000000002 0.0 0.0 0.0 0.0 88-89 1.6 0.0 0.0 0.0 0.0 90-91 1.925 0.0 0.0 0.0 0.0 92-93 2.1375 0.0 0.0 0.0 0.0 94-95 2.45 0.0 0.0 0.0 0.0 96-97 2.9875 0.0 0.0 0.0 0.0 98-99 3.2625 0.0 0.0 0.0 0.0 100-101 3.625 0.0 0.0 0.0 0.0 102-103 4.1875 0.0 0.0 0.0 0.0 104-105 4.800000000000001 0.0 0.0 0.0 0.0 106-107 5.55 0.0 0.0 0.0 0.0 108-109 5.9875 0.0 0.0 0.0 0.0 110-111 6.45 0.0 0.0 0.0 0.0 112-113 6.825 0.0 0.0 0.0 0.0 114-115 7.175 0.0 0.0 0.0 0.0 116-117 7.887499999999999 0.0 0.0 0.0 0.0 118-119 8.6375 0.0 0.0 0.0 0.0 120-121 9.3 0.0 0.0 0.0 0.0 122-123 9.8625 0.0 0.0 0.0 0.0 124-125 10.475 0.0 0.0 0.0 0.0 126-127 11.225000000000001 0.0 0.0 0.0 0.0 128-129 11.95 0.0 0.0 0.0 0.0 130-131 12.65 0.0 0.0 0.0 0.0 132-133 13.1375 0.0 0.0 0.0 0.0 134-135 13.912500000000001 0.0 0.0 0.0 0.0 136-137 14.4375 0.0 0.0 0.0 0.0 138-139 15.0125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTCGCCT 10 0.006830828 145.0 8 CGAGCTT 10 0.006830828 145.0 2 GCTTTCG 10 0.006830828 145.0 5 CGCCGGT 10 0.006830828 145.0 8 TTTCGCC 10 0.006830828 145.0 7 CTTTCGC 10 0.006830828 145.0 6 GGGGGGG 155 2.875396E-4 14.032258 145 >>END_MODULE Read 1669334 spots for SRR13165389.sra Written 1669334 spots for SRR13165389.sra Read 1669334 spots for SRR13165389.sra Written 1669334 spots for SRR13165389.sra Read 1669334 spots for SRR13165389.sra Written 1669334 spots for SRR13165389.sra Read 1669334 spots for SRR13165389.sra Written 1669334 spots for SRR13165389.sra Read 1669334 spots for SRR13165389.sra Written 1669334 spots for SRR13165389.sra Read 1669334 spots for SRR13165389.sra Written 1669334 spots for SRR13165389.sra Read 1669334 spots for SRR13165389.sra Written 1669334 spots for SRR13165389.sra Read 1669334 spots for SRR13165389.sra Written 1669334 spots for SRR13165389.sra Read 1669334 spots for SRR13165389.sra Written 1669334 spots for SRR13165389.sra Read 1669334 spots for SRR13165389.sra Written 1669334 spots for SRR13165389.sra Read 1669334 spots for SRR13165389.sra Written 1669334 spots for SRR13165389.sra Read 1669334 spots for SRR13165389.sra Written 1669334 spots for SRR13165389.sra Read 1669334 spots for SRR13165389.sra Written 1669334 spots for SRR13165389.sra Read 1669334 spots for SRR13165389.sra Written 1669334 spots for SRR13165389.sra Read 1669334 spots for SRR13165389.sra Written 1669334 spots for SRR13165389.sra Read 1669334 spots for SRR13165389.sra Written 1669334 spots for SRR13165389.sra Read 1669349 spots for SRR13165389.sra Written 1669349 spots for SRR13165389.sra Read 1669334 spots for SRR13165389.sra Written 1669334 spots for SRR13165389.sra Read 1669334 spots for SRR13165389.sra Written 1669334 spots for SRR13165389.sra Read 1669334 spots for SRR13165389.sra Written 1669334 spots for SRR13165389.sra SRR ids: ['SRR13165389.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_7um30mrl SRR13165389.sra spots: 33386695 blocks: [[1, 1669334], [1669335, 3338668], [3338669, 5008002], [5008003, 6677336], [6677337, 8346670], [8346671, 10016004], [10016005, 11685338], [11685339, 13354672], [13354673, 15024006], [15024007, 16693340], [16693341, 18362674], [18362675, 20032008], [20032009, 21701342], [21701343, 23370676], [23370677, 25040010], [25040011, 26709344], [26709345, 28378678], [28378679, 30048012], [30048013, 31717346], [31717347, 33386695]] SRR13165389 file size 11324559 SRR13165389 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 SRR13165389 SRR13165389_1.fastq SRR13165389_2.fastq Input file: SRR13165389_1.fastq Paired file: SRR13165389_2.fastq trimmed: SRR13165389-trimmed-pair1.fastq, SRR13165389-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 17:33:10 2024 >> started Sat Dec 7 17:33:48 2024 >> done (37.775s) 33386695 read pairs processed; of these: 997 ( 0.00%) short read pairs filtered out after trimming by size control 36388 ( 0.11%) empty read pairs filtered out after trimming by size control 33349310 (99.89%) read pairs available; of these: 6454201 (19.35%) trimmed read pairs available after processing 26895109 (80.65%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 59 0.00% 19 66 0.00% 20 80 0.00% 21 105 0.00% 22 131 0.00% 23 132 0.00% 24 154 0.00% 25 205 0.00% 26 159 0.00% 27 227 0.00% 28 245 0.00% 29 226 0.00% 30 273 0.00% 31 269 0.00% 32 217 0.00% 33 280 0.00% 34 268 0.00% 35 302 0.00% 36 278 0.00% 37 329 0.00% 38 335 0.00% 39 373 0.00% 40 418 0.00% 41 469 0.00% 42 538 0.00% 43 541 0.00% 44 599 0.00% 45 601 0.00% 46 647 0.00% 47 778 0.00% 48 859 0.00% 49 954 0.00% 50 1110 0.00% 51 1217 0.00% 52 1457 0.00% 53 1490 0.00% 54 1760 0.01% 55 1862 0.01% 56 2081 0.01% 57 2392 0.01% 58 2720 0.01% 59 2971 0.01% 60 3525 0.01% 61 4013 0.01% 62 4555 0.01% 63 5251 0.02% 64 5799 0.02% 65 6338 0.02% 66 6941 0.02% 67 7734 0.02% 68 8272 0.02% 69 9245 0.03% 70 10623 0.03% 71 11868 0.04% 72 13353 0.04% 73 14726 0.04% 74 16232 0.05% 75 18338 0.05% 76 19861 0.06% 77 21353 0.06% 78 23050 0.07% 79 24639 0.07% 80 26463 0.08% 81 29079 0.09% 82 30820 0.09% 83 33596 0.10% 84 36328 0.11% 85 38758 0.12% 86 40777 0.12% 87 42893 0.13% 88 45047 0.14% 89 46712 0.14% 90 49442 0.15% 91 51108 0.15% 92 53251 0.16% 93 55773 0.17% 94 58337 0.17% 95 59940 0.18% 96 62299 0.19% 97 64154 0.19% 98 65941 0.20% 99 67454 0.20% 100 68470 0.21% 101 69539 0.21% 102 71986 0.22% 103 73802 0.22% 104 74786 0.22% 105 77931 0.23% 106 78509 0.24% 107 79991 0.24% 108 82731 0.25% 109 84211 0.25% 110 84391 0.25% 111 87022 0.26% 112 88116 0.26% 113 88149 0.26% 114 90816 0.27% 115 91857 0.28% 116 92890 0.28% 117 95025 0.28% 118 96751 0.29% 119 97076 0.29% 120 99031 0.30% 121 100794 0.30% 122 100651 0.30% 123 101978 0.31% 124 104666 0.31% 125 104988 0.31% 126 106800 0.32% 127 107057 0.32% 128 107871 0.32% 129 109634 0.33% 130 109512 0.33% 131 110617 0.33% 132 112923 0.34% 133 114118 0.34% 134 115008 0.34% 135 115950 0.35% 136 115860 0.35% 137 115738 0.35% 138 117814 0.35% 139 119226 0.36% 140 119049 0.36% 141 121344 0.36% 142 121430 0.36% 143 122098 0.37% 144 124775 0.37% 145 125568 0.38% 146 124773 0.37% 147 125784 0.38% 148 125996 0.38% 149 126367 0.38% 150 128667 0.39% 151 26895109 80.65% 33349310 reads passed initial QC criterion=sequence-density sequence-density=0.17 sequence-density-rank=1 fanout-score=18.53 fanout-score-rank=6 prefix-density=0.40 prefix-fanout=7.8 sequence=TCTCCAGCTCCTT criterion=fanout-score sequence-density=0.06 sequence-density-rank=32 fanout-score=316.60 fanout-score-rank=1 prefix-density=0.86 prefix-fanout=23.3 sequence=CTTCTTCTTCCCTGCCTCAATCGCCATCTTCTTCGTCTTCCCCAGCTGCTGC criterion=sequence-density sequence-density=0.38 sequence-density-rank=1 fanout-score=2.14 fanout-score-rank=35 prefix-density=0.39 prefix-fanout=2.1 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.05 sequence-density-rank=34 fanout-score=152.09 fanout-score-rank=1 prefix-density=0.43 prefix-fanout=16.4 sequence=AAGGAGGAGGAAGAAGA SRR13165389 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 17:34:31 Started mapping on | Dec 07 17:34:31 Finished on | Dec 07 17:37:23 Mapping speed, Million of reads per hour | 698.01 Number of input reads | 33349310 Average input read length | 289 UNIQUE READS: Uniquely mapped reads number | 31612796 Uniquely mapped reads % | 94.79% Average mapped length | 288.50 Number of splices: Total | 30080508 Number of splices: Annotated (sjdb) | 27891237 Number of splices: GT/AG | 29591993 Number of splices: GC/AG | 416405 Number of splices: AT/AC | 16675 Number of splices: Non-canonical | 55435 Mismatch rate per base, % | 0.25% Deletion rate per base | 0.01% Deletion average length | 2.46 Insertion rate per base | 0.01% Insertion average length | 2.44 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 423469 % of reads mapped to multiple loci | 1.27% Number of reads mapped to too many loci | 51277 % of reads mapped to too many loci | 0.15% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.08% % of reads unmapped: other | 0.71% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1313450 1313450 1313450 N_multimapping 423469 423469 423469 N_noFeature 1518625 30714342 1853947 N_ambiguous 674639 3902 112078 UnstrandedReadsAssigned:29419532 PositiveStrandReadsAssigned:894552 NegativeStrandReadsAssigned:29646771 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR13165389 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: SRR13165389-trimmed-pair1.fastq SRR13165389-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 33,349,310 reads, 30,143,100 reads pseudoaligned [quant] estimated average fragment length: 241.58 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,207 rounds 52973 SRR13165389.ke.tsv 35125 SRR13165389.se.tsv 88098 total ==> SRR13165389.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 696 0 0 PNS24247 1044 803.42 146.595 9.27686 PNS24249 1928 1687.42 187.158 5.6391 PNS24246 1044 803.42 146.595 9.27686 PNS24248 1044 803.42 146.595 9.27686 PNS24244 1471 1230.42 251.057 10.3739 PNS24243 293 111.973 0 0 KQK14069 1603 1362.42 54321.9 2027.16 KQK14071 474 254.771 938.723 187.331 ==> SRR13165389.se.tsv <== BRADI_1g14170v3 59261 BRADI_1g53295v3 844 BRADI_1g59795v3 1442 BRADI_1g07683v3 0 BRADI_1g00485v3 3 BRADI_1g20270v3 526 BRADI_1g74790v3 612 BRADI_1g09890v3 0 BRADI_1g77505v3 476 BRADI_1g48960v3 0 SRR13165389 completed mapping pipeline successfully