Starting /dee2/code/volunteer_pipeline.sh SRR7473330 current disk space = 1542975422464 free memory = 1603246032 SRR7473330 SRAfilesize bea877c66571a881e06940579c209cac SRR7473330.sra SRR7473330.sra file validated SRR7473330 is paired end SRR7473330 is conventional basespace SRR7473330 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7473330_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.46875 34.0 34.0 34.0 33.0 34.0 2 33.4875 34.0 34.0 34.0 33.0 34.0 3 33.5585 34.0 34.0 34.0 33.0 34.0 4 33.50925 34.0 34.0 34.0 33.0 34.0 5 33.544 34.0 34.0 34.0 33.0 34.0 6 37.29 38.0 38.0 38.0 36.0 38.0 7 37.491 38.0 38.0 38.0 37.0 38.0 8 37.6105 38.0 38.0 38.0 38.0 38.0 9 37.59925 38.0 38.0 38.0 38.0 38.0 10-14 37.483850000000004 38.0 38.0 38.0 37.8 38.0 15-19 37.57355 38.0 38.0 38.0 38.0 38.0 20-24 37.55195 38.0 38.0 38.0 38.0 38.0 25-29 37.4764 38.0 38.0 38.0 37.8 38.0 30-34 37.3609 38.0 38.0 38.0 37.4 38.0 35-39 37.46835 38.0 38.0 38.0 38.0 38.0 40-44 37.101549999999996 38.0 38.0 38.0 36.6 38.0 45-49 37.240300000000005 38.0 38.0 38.0 37.0 38.0 50-54 37.0728 38.0 38.0 38.0 36.4 38.0 55-59 37.048500000000004 38.0 38.0 38.0 36.2 38.0 60-64 37.229 38.0 38.0 38.0 37.0 38.0 65-69 37.048649999999995 38.0 38.0 38.0 36.4 38.0 70-74 37.117200000000004 38.0 38.0 38.0 37.0 38.0 75-79 36.9584 38.0 38.0 38.0 36.8 38.0 80-84 36.833299999999994 38.0 38.0 38.0 36.0 38.0 85-89 36.8435 38.0 38.0 38.0 36.0 38.0 90-94 36.7971 38.0 38.0 38.0 35.8 38.0 95-99 36.697199999999995 38.0 38.0 38.0 35.6 38.0 100-104 36.620999999999995 38.0 38.0 38.0 35.2 38.0 105-109 36.3957 38.0 38.0 38.0 34.6 38.0 110-114 36.34275000000001 38.0 38.0 38.0 34.0 38.0 115-119 36.2338 38.0 38.0 38.0 34.0 38.0 120-124 36.08335 38.0 38.0 38.0 33.6 38.0 125-129 35.84295000000001 38.0 37.6 38.0 33.0 38.0 130-134 35.60715 38.0 37.2 38.0 32.4 38.0 135-139 35.253750000000004 38.0 36.0 38.0 30.6 38.0 140-144 35.13545 38.0 36.0 38.0 30.6 38.0 145-149 34.618 38.0 35.4 38.0 28.0 38.0 150-151 30.88925 36.5 30.0 38.0 11.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 7 1.0 8 1.0 9 0.0 10 3.0 11 1.0 12 0.0 13 3.0 14 2.0 15 4.0 16 7.0 17 4.0 18 6.0 19 12.0 20 4.0 21 6.0 22 9.0 23 6.0 24 3.0 25 11.0 26 14.0 27 9.0 28 18.0 29 28.0 30 33.0 31 43.0 32 48.0 33 71.0 34 100.0 35 191.0 36 478.0 37 2884.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.25 10.65 11.475 38.625 2 24.36827620715537 14.83612709532149 31.37353014761071 29.422066549912433 3 21.75 20.1 24.5 33.650000000000006 4 26.05 26.625 21.925 25.4 5 26.450000000000003 29.625 23.225 20.7 6 21.525 31.85 25.275 21.349999999999998 7 15.9 22.400000000000002 41.725 19.975 8 20.075000000000003 23.200000000000003 29.7 27.025 9 18.675 22.1 33.1 26.125 10-14 21.515 26.715 25.385 26.384999999999998 15-19 21.78 24.94 26.85 26.43 20-24 21.68 25.885 26.855 25.580000000000002 25-29 21.845 25.485000000000003 26.47 26.200000000000003 30-34 21.52 25.525 26.52 26.435 35-39 22.439999999999998 25.56 26.02 25.979999999999997 40-44 22.185 25.119999999999997 26.87 25.825 45-49 22.189999999999998 25.335 26.919999999999998 25.555 50-54 22.7 25.495 25.94 25.865 55-59 22.23 25.395 26.419999999999998 25.955000000000002 60-64 22.040000000000003 24.92 26.525 26.515 65-69 21.75 25.335 26.565 26.35 70-74 21.915000000000003 26.44 25.395 26.25 75-79 21.82 26.345000000000002 25.480000000000004 26.355 80-84 21.505 26.005 26.125 26.365 85-89 22.085 25.465 26.064999999999998 26.384999999999998 90-94 22.805 24.87 25.674999999999997 26.650000000000002 95-99 22.005 25.005 26.77 26.22 100-104 22.39 25.53 25.75 26.33 105-109 22.285 25.86 25.105 26.75 110-114 22.435 25.71 25.415 26.44 115-119 22.49 25.61 25.53 26.369999999999997 120-124 22.415 25.3 24.959999999999997 27.325 125-129 22.955000000000002 25.105 25.729999999999997 26.21 130-134 22.915 25.165 25.635 26.284999999999997 135-139 22.6 25.66 25.195 26.545 140-144 23.535 25.669999999999998 24.195 26.6 145-149 23.40638446912839 25.75302711898329 24.587211047733412 26.253377364154908 150-151 23.125 25.275 24.637500000000003 26.9625 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.5 4 0.5 5 0.0 6 1.5 7 2.0 8 0.5 9 0.5 10 1.0 11 0.5 12 0.5 13 1.0 14 0.5 15 1.0 16 1.0 17 1.0 18 1.0 19 0.5 20 0.5 21 0.5 22 1.0 23 0.5 24 1.5 25 3.0 26 4.5 27 6.0 28 8.5 29 13.5 30 21.5 31 26.5 32 29.0 33 40.0 34 50.5 35 55.0 36 65.0 37 82.5 38 98.0 39 100.0 40 100.5 41 116.5 42 148.0 43 161.5 44 165.0 45 168.0 46 161.0 47 142.0 48 149.0 49 159.0 50 146.5 51 155.5 52 160.0 53 170.0 54 186.0 55 175.0 56 141.0 57 117.0 58 93.5 59 80.5 60 76.5 61 63.0 62 61.0 63 48.5 64 37.0 65 33.0 66 26.0 67 23.0 68 16.5 69 14.5 70 16.0 71 15.5 72 11.5 73 9.5 74 9.5 75 7.5 76 5.5 77 4.0 78 2.0 79 1.0 80 0.5 81 0.5 82 0.5 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.075 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 0.06999999999999999 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 89.14999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 92.93325855300057 82.85 2 4.8233314638250135 8.6 3 1.1777902411665733 3.15 4 0.532809871003926 1.9 5 0.11217049915872125 0.5 6 0.2243409983174425 1.2 7 0.028042624789680313 0.17500000000000002 8 0.056085249579360626 0.4 9 0.028042624789680313 0.22499999999999998 >10 0.08412787436904094 1.0 >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 GTCGGTTCGGTCCTCCAGTTAGTGTTACCCAACCTTCAACCTGCCCATGG 14 0.35000000000000003 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATCTCGTATGC 14 0.35000000000000003 TruSeq Adapter, Index 7 (97% over 36bp) CCCCACTGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGT 12 0.3 No Hit CCCACTGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTG 9 0.22499999999999998 No Hit GTTGATTTCTTTTCCTCGGGGTACTTAGATGTTTCAGTTCCCCCGGTTCG 8 0.2 No Hit CGGGGATTTCACATCTGACTTAACAAACCGCCTGCGTGCGCTTTACGCCC 8 0.2 No Hit GGGGATTTCACATCTGACTTAACAAACCGCCTGCGTGCGCTTTACGCCCA 7 0.17500000000000002 No Hit CCCACGCTTTCGCACCTGAGCGTCAGTCTTCGTCCAGGGGGCCGCCTTCG 6 0.15 No Hit CCACGCTTTCGCACCTGAGCGTCAGTCTTCGTCCAGGGGGCCGCCTTCGC 6 0.15 No Hit CCCCCCTCTACGAGACTCAAGCTTGCCAGTATCAGATGCAGTTCCCAGGT 6 0.15 No Hit GTCAGTCAGGAGTATTTAGCCTTGGAGGATGGTCCCCCCATATTCAGACA 6 0.15 No Hit CTTCGCAGTAACACCAAGTACAGGAATATTAACCTGTTTCCCATCGACTA 6 0.15 No Hit CCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCT 6 0.15 No Hit GGAAGCTATACTATATAGGTGGCTATCTATCCCTACCAAGGCTTATATTG 6 0.15 No Hit CCCATATTCAGACAGGATACCACGTGTCCCGCCCTACTCATCGAGCTCAC 6 0.15 No Hit GTCCGCTTGCTCTCGCGAGGTCGCTTCTCTTTGTATGCGCCATTGTAGCA 5 0.125 No Hit CTTGGTCTTCCGGCGAGCGGGCTTTTCACCCGCTTTATCGTTACTTATGT 5 0.125 No Hit CCCCGGTTCGCCTCATTAACCTATGGATTCAGTTAATGATAGTGTGTCGA 5 0.125 No Hit CCCCTTCGCAGTAACACCAAGTACAGGAATATTAACCTGTTTCCCATCGA 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 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.037500000000000006 0.0 0.0 0.0 0.0 68-69 0.0625 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.1125 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0 0.0 78-79 0.1375 0.0 0.0 0.0 0.0 80-81 0.21250000000000002 0.0 0.0 0.0 0.0 82-83 0.3375 0.0 0.0 0.0 0.0 84-85 0.4625 0.0 0.0 0.0 0.0 86-87 0.5125 0.0 0.0 0.0 0.0 88-89 0.65 0.0 0.0 0.0 0.0 90-91 0.7375 0.0 0.0 0.0 0.0 92-93 0.9125 0.0 0.0 0.0 0.0 94-95 1.075 0.0 0.0 0.0 0.0 96-97 1.2375 0.0 0.0 0.0 0.0 98-99 1.3625 0.0 0.0 0.0 0.0 100-101 1.6 0.0 0.0 0.0 0.0 102-103 1.8625 0.0 0.0 0.0 0.0 104-105 2.1875 0.0 0.0 0.0 0.0 106-107 2.525 0.0 0.0 0.0 0.0 108-109 2.9124999999999996 0.0 0.0 0.0 0.0 110-111 3.2874999999999996 0.0 0.0 0.0 0.0 112-113 3.8125 0.0 0.0 0.0 0.0 114-115 4.275 0.0 0.0 0.0 0.0 116-117 4.8125 0.0 0.0 0.0 0.0 118-119 5.225 0.0 0.0 0.0 0.0 120-121 5.612500000000001 0.0 0.0 0.0 0.0 122-123 5.9125 0.0 0.0 0.0 0.0 124-125 6.2875 0.0 0.0 0.0 0.0 126-127 6.7375 0.0 0.0 0.0 0.0 128-129 7.2125 0.0 0.0 0.0 0.0 130-131 7.975 0.0 0.0 0.0 0.0 132-133 8.4875 0.0 0.0 0.0 0.0 134-135 9.0 0.0 0.0 0.0 0.0 136-137 9.6875 0.0 0.0 0.0 0.0 138-139 10.4625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTGTATA 10 0.006830828 145.0 1 CACAAAT 10 0.006830828 145.0 1 >>END_MODULE SRR7473330 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7473330_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.15275 34.0 33.0 34.0 32.0 34.0 2 33.21325 34.0 33.0 34.0 33.0 34.0 3 33.15125 34.0 33.0 34.0 33.0 34.0 4 33.08375 34.0 33.0 34.0 33.0 34.0 5 33.071 34.0 33.0 34.0 33.0 34.0 6 37.17375 38.0 38.0 38.0 37.0 38.0 7 37.068 38.0 38.0 38.0 37.0 38.0 8 37.14575 38.0 38.0 38.0 37.0 38.0 9 37.16 38.0 38.0 38.0 37.0 38.0 10-14 37.053 38.0 38.0 38.0 37.0 38.0 15-19 37.1625 38.0 38.0 38.0 37.2 38.0 20-24 37.13765 38.0 38.0 38.0 37.2 38.0 25-29 37.1707 38.0 38.0 38.0 37.6 38.0 30-34 37.1936 38.0 38.0 38.0 38.0 38.0 35-39 37.0064 38.0 38.0 38.0 37.0 38.0 40-44 37.07595 38.0 38.0 38.0 37.0 38.0 45-49 37.1169 38.0 38.0 38.0 37.2 38.0 50-54 37.1142 38.0 38.0 38.0 37.0 38.0 55-59 37.10365 38.0 38.0 38.0 37.0 38.0 60-64 37.05395 38.0 38.0 38.0 37.0 38.0 65-69 36.8262 38.0 38.0 38.0 36.4 38.0 70-74 36.74025 38.0 38.0 38.0 36.0 38.0 75-79 36.7462 38.0 38.0 38.0 36.0 38.0 80-84 36.66665 38.0 38.0 38.0 36.0 38.0 85-89 36.61815 38.0 38.0 38.0 35.8 38.0 90-94 36.41365 38.0 38.0 38.0 35.0 38.0 95-99 36.45635 38.0 38.0 38.0 35.0 38.0 100-104 36.298700000000004 38.0 38.0 38.0 34.6 38.0 105-109 36.12925 38.0 38.0 38.0 34.2 38.0 110-114 35.89784999999999 38.0 38.0 38.0 33.6 38.0 115-119 35.4415 38.0 37.4 38.0 31.2 38.0 120-124 35.7362 38.0 38.0 38.0 33.2 38.0 125-129 35.5007 38.0 37.4 38.0 32.6 38.0 130-134 35.13520000000001 38.0 36.2 38.0 29.8 38.0 135-139 34.909099999999995 38.0 36.0 38.0 29.4 38.0 140-144 34.35345 38.0 35.2 38.0 27.2 38.0 145-149 33.71785 38.0 34.2 38.0 21.6 38.0 150-151 29.509375 35.5 27.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 6.0 3 4.0 4 3.0 5 0.0 6 1.0 7 0.0 8 1.0 9 2.0 10 1.0 11 4.0 12 8.0 13 2.0 14 3.0 15 5.0 16 5.0 17 19.0 18 9.0 19 6.0 20 4.0 21 7.0 22 7.0 23 12.0 24 10.0 25 15.0 26 23.0 27 19.0 28 28.0 29 20.0 30 26.0 31 33.0 32 47.0 33 78.0 34 121.0 35 189.0 36 471.0 37 2811.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.4 18.65 14.2 27.750000000000004 2 32.299224418313734 22.61696272204153 24.69352014010508 20.390292719539655 3 24.0990990990991 26.45145145145145 26.401401401401404 23.04804804804805 4 27.89882294014525 31.129476584022036 20.33558727773604 20.63611319809667 5 27.7027027027027 31.356356356356358 19.094094094094093 21.846846846846844 6 22.8 35.425000000000004 20.65 21.125 7 22.025 19.2 36.875 21.9 8 25.7 23.525 22.475 28.299999999999997 9 24.975 23.925 24.625 26.474999999999998 10-14 27.145858343337338 25.890356142456984 21.998799519807925 24.964985994397757 15-19 26.9480844253276 26.067820346103833 23.507052115634693 23.477043112933877 20-24 27.457745774577457 26.547654765476548 22.597259725972595 23.397339733973396 25-29 26.71167791947987 26.156539134783696 24.0960240060015 23.035758939734936 30-34 27.095000000000002 26.295 24.235 22.375 35-39 27.60552110422084 25.69013802760552 23.73474694938988 22.969593918783758 40-44 27.459118867830174 26.048907336100413 23.933590038505777 22.558383757563636 45-49 26.74302290687206 26.15784735420626 24.487346203861158 22.611783535060518 50-54 26.678003401020305 25.682704811443436 24.67740322096629 22.96188856656997 55-59 26.42028405681136 26.14022804560912 24.93998799759952 22.499499899979998 60-64 26.68700915411935 25.916662498124154 24.466009704366964 22.930318643389526 65-69 26.95021265949462 25.94445834375782 24.563422566925194 22.54190642982237 70-74 27.011752938234558 26.296574143535885 24.646161540385098 22.045511377844463 75-79 26.21893283992599 26.1039155873381 25.143771565734863 22.53338000700105 80-84 27.224083612541882 26.35895384307646 24.108616292443866 22.30834625193779 85-89 27.045 25.765 24.285 22.905 90-94 26.851712928232057 26.296574143535885 24.491122780695175 22.360590147536886 95-99 26.3913195659783 26.721336066803342 24.351217560878045 22.536126806340317 100-104 27.765 26.6 24.545 21.09 105-109 26.65933076576802 26.984444555594457 23.868353923873357 22.487870754764167 110-114 26.30656788145775 27.723267921505805 24.279134961954345 21.691029235082098 115-119 26.816565676799037 27.612799839751617 23.81190845811007 21.758726025339275 120-124 27.063531765882942 26.848424212106053 24.542271135567784 21.54577288644322 125-129 27.41 27.42 23.97 21.2 130-134 26.895000000000003 26.474999999999998 24.645 21.985 135-139 27.689999999999998 26.83 23.835 21.645 140-144 27.284999999999997 26.76 24.395 21.560000000000002 145-149 27.735 26.55 24.04 21.675 150-151 27.4125 27.8625 22.5625 22.162499999999998 >>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 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 1.0 21 3.0 22 3.5 23 3.5 24 3.5 25 4.0 26 5.0 27 6.5 28 6.5 29 8.5 30 12.0 31 18.5 32 22.0 33 21.0 34 35.0 35 48.5 36 52.0 37 59.0 38 80.0 39 103.0 40 101.5 41 98.5 42 115.0 43 125.0 44 136.0 45 139.5 46 149.0 47 165.0 48 159.5 49 159.5 50 158.0 51 147.0 52 154.5 53 204.5 54 213.5 55 196.0 56 176.5 57 129.0 58 100.0 59 93.5 60 80.0 61 68.5 62 70.0 63 56.0 64 39.0 65 26.5 66 31.5 67 37.0 68 29.0 69 25.5 70 27.5 71 25.0 72 16.0 73 13.0 74 13.5 75 8.0 76 5.5 77 4.0 78 3.0 79 3.5 80 1.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.075 3 0.1 4 0.17500000000000002 5 0.1 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.04 15-19 0.03 20-24 0.01 25-29 0.025 30-34 0.0 35-39 0.02 40-44 0.015 45-49 0.03 50-54 0.03 55-59 0.02 60-64 0.045 65-69 0.075 70-74 0.025 75-79 0.015 80-84 0.015 85-89 0.0 90-94 0.025 95-99 0.005 100-104 0.0 105-109 0.034999999999999996 110-114 0.12 115-119 0.155 120-124 0.05 125-129 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 89.075 #Duplication Level Percentage of deduplicated Percentage of total 1 93.32023575638507 83.125 2 4.602862756104406 8.200000000000001 3 1.094583216390682 2.9250000000000003 4 0.36486107213022734 1.3 5 0.25259612685938815 1.125 6 0.028066236317709797 0.15 7 0.11226494527083919 0.7000000000000001 8 0.028066236317709797 0.2 9 0.028066236317709797 0.22499999999999998 >10 0.16839741790625876 2.0500000000000003 >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 GCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAG 16 0.4 No Hit CTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAA 15 0.375 No Hit GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 15 0.375 Illumina Single End PCR Primer 1 (100% over 50bp) GCGACTTATATTCTGTAGCAAGGTTAACCGAATAGGGGAGCCGAAGGGAA 13 0.325 No Hit GGTGGATGCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGAT 12 0.3 No Hit GGTGAGTCGACCCCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGGAAACA 11 0.27499999999999997 No Hit GGGAAACCGAGTCTTAACTGGGCGTTAAGTTGCAGGGTATAGACCCGAAA 9 0.22499999999999998 No Hit CAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTA 8 0.2 No Hit GTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAA 7 0.17500000000000002 No Hit GGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTA 7 0.17500000000000002 No Hit CAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCC 7 0.17500000000000002 No Hit CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGAT 7 0.17500000000000002 No Hit GGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGATAAGCGTCGGTAA 6 0.15 No Hit GCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAG 5 0.125 No Hit CGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGT 5 0.125 No Hit GGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTT 5 0.125 No Hit CTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTG 5 0.125 No Hit CCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATGG 5 0.125 No Hit GTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTT 5 0.125 No Hit CGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATG 5 0.125 No Hit CCCGGTTTAAGCGTGTAGGCTGGTTTTCCAGGCAAATCCGGAAAATCAAG 5 0.125 No Hit GGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATG 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 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.037500000000000006 0.0 0.0 0.0 0.0 68-69 0.0625 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.1125 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.1875 0.0 0.0 0.0 0.0 82-83 0.3125 0.0 0.0 0.0 0.0 84-85 0.4375 0.0 0.0 0.0 0.0 86-87 0.4875 0.0 0.0 0.0 0.0 88-89 0.625 0.0 0.0 0.0 0.0 90-91 0.7125 0.0 0.0 0.0 0.0 92-93 0.8875 0.0 0.0 0.0 0.0 94-95 1.05 0.0 0.0 0.0 0.0 96-97 1.2125 0.0 0.0 0.0 0.0 98-99 1.3250000000000002 0.0 0.0 0.0 0.0 100-101 1.55 0.0 0.0 0.0 0.0 102-103 1.7999999999999998 0.0 0.0 0.0 0.0 104-105 2.1 0.0 0.0 0.0 0.0 106-107 2.425 0.0 0.0 0.0 0.0 108-109 2.8375000000000004 0.0 0.0 0.0 0.0 110-111 3.2125000000000004 0.0 0.0 0.0 0.0 112-113 3.7375 0.0 0.0 0.0 0.0 114-115 4.175 0.0 0.0 0.0 0.0 116-117 4.75 0.0 0.0 0.0 0.0 118-119 5.1375 0.0 0.0 0.0 0.0 120-121 5.487500000000001 0.0 0.0 0.0 0.0 122-123 5.775 0.0 0.0 0.0 0.0 124-125 6.1625 0.0 0.0 0.0 0.0 126-127 6.574999999999999 0.0 0.0 0.0 0.0 128-129 7.025 0.0 0.0 0.0 0.0 130-131 7.7625 0.0 0.0 0.0 0.0 132-133 8.337499999999999 0.0 0.0 0.0 0.0 134-135 8.837499999999999 0.0 0.0 0.0 0.0 136-137 9.475000000000001 0.0 0.0 0.0 0.0 138-139 10.2875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 797096 spots for SRR7473330.sra Written 797096 spots for SRR7473330.sra Read 797096 spots for SRR7473330.sra Written 797096 spots for SRR7473330.sra Read 797096 spots for SRR7473330.sra Written 797096 spots for SRR7473330.sra Read 797096 spots for SRR7473330.sra Written 797096 spots for SRR7473330.sra Read 797096 spots for SRR7473330.sra Written 797096 spots for SRR7473330.sra Read 797096 spots for SRR7473330.sra Written 797096 spots for SRR7473330.sra Read 797096 spots for SRR7473330.sra Written 797096 spots for SRR7473330.sra Read 797096 spots for SRR7473330.sra Written 797096 spots for SRR7473330.sra Read 797096 spots for SRR7473330.sra Written 797096 spots for SRR7473330.sra Read 797096 spots for SRR7473330.sra Written 797096 spots for SRR7473330.sra Read 797096 spots for SRR7473330.sra Written 797096 spots for SRR7473330.sra Read 797096 spots for SRR7473330.sra Written 797096 spots for SRR7473330.sra Read 797096 spots for SRR7473330.sra Written 797096 spots for SRR7473330.sra Read 797115 spots for SRR7473330.sra Written 797115 spots for SRR7473330.sra Read 797096 spots for SRR7473330.sra Written 797096 spots for SRR7473330.sra Read 797096 spots for SRR7473330.sra Written 797096 spots for SRR7473330.sra Read 797096 spots for SRR7473330.sra Written 797096 spots for SRR7473330.sra Read 797096 spots for SRR7473330.sra Written 797096 spots for SRR7473330.sra Read 797096 spots for SRR7473330.sra Written 797096 spots for SRR7473330.sra Read 797096 spots for SRR7473330.sra Written 797096 spots for SRR7473330.sra SRR ids: ['SRR7473330.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_4z529m2w SRR7473330.sra spots: 15941939 blocks: [[1, 797096], [797097, 1594192], [1594193, 2391288], [2391289, 3188384], [3188385, 3985480], [3985481, 4782576], [4782577, 5579672], [5579673, 6376768], [6376769, 7173864], [7173865, 7970960], [7970961, 8768056], [8768057, 9565152], [9565153, 10362248], [10362249, 11159344], [11159345, 11956440], [11956441, 12753536], [12753537, 13550632], [13550633, 14347728], [14347729, 15144824], [15144825, 15941939]] SRR7473330 file size 5380499 SRR7473330 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 SRR7473330 SRR7473330_1.fastq SRR7473330_2.fastq Input file: SRR7473330_1.fastq Paired file: SRR7473330_2.fastq trimmed: SRR7473330-trimmed-pair1.fastq, SRR7473330-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 13:36:07 2024 >> started Sat Dec 7 13:36:31 2024 >> done (24.558s) 15941939 read pairs processed; of these: 30656 ( 0.19%) short read pairs filtered out after trimming by size control 84280 ( 0.53%) empty read pairs filtered out after trimming by size control 15827003 (99.28%) read pairs available; of these: 7604378 (48.05%) trimmed read pairs available after processing 8222625 (51.95%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 10 0.00% 19 16 0.00% 20 17 0.00% 21 13 0.00% 22 21 0.00% 23 18 0.00% 24 72 0.00% 25 17 0.00% 26 26 0.00% 27 18 0.00% 28 48 0.00% 29 34 0.00% 30 23 0.00% 31 37 0.00% 32 28 0.00% 33 29 0.00% 34 30 0.00% 35 47 0.00% 36 54 0.00% 37 41 0.00% 38 57 0.00% 39 52 0.00% 40 69 0.00% 41 63 0.00% 42 71 0.00% 43 73 0.00% 44 105 0.00% 45 124 0.00% 46 138 0.00% 47 135 0.00% 48 169 0.00% 49 175 0.00% 50 194 0.00% 51 231 0.00% 52 270 0.00% 53 247 0.00% 54 264 0.00% 55 300 0.00% 56 268 0.00% 57 340 0.00% 58 347 0.00% 59 431 0.00% 60 468 0.00% 61 547 0.00% 62 579 0.00% 63 785 0.00% 64 785 0.00% 65 1021 0.01% 66 1173 0.01% 67 2056 0.01% 68 3462 0.02% 69 15305 0.10% 70 15017 0.09% 71 5143 0.03% 72 3450 0.02% 73 3277 0.02% 74 3085 0.02% 75 3046 0.02% 76 3057 0.02% 77 3337 0.02% 78 3579 0.02% 79 4331 0.03% 80 4571 0.03% 81 4953 0.03% 82 5481 0.03% 83 6763 0.04% 84 9180 0.06% 85 9941 0.06% 86 10961 0.07% 87 11773 0.07% 88 13323 0.08% 89 13680 0.09% 90 14413 0.09% 91 15391 0.10% 92 14764 0.09% 93 17737 0.11% 94 18224 0.12% 95 20285 0.13% 96 20366 0.13% 97 20740 0.13% 98 20849 0.13% 99 22312 0.14% 100 25131 0.16% 101 23781 0.15% 102 24965 0.16% 103 25665 0.16% 104 27831 0.18% 105 31517 0.20% 106 30448 0.19% 107 30327 0.19% 108 32897 0.21% 109 38152 0.24% 110 39384 0.25% 111 35091 0.22% 112 36610 0.23% 113 43123 0.27% 114 39977 0.25% 115 43072 0.27% 116 44737 0.28% 117 42606 0.27% 118 43906 0.28% 119 45293 0.29% 120 47983 0.30% 121 45895 0.29% 122 49774 0.31% 123 52462 0.33% 124 52650 0.33% 125 53154 0.34% 126 53928 0.34% 127 56409 0.36% 128 56011 0.35% 129 56894 0.36% 130 60268 0.38% 131 60810 0.38% 132 62798 0.40% 133 65520 0.41% 134 69568 0.44% 135 72033 0.46% 136 72289 0.46% 137 78884 0.50% 138 81611 0.52% 139 84480 0.53% 140 86444 0.55% 141 95185 0.60% 142 99563 0.63% 143 106766 0.67% 144 118846 0.75% 145 135218 0.85% 146 161143 1.02% 147 206252 1.30% 148 301078 1.90% 149 600946 3.80% 150 3401071 21.49% 151 8222625 51.95% 15827003 reads passed initial QC criterion=sequence-density sequence-density=0.48 sequence-density-rank=1 fanout-score=1.69 fanout-score-rank=40 prefix-density=0.81 prefix-fanout=1.0 sequence=TAATTTTTCAACATTAGTCGGTTCGGTCCTCCAGTTAGTGTTACCCAACCTTCAACCTGCCCATGGCTAGATCACCGGGTTTCGGGTCTATACCCTGCAACTTAACGCCCAGTTAAGACTCGGTTTCCCTTCGGCTCCCCTATTCGGTTAACCTTGCTACAGAATATAAGTCGCTGACCCATTATACAAAAGGTACGCAGTCACACGCCTAAGCGTGCTCCCACTGCTTGTACGTACACGGTTTCAGGTTCTTTTTCACTCCCCTCGCCGGGGTTCTTTTCGCCTTTCCCTCACGGTACTGGTTCACTATCGGTCAGTCAGGAGTATTTAGCCTTGGAGGATGGTCCCCCCATATTCAGACAGGATACCACGTGTCCCGCCCTACTCATCGAGCTCACAGCATGTGCATTTTTGTGTACGGGGCTGTCACCCTGTATCGCGCGCCTTTCCAGACGCTTCCACTAACACACACACTGATTCAGGCTCTGGGCTGCTCCCCGTTCGCTCGCCG criterion=fanout-score sequence-density=0.01 sequence-density-rank=41 fanout-score=28.83 fanout-score-rank=1 prefix-density=0.05 prefix-fanout=5.5 sequence=TGTTCACCAAATGAATATACTCAATATCTTTATATATGAACAAAAACTTTTCATGCCCAGCAATTGCTTGGATGCAATGCGGTACTTAGGTACAAAGAGTGAAACATCAGAATAATTAAAGTGGCATGCTTAAAAGGTGTAAAGGCAGCTGCCGTCGTCACTCCTTGCTGTTGGGTCGTAGTTCTCGGCATTCCGGTCAGTGCAACCTTCTGGGACGGGCAAATTACCTTGTTGTGCTCCTTTACCTCCTCCTATGCAGCTAGAGATGGTGTGTGTATGAAGAGTGTTCTAACCGTAGAAGGAACCAGTCTTCATGGCATCTGAGTTAGCATCTCCCAGAGCAGCCTCGCTCATGTACTTGTCAGCAAGCTGCACACGCTTGACATTGTCCTGCTCTTGGACGAGCATGTGGCCGTACTCCAGGAGCTTCTCGATTGTCATCTTTGGCTGCTCAAAGGACACCGGTCCATCCTTCGAGTTCACCAGCTTCTTGCCGATGTTCTCTATTCCG criterion=sequence-density sequence-density=0.61 sequence-density-rank=1 fanout-score=3.14 fanout-score-rank=24 prefix-density=1.91 prefix-fanout=1.0 sequence=GGTAACAGGAAACAGCTTGCTGTTTCGCTGACGAGTG criterion=fanout-score sequence-density=0.04 sequence-density-rank=34 fanout-score=24.65 fanout-score-rank=1 prefix-density=1.08 prefix-fanout=1.0 sequence=CGTCGCAAGACGAAAAATGAATACCAAGTCTCAAGAGTGAACACGTAATTCATTACGAAGTTTAATTCTTTGAGCATCAAACTTTTAAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGG SRR7473330 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 13:38:07 Started mapping on | Dec 07 13:38:07 Finished on | Dec 07 13:55:02 Mapping speed, Million of reads per hour | 56.14 Number of input reads | 15827003 Average input read length | 291 UNIQUE READS: Uniquely mapped reads number | 9598015 Uniquely mapped reads % | 60.64% Average mapped length | 293.15 Number of splices: Total | 9584402 Number of splices: Annotated (sjdb) | 8877162 Number of splices: GT/AG | 9456477 Number of splices: GC/AG | 111741 Number of splices: AT/AC | 5949 Number of splices: Non-canonical | 10235 Mismatch rate per base, % | 0.12% Deletion rate per base | 0.01% Deletion average length | 1.44 Insertion rate per base | 0.01% Insertion average length | 1.64 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 150153 % of reads mapped to multiple loci | 0.95% Number of reads mapped to too many loci | 8496 % of reads mapped to too many loci | 0.05% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 36.77% % of reads unmapped: other | 1.59% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 6091574 6091574 6091574 N_multimapping 150153 150153 150153 N_noFeature 387975 9261831 487514 N_ambiguous 292876 1550 56524 UnstrandedReadsAssigned:8917164 PositiveStrandReadsAssigned:334634 NegativeStrandReadsAssigned:9053977 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=148 echo kmer=143 SRR7473330 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: SRR7473330-trimmed-pair1.fastq SRR7473330-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 15,827,003 reads, 9,239,002 reads pseudoaligned [quant] estimated average fragment length: 247.205 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,079 rounds 52973 SRR7473330.ke.tsv 35125 SRR7473330.se.tsv 88098 total ==> SRR7473330.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 690.239 0 0 PNS24247 1044 797.795 9.71718 1.48383 PNS24249 1928 1681.79 23.5566 1.70638 PNS24246 1044 797.795 9.71718 1.48383 PNS24248 1044 797.795 9.71718 1.48383 PNS24244 1471 1224.79 57.2919 5.69856 PNS24243 293 97.3083 0 0 KQK14069 1603 1356.79 3215.24 288.692 KQK14071 474 243.481 73.314 36.6824 ==> SRR7473330.se.tsv <== BRADI_1g14170v3 3577 BRADI_1g53295v3 29 BRADI_1g59795v3 383 BRADI_1g07683v3 0 BRADI_1g00485v3 30 BRADI_1g20270v3 1076 BRADI_1g74790v3 79 BRADI_1g09890v3 1 BRADI_1g77505v3 433 BRADI_1g48960v3 0 SRR7473330 completed mapping pipeline successfully