Starting /dee2/code/volunteer_pipeline.sh SRR1797582 current disk space = 1515176775680 free memory = 1597851928 SRR1797582 SRAfilesize 2c0b3375389c4173715b1c24292b922a SRR1797582.sra SRR1797582.sra file validated SRR1797582 is paired end SRR1797582 is conventional basespace SRR1797582 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1797582_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 60 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.735 34.0 31.0 34.0 31.0 34.0 2 33.30375 34.0 33.0 34.0 31.0 34.0 3 32.82725 34.0 33.0 34.0 31.0 34.0 4 36.59675 37.0 37.0 37.0 35.0 37.0 5 36.6435 37.0 37.0 37.0 35.0 37.0 6 36.65 37.0 37.0 37.0 35.0 37.0 7 36.63925 37.0 37.0 37.0 35.0 37.0 8 36.544 37.0 37.0 37.0 35.0 37.0 9 38.45125 39.0 39.0 39.0 37.0 39.0 10-14 38.865050000000004 39.4 39.2 39.4 37.8 39.4 15-19 40.144349999999996 41.0 40.0 41.0 38.0 41.0 20-24 39.92955 41.0 40.0 41.0 37.8 41.0 25-29 39.5887 41.0 39.8 41.0 36.6 41.0 30-34 39.41975000000001 41.0 39.4 41.0 35.2 41.0 35-39 38.8819 40.6 38.0 41.0 35.0 41.0 40-44 38.1671 40.0 35.6 41.0 35.0 41.0 45-49 37.43125 38.8 35.0 41.0 33.6 41.0 50-54 36.594300000000004 37.0 35.0 40.4 33.0 41.0 55-59 35.981100000000005 35.2 35.0 39.6 32.8 41.0 60-64 35.50105 35.0 35.0 38.6 32.6 41.0 65-69 34.698350000000005 35.0 34.8 36.6 31.6 39.4 70-74 33.6568 35.0 33.8 35.2 30.0 37.6 75-79 32.925650000000005 35.0 33.2 35.0 29.0 36.2 80-84 32.436699999999995 35.0 33.0 35.0 28.0 35.4 85-89 31.921249999999997 35.0 33.0 35.0 27.0 35.0 90-94 31.352099999999997 34.4 31.8 35.0 24.4 35.0 95-99 30.7118 34.0 31.0 35.0 22.0 35.0 100-104 29.896499999999996 33.8 29.8 35.0 18.2 35.0 105-109 28.625400000000003 33.0 27.4 35.0 7.2 35.0 110-114 27.406599999999997 32.8 25.6 34.6 2.0 35.0 115-119 25.864300000000004 31.2 22.8 34.0 2.0 35.0 120-124 24.432450000000003 30.4 18.2 34.0 2.0 35.0 125-129 22.459049999999998 28.6 7.4 33.0 2.0 34.8 130-134 20.5282 26.2 2.0 32.6 2.0 34.0 135-139 18.8079 24.2 2.0 32.0 2.0 34.0 140-144 16.915799999999997 19.2 2.0 31.0 2.0 34.0 145-149 13.529850000000001 2.0 2.0 30.0 2.0 33.6 150 8.0 2.0 2.0 16.0 2.0 27.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 4 1.0 5 0.0 6 2.0 7 1.0 8 7.0 9 3.0 10 5.0 11 2.0 12 4.0 13 6.0 14 14.0 15 10.0 16 14.0 17 32.0 18 35.0 19 35.0 20 28.0 21 28.0 22 40.0 23 63.0 24 82.0 25 115.0 26 124.0 27 148.0 28 155.0 29 199.0 30 215.0 31 275.0 32 383.0 33 450.0 34 542.0 35 604.0 36 338.0 37 40.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 36.43643643643644 7.632632632632633 12.537537537537538 43.393393393393396 2 29.225 8.674999999999999 22.475 39.625 3 30.407601900475118 8.752188047011753 18.104526131532882 42.73568392098024 4 34.8 12.5 15.425 37.275000000000006 5 34.55 17.65 19.025 28.775000000000002 6 35.275 18.35 19.900000000000002 26.474999999999998 7 22.975 26.575 28.325 22.125 8 26.10330992978937 19.80942828485456 27.00601805416249 27.08124373119358 9 27.800000000000004 16.975 27.250000000000004 27.975 10-14 27.74 21.86 22.78 27.62 15-19 28.055000000000003 20.919999999999998 21.975 29.049999999999997 20-24 28.325 20.645 22.505 28.525 25-29 28.33 20.21 21.545 29.915000000000003 30-34 28.175 20.335 21.73 29.759999999999998 35-39 28.775000000000002 19.89 21.335 30.0 40-44 28.389999999999997 19.93 21.21 30.470000000000002 45-49 29.34 19.675 21.455 29.53 50-54 28.575 19.305 21.075 31.045 55-59 28.48 19.07 22.035 30.415 60-64 28.720000000000002 19.615 21.235 30.43 65-69 28.925 20.205000000000002 20.785 30.085 70-74 29.354999999999997 19.919999999999998 20.630000000000003 30.095 75-79 29.110000000000003 19.62 20.5 30.769999999999996 80-84 29.645 19.08 20.695 30.580000000000002 85-89 29.07 19.36 20.4 31.169999999999998 90-94 29.81 18.790000000000003 20.580000000000002 30.819999999999997 95-99 29.830000000000002 19.11 20.575 30.485 100-104 29.830000000000002 19.220000000000002 19.84 31.11 105-109 30.04 18.82 20.205000000000002 30.935000000000002 110-114 30.075000000000003 19.075 19.564999999999998 31.285 115-119 30.415 19.145 19.79 30.65 120-124 30.28 18.725 19.765 31.230000000000004 125-129 30.37 19.34 18.675 31.615 130-134 30.211510575528777 18.48592429621481 20.131006550327516 31.1715585779289 135-139 31.181559077953896 18.575928796439822 19.175958797939895 31.066553327666384 140-144 31.069999999999997 18.345 19.470000000000002 31.115 145-149 31.130000000000003 18.77 18.915000000000003 31.185000000000002 150 30.755755755755754 18.293293293293296 14.43943943943944 36.511511511511515 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 0.5 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 0.5 11 0.5 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.5 18 0.5 19 0.0 20 0.0 21 0.5 22 0.5 23 0.0 24 0.0 25 0.5 26 0.5 27 0.5 28 0.5 29 0.0 30 0.0 31 0.0 32 0.0 33 0.0 34 2.0 35 4.0 36 5.5 37 8.5 38 12.5 39 22.5 40 35.0 41 38.0 42 47.0 43 63.0 44 73.0 45 84.5 46 98.5 47 107.5 48 114.5 49 114.5 50 131.5 51 136.5 52 113.5 53 108.5 54 101.5 55 104.0 56 116.5 57 117.5 58 105.5 59 92.0 60 106.5 61 112.0 62 91.5 63 98.0 64 105.0 65 113.0 66 124.5 67 121.5 68 122.0 69 123.5 70 125.5 71 129.0 72 116.5 73 94.5 74 95.5 75 80.5 76 53.0 77 43.0 78 40.0 79 35.5 80 32.5 81 23.5 82 15.0 83 12.0 84 7.0 85 6.5 86 4.5 87 2.5 88 1.5 89 1.0 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 0.1 2 0.0 3 0.025 4 0.0 5 0.0 6 0.0 7 0.0 8 0.3 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 0.005 135-139 0.005 140-144 0.0 145-149 0.0 150 0.1 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 95.625 #Duplication Level Percentage of deduplicated Percentage of total 1 97.77777777777777 93.5 2 1.4640522875816993 2.8000000000000003 3 0.4183006535947713 1.2 4 0.130718954248366 0.5 5 0.0784313725490196 0.375 6 0.026143790849673207 0.15 7 0.052287581699346414 0.35000000000000003 8 0.026143790849673207 0.2 9 0.0 0.0 >10 0.026143790849673207 0.9249999999999999 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGC 37 0.9249999999999999 TruSeq Adapter, Index 4 (100% over 50bp) GCGGCGATGGTGGGTGCATGCTTGCAGTGCAGTTGTCCTAGATCCTGGAT 8 0.2 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGC 7 0.17500000000000002 TruSeq Adapter, Index 2 (100% over 50bp) GGCGGCGATGGTGGGTGCATGCTTGCAGTGCAGTTGTCCTAGATCCTGGA 7 0.17500000000000002 No Hit GGCGATTTTATTTATGGGGGGTTACAAGCATGGCATGGGATGGCATGCAT 6 0.15 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGC 5 0.125 TruSeq Adapter, Index 1 (100% over 50bp) TCTAGTTGCAGGTGCAGCAGGAGCAGCCGCAGGCGGTGCCGCACTTGCAG 5 0.125 No Hit GCGACGACGAGGAGGCTGGAGGTCTGGACCTCGGCTTCAGGGTACATGTT 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 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 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.025 0.0 0.0 0.0 0.0 102-103 0.025 0.0 0.0 0.0 0.0 104-105 0.05 0.0 0.0 0.0 0.0 106-107 0.075 0.0 0.0 0.0 0.0 108-109 0.0875 0.0 0.0 0.0 0.0 110-111 0.1125 0.0 0.0 0.0 0.0 112-113 0.125 0.0 0.0 0.0 0.0 114-115 0.1875 0.0 0.0 0.0 0.0 116-117 0.225 0.0 0.0 0.0 0.0 118-119 0.225 0.0 0.0 0.0 0.0 120-121 0.2375 0.0 0.0 0.0 0.0 122-123 0.2875 0.0 0.0 0.0 0.0 124-125 0.45 0.0 0.0 0.0 0.0 126-127 0.5 0.0 0.0 0.0 0.0 128-129 0.65 0.0 0.0 0.0 0.0 130-131 0.775 0.0 0.0 0.0 0.0 132-133 1.0625 0.0 0.0 0.0 0.0 134-135 1.375 0.0 0.0 0.0 0.0 136-137 1.625 0.0 0.0 0.0 0.0 138 2.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTGGGAT 10 0.006973645 144.0 1 TGGGGAG 10 0.006973645 144.0 2 GGGATCG 10 0.006973645 144.0 3 CGATCTA 10 0.006973645 144.0 8 GAGCACA 35 3.1411873E-5 82.28571 9 AGAGCAC 35 3.1411873E-5 82.28571 8 ATCGGAA 35 3.1411873E-5 82.28571 2 AAGAGCA 40 6.0911432E-5 72.0 7 GAAGAGC 50 1.9936197E-6 72.0 6 GATCGGA 45 1.0917089E-4 64.0 1 TCGGAAG 45 1.0917089E-4 64.0 3 CGGAAGA 45 1.0917089E-4 64.0 4 GGAAGAG 50 1.838823E-4 57.6 5 ACACGTC 20 0.006139246 28.8 10-14 GTATGCC 20 0.006139246 28.8 45-49 CAGTCAC 20 0.006139246 28.8 25-29 TGCCGTC 20 0.006139246 28.8 45-49 CCAGTCA 20 0.006139246 28.8 25-29 CACGTCT 20 0.006139246 28.8 10-14 TATGCCG 20 0.006139246 28.8 45-49 >>END_MODULE SRR1797582 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1797582_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 60 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.51575 34.0 31.0 34.0 31.0 34.0 2 32.92675 34.0 33.0 34.0 31.0 34.0 3 32.953 34.0 34.0 34.0 31.0 34.0 4 36.242 37.0 37.0 37.0 35.0 37.0 5 36.217 37.0 37.0 37.0 35.0 37.0 6 36.2625 37.0 37.0 37.0 36.0 37.0 7 36.20625 37.0 37.0 37.0 35.0 37.0 8 36.24975 37.0 37.0 37.0 36.0 37.0 9 38.066 39.0 39.0 39.0 38.0 39.0 10-14 38.293150000000004 39.4 39.2 39.4 37.4 39.4 15-19 39.539300000000004 41.0 40.0 41.0 38.0 41.0 20-24 39.25664999999999 41.0 40.0 41.0 37.2 41.0 25-29 38.80135 41.0 39.4 41.0 35.4 41.0 30-34 38.196600000000004 40.2 38.0 41.0 34.8 41.0 35-39 37.40625 40.0 36.0 41.0 33.2 41.0 40-44 36.49995 38.6 35.0 40.8 32.8 41.0 45-49 35.4516 36.6 34.8 40.0 30.8 41.0 50-54 34.66205 35.0 33.8 39.2 29.6 40.8 55-59 34.1771 35.0 34.0 38.4 29.0 40.6 60-64 33.36105 35.0 33.0 36.6 27.0 39.8 65-69 32.6085 35.0 33.0 35.2 25.6 38.6 70-74 31.8613 35.0 32.6 35.0 24.8 36.6 75-79 31.286250000000003 34.2 31.6 35.0 24.0 35.4 80-84 30.5542 34.0 31.0 35.0 21.2 35.0 85-89 29.72665 33.4 29.8 35.0 17.6 35.0 90-94 28.9808 33.0 29.0 35.0 10.6 35.0 95-99 27.675349999999998 32.8 26.6 34.2 2.0 35.0 100-104 26.6466 32.0 24.4 34.0 2.0 35.0 105-109 25.08755 30.6 21.0 34.0 2.0 35.0 110-114 23.91735 29.6 17.6 33.4 2.0 35.0 115-119 22.51545 28.2 9.8 33.0 2.0 34.0 120-124 21.192 27.0 2.0 32.4 2.0 34.0 125-129 19.38555 25.0 2.0 31.4 2.0 34.0 130-134 17.7416 22.6 2.0 31.0 2.0 34.0 135-139 15.541150000000002 13.6 2.0 29.8 2.0 33.4 140-144 13.0821 2.0 2.0 28.2 2.0 32.6 145-149 8.767749999999998 2.0 2.0 14.4 2.0 30.2 150 4.718 2.0 2.0 2.0 2.0 18.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 53.0 3 5.0 4 3.0 5 5.0 6 9.0 7 7.0 8 7.0 9 13.0 10 13.0 11 7.0 12 8.0 13 16.0 14 18.0 15 16.0 16 23.0 17 34.0 18 48.0 19 56.0 20 69.0 21 66.0 22 65.0 23 99.0 24 113.0 25 113.0 26 150.0 27 190.0 28 206.0 29 227.0 30 279.0 31 341.0 32 407.0 33 501.0 34 479.0 35 290.0 36 64.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 33.575 14.725 10.5 41.199999999999996 2 35.5 20.7 16.675 27.125 3 26.525 23.724999999999998 19.05 30.7 4 29.549999999999997 23.3 17.325 29.825000000000003 5 33.5 23.575 16.175 26.75 6 28.775000000000002 28.849999999999998 15.15 27.224999999999998 7 27.825 15.275 25.85 31.05 8 28.799999999999997 20.575 18.224999999999998 32.4 9 29.549999999999997 19.55 19.5 31.4 10-14 30.615 21.375 18.27 29.74 15-19 30.259999999999998 20.755000000000003 19.139999999999997 29.845 20-24 30.89 20.805 19.18 29.125 25-29 30.335 21.61 18.375 29.68 30-34 31.3 20.51 18.175 30.014999999999997 35-39 30.055 21.175 18.955 29.815 40-44 31.540000000000003 19.86 18.095 30.505 45-49 30.39303930393039 20.602060206020603 18.59185918591859 30.413041304130413 50-54 30.72153607680384 20.541027051352568 18.81594079703985 29.921496074803738 55-59 30.55805580558056 20.692069206920692 18.731873187318733 30.018001800180016 60-64 30.43 21.51 18.315 29.744999999999997 65-69 31.145 21.82 18.125 28.910000000000004 70-74 31.1 20.465 18.915000000000003 29.520000000000003 75-79 31.06 20.455000000000002 19.175 29.310000000000002 80-84 31.53 20.79 18.565 29.115000000000002 85-89 30.94 20.560000000000002 18.81 29.69 90-94 31.430000000000003 20.54 18.92 29.110000000000003 95-99 32.28 20.415 18.09 29.215000000000003 100-104 31.353003055652955 20.27751339978961 18.409056754996744 29.960426789560685 105-109 30.498548403243568 20.757833616978676 18.89077985784363 29.852838121934127 110-114 31.059658948842326 20.383057458618794 18.282742411361706 30.274541181177177 115-119 31.146557327866393 20.131006550327516 18.205910295514776 30.516525826291314 120-124 30.805 20.635 18.385 30.175 125-129 31.564999999999998 20.415 17.985 30.035 130-134 31.430000000000003 20.77 18.265 29.535 135-139 30.7 20.94 18.25 30.11 140-144 31.245 20.830000000000002 18.305 29.62 145-149 31.755 21.035 17.83 29.38 150 34.825 20.1 13.175 31.900000000000002 >>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 0.5 23 0.5 24 0.0 25 0.5 26 0.5 27 0.0 28 0.0 29 0.0 30 0.5 31 0.5 32 0.5 33 1.0 34 2.0 35 3.0 36 3.5 37 6.0 38 6.5 39 10.5 40 18.5 41 26.0 42 33.5 43 44.5 44 58.5 45 75.0 46 89.5 47 94.0 48 98.0 49 99.5 50 109.0 51 112.5 52 109.0 53 118.0 54 119.5 55 117.0 56 109.5 57 98.0 58 101.5 59 112.5 60 109.5 61 104.0 62 100.0 63 105.5 64 118.5 65 126.0 66 146.0 67 143.0 68 126.5 69 124.5 70 117.0 71 116.5 72 120.0 73 117.0 74 115.0 75 88.0 76 66.5 77 64.5 78 49.5 79 43.0 80 36.0 81 23.0 82 16.0 83 12.0 84 9.0 85 5.5 86 3.5 87 3.0 88 2.5 89 2.0 90 1.5 91 2.0 92 1.5 93 1.0 94 0.5 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 0.0 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 0.01 50-54 0.005 55-59 0.01 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 0.185 105-109 0.11 110-114 0.015 115-119 0.005 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 97.475 #Duplication Level Percentage of deduplicated Percentage of total 1 97.99948704796103 95.525 2 1.6414465247499357 3.2 3 0.25647601949217746 0.75 4 0.025647601949217745 0.1 5 0.05129520389843549 0.25 6 0.0 0.0 7 0.025647601949217745 0.17500000000000002 8 0.0 0.0 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 GAAACATCCTTAACTGAGCTCCTCACTCACTCACTGCAGCTAGCCTCTTC 7 0.17500000000000002 No Hit CTGGTGGGCTGGAGATGGCCGGCGGGGAGGAGAGCGGCGGCTGCGACTGC 5 0.125 No Hit CCTTAACTGAGCTCCTCACTCACTCACTGCAGCTAGCCTCTTCTTCCTCA 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 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 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.025 0.0 0.0 0.0 0.0 102-103 0.025 0.0 0.0 0.0 0.0 104-105 0.037500000000000006 0.0 0.0 0.0 0.0 106-107 0.05 0.0 0.0 0.0 0.0 108-109 0.05 0.0 0.0 0.0 0.0 110-111 0.05 0.0 0.0 0.0 0.0 112-113 0.05 0.0 0.0 0.0 0.0 114-115 0.1 0.0 0.0 0.0 0.0 116-117 0.15 0.0 0.0 0.0 0.0 118-119 0.15 0.0 0.0 0.0 0.0 120-121 0.16249999999999998 0.0 0.0 0.0 0.0 122-123 0.2 0.0 0.0 0.0 0.0 124-125 0.35 0.0 0.0 0.0 0.0 126-127 0.375 0.0 0.0 0.0 0.0 128-129 0.5 0.0 0.0 0.0 0.0 130-131 0.575 0.0 0.0 0.0 0.0 132-133 0.7875 0.0 0.0 0.0 0.0 134-135 1.0125 0.0 0.0 0.0 0.0 136-137 1.2375 0.0 0.0 0.0 0.0 138 1.525 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAAAGGG 10 0.006973645 144.0 7 GGAAAGG 10 0.006973645 144.0 6 AAAAAAA 110 8.54925E-11 18.327272 60-64 >>END_MODULE Read 1302053 spots for SRR1797582.sra Written 1302053 spots for SRR1797582.sra Read 1302053 spots for SRR1797582.sra Written 1302053 spots for SRR1797582.sra Read 1302053 spots for SRR1797582.sra Written 1302053 spots for SRR1797582.sra Read 1302053 spots for SRR1797582.sra Written 1302053 spots for SRR1797582.sra Read 1302053 spots for SRR1797582.sra Written 1302053 spots for SRR1797582.sra Read 1302053 spots for SRR1797582.sra Written 1302053 spots for SRR1797582.sra Read 1302053 spots for SRR1797582.sra Written 1302053 spots for SRR1797582.sra Read 1302053 spots for SRR1797582.sra Written 1302053 spots for SRR1797582.sra Read 1302053 spots for SRR1797582.sra Written 1302053 spots for SRR1797582.sra Read 1302053 spots for SRR1797582.sra Written 1302053 spots for SRR1797582.sra Read 1302053 spots for SRR1797582.sra Written 1302053 spots for SRR1797582.sra Read 1302053 spots for SRR1797582.sra Written 1302053 spots for SRR1797582.sra Read 1302053 spots for SRR1797582.sra Written 1302053 spots for SRR1797582.sra Read 1302053 spots for SRR1797582.sra Written 1302053 spots for SRR1797582.sra Read 1302053 spots for SRR1797582.sra Written 1302053 spots for SRR1797582.sra Read 1302053 spots for SRR1797582.sra Written 1302053 spots for SRR1797582.sra Read 1302053 spots for SRR1797582.sra Written 1302053 spots for SRR1797582.sra Read 1302053 spots for SRR1797582.sra Written 1302053 spots for SRR1797582.sra Read 1302063 spots for SRR1797582.sra Written 1302063 spots for SRR1797582.sra Read 1302053 spots for SRR1797582.sra Written 1302053 spots for SRR1797582.sra SRR ids: ['SRR1797582.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_jujarpm3 SRR1797582.sra spots: 26041070 blocks: [[1, 1302053], [1302054, 2604106], [2604107, 3906159], [3906160, 5208212], [5208213, 6510265], [6510266, 7812318], [7812319, 9114371], [9114372, 10416424], [10416425, 11718477], [11718478, 13020530], [13020531, 14322583], [14322584, 15624636], [15624637, 16926689], [16926690, 18228742], [18228743, 19530795], [19530796, 20832848], [20832849, 22134901], [22134902, 23436954], [23436955, 24739007], [24739008, 26041070]] SRR1797582 file size 8751902 SRR1797582 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 SRR1797582 SRR1797582_1.fastq SRR1797582_2.fastq Input file: SRR1797582_1.fastq Paired file: SRR1797582_2.fastq trimmed: SRR1797582-trimmed-pair1.fastq, SRR1797582-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 Thu Dec 12 03:18:42 2024 >> started Thu Dec 12 03:19:16 2024 >> done (33.370s) 26041070 read pairs processed; of these: 69467 ( 0.27%) short read pairs filtered out after trimming by size control 408533 ( 1.57%) empty read pairs filtered out after trimming by size control 25563070 (98.16%) read pairs available; of these: 25107275 (98.22%) trimmed read pairs available after processing 455795 ( 1.78%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 13 0.00% 19 38 0.00% 20 74 0.00% 21 117 0.00% 22 184 0.00% 23 213 0.00% 24 306 0.00% 25 422 0.00% 26 457 0.00% 27 593 0.00% 28 739 0.00% 29 903 0.00% 30 1009 0.00% 31 1084 0.00% 32 1303 0.01% 33 1461 0.01% 34 1676 0.01% 35 1817 0.01% 36 1913 0.01% 37 2197 0.01% 38 2347 0.01% 39 2635 0.01% 40 2733 0.01% 41 3070 0.01% 42 3382 0.01% 43 3806 0.01% 44 4143 0.02% 45 4463 0.02% 46 4848 0.02% 47 5202 0.02% 48 5476 0.02% 49 5975 0.02% 50 6415 0.03% 51 6847 0.03% 52 7448 0.03% 53 7987 0.03% 54 8628 0.03% 55 9168 0.04% 56 9863 0.04% 57 10529 0.04% 58 11272 0.04% 59 12091 0.05% 60 13055 0.05% 61 14161 0.06% 62 15277 0.06% 63 16143 0.06% 64 17917 0.07% 65 18990 0.07% 66 20106 0.08% 67 21586 0.08% 68 23268 0.09% 69 25380 0.10% 70 26937 0.11% 71 29314 0.11% 72 30623 0.12% 73 33190 0.13% 74 35712 0.14% 75 37957 0.15% 76 40741 0.16% 77 43561 0.17% 78 47040 0.18% 79 50562 0.20% 80 54433 0.21% 81 58604 0.23% 82 62751 0.25% 83 67586 0.26% 84 73384 0.29% 85 78510 0.31% 86 83432 0.33% 87 88976 0.35% 88 94054 0.37% 89 100308 0.39% 90 105327 0.41% 91 112006 0.44% 92 117933 0.46% 93 124891 0.49% 94 131519 0.51% 95 137249 0.54% 96 144368 0.56% 97 152146 0.60% 98 159046 0.62% 99 168943 0.66% 100 177327 0.69% 101 186584 0.73% 102 197728 0.77% 103 208710 0.82% 104 218993 0.86% 105 229887 0.90% 106 240944 0.94% 107 250365 0.98% 108 260953 1.02% 109 273346 1.07% 110 285561 1.12% 111 297498 1.16% 112 309372 1.21% 113 320150 1.25% 114 334776 1.31% 115 348422 1.36% 116 360024 1.41% 117 369142 1.44% 118 383676 1.50% 119 394363 1.54% 120 408420 1.60% 121 424972 1.66% 122 442010 1.73% 123 456549 1.79% 124 467240 1.83% 125 467414 1.83% 126 475462 1.86% 127 484841 1.90% 128 494756 1.94% 129 502695 1.97% 130 512009 2.00% 131 517859 2.03% 132 525063 2.05% 133 536803 2.10% 134 545290 2.13% 135 552577 2.16% 136 561399 2.20% 137 568884 2.23% 138 575752 2.25% 139 583109 2.28% 140 590835 2.31% 141 599718 2.35% 142 609268 2.38% 143 621886 2.43% 144 642097 2.51% 145 662647 2.59% 146 686401 2.69% 147 707852 2.77% 148 730722 2.86% 149 673091 2.63% 150 455795 1.78% 25563070 reads passed initial QC criterion=sequence-density sequence-density=1.76 sequence-density-rank=1 fanout-score=3.50 fanout-score-rank=27 prefix-density=1.81 prefix-fanout=3.4 sequence=TGCCGCACTTGCAG criterion=fanout-score sequence-density=0.02 sequence-density-rank=32 fanout-score=2101.28 fanout-score-rank=1 prefix-density=1.28 prefix-fanout=27.8 sequence=GCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAGT criterion=sequence-density sequence-density=1.42 sequence-density-rank=1 fanout-score=3.22 fanout-score-rank=30 prefix-density=1.53 prefix-fanout=3.0 sequence=CCTGCAAGTGCGGCA criterion=fanout-score sequence-density=0.17 sequence-density-rank=27 fanout-score=359.03 fanout-score-rank=1 prefix-density=2.38 prefix-fanout=24.9 sequence=CGGCGGCGGCGC SRR1797582 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 12 03:19:52 Started mapping on | Dec 12 03:19:52 Finished on | Dec 12 03:22:05 Mapping speed, Million of reads per hour | 691.93 Number of input reads | 25563070 Average input read length | 250 UNIQUE READS: Uniquely mapped reads number | 23789379 Uniquely mapped reads % | 93.06% Average mapped length | 249.68 Number of splices: Total | 15339035 Number of splices: Annotated (sjdb) | 14422115 Number of splices: GT/AG | 15139114 Number of splices: GC/AG | 169555 Number of splices: AT/AC | 9214 Number of splices: Non-canonical | 21152 Mismatch rate per base, % | 0.33% Deletion rate per base | 0.01% Deletion average length | 3.01 Insertion rate per base | 0.01% Insertion average length | 3.06 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 227607 % of reads mapped to multiple loci | 0.89% Number of reads mapped to too many loci | 160597 % of reads mapped to too many loci | 0.63% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.37% % of reads unmapped: other | 3.05% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1568032 1568032 1568032 N_multimapping 227607 227607 227607 N_noFeature 375489 23220431 613154 N_ambiguous 383889 2244 54174 UnstrandedReadsAssigned:23030001 PositiveStrandReadsAssigned:566704 NegativeStrandReadsAssigned:23122051 Dataset is classified negative stranded MeadianReadLen=141 20thPercentileLength=122 echo kmer=117 SRR1797582 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: SRR1797582-trimmed-pair1.fastq SRR1797582-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 25,563,070 reads, 23,231,758 reads pseudoaligned [quant] estimated average fragment length: 205.459 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,186 rounds 52973 SRR1797582.ke.tsv 35125 SRR1797582.se.tsv 88098 total ==> SRR1797582.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 731.73 1.74484e-07 1.26522e-08 PNS24247 1044 839.541 7.85336 0.496333 PNS24249 1928 1723.54 535.103 16.4731 PNS24246 1044 839.541 7.85336 0.496333 PNS24248 1044 839.541 7.85336 0.496333 PNS24244 1471 1266.54 10.3373 0.433059 PNS24243 293 95.5331 0 0 KQK14069 1603 1398.54 5760 218.528 KQK14071 474 271.124 902.393 176.598 ==> SRR1797582.se.tsv <== BRADI_1g14170v3 6779 BRADI_1g53295v3 73 BRADI_1g59795v3 109 BRADI_1g07683v3 0 BRADI_1g00485v3 3 BRADI_1g20270v3 1233 BRADI_1g74790v3 137 BRADI_1g09890v3 1 BRADI_1g77505v3 210 BRADI_1g48960v3 2 SRR1797582 completed mapping pipeline successfully