Starting /dee2/code/volunteer_pipeline.sh SRR8096888 current disk space = 1543049568256 free memory = 1596648204 SRR8096888 SRAfilesize d2699a1bec3671e5199a0e2d59dd061c SRR8096888.sra SRR8096888.sra file validated SRR8096888 is paired end SRR8096888 is conventional basespace SRR8096888 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8096888_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.76725 34.0 33.0 34.0 32.0 34.0 2 33.015 34.0 33.0 34.0 32.0 34.0 3 33.11875 34.0 33.0 34.0 32.0 34.0 4 33.219 34.0 33.0 34.0 32.0 34.0 5 33.34825 34.0 33.0 34.0 33.0 34.0 6 37.05275 38.0 37.0 38.0 36.0 38.0 7 37.395 38.0 38.0 38.0 37.0 38.0 8 37.4225 38.0 38.0 38.0 37.0 38.0 9 37.46325 38.0 38.0 38.0 37.0 38.0 10-14 37.481 38.0 38.0 38.0 37.0 38.0 15-19 37.29165 38.0 38.0 38.0 36.6 38.0 20-24 37.39149999999999 38.0 38.0 38.0 37.0 38.0 25-29 37.3795 38.0 38.0 38.0 37.0 38.0 30-34 37.331849999999996 38.0 38.0 38.0 37.0 38.0 35-39 37.24915 38.0 38.0 38.0 37.0 38.0 40-44 37.1643 38.0 38.0 38.0 36.8 38.0 45-49 37.14405000000001 38.0 38.0 38.0 37.0 38.0 50-54 37.17695 38.0 38.0 38.0 37.0 38.0 55-59 37.0741 38.0 38.0 38.0 36.4 38.0 60-64 37.01115 38.0 38.0 38.0 36.4 38.0 65-69 36.76115 38.0 38.0 38.0 35.6 38.0 70-74 36.66605 38.0 38.0 38.0 35.4 38.0 75-79 36.360749999999996 38.0 38.0 38.0 35.0 38.0 80-84 36.3455 38.0 38.0 38.0 35.2 38.0 85-89 36.27230000000001 38.0 38.0 38.0 35.0 38.0 90-94 36.28340000000001 38.0 38.0 38.0 34.8 38.0 95-99 36.19335 38.0 38.0 38.0 34.6 38.0 100-104 35.9533 38.0 38.0 38.0 33.8 38.0 105-109 35.7911 38.0 38.0 38.0 33.8 38.0 110-114 35.76195 38.0 38.0 38.0 33.4 38.0 115-119 35.6202 38.0 38.0 38.0 32.8 38.0 120-124 35.52185000000001 38.0 38.0 38.0 32.6 38.0 125-129 35.23705 38.0 37.6 38.0 31.2 38.0 130-134 35.09595 38.0 37.4 38.0 30.8 38.0 135-139 34.84015 38.0 36.8 38.0 28.8 38.0 140-144 34.60080000000001 38.0 36.2 38.0 28.4 38.0 145-149 33.8369 38.0 35.6 38.0 20.8 38.0 150 28.41475 35.0 25.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 5 1.0 6 0.0 7 3.0 8 2.0 9 0.0 10 3.0 11 0.0 12 4.0 13 6.0 14 3.0 15 3.0 16 3.0 17 6.0 18 17.0 19 33.0 20 3.0 21 7.0 22 8.0 23 12.0 24 13.0 25 10.0 26 17.0 27 23.0 28 30.0 29 42.0 30 37.0 31 49.0 32 49.0 33 59.0 34 107.0 35 180.0 36 440.0 37 2830.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.499342969776606 11.038107752956636 7.805519053876478 40.65703022339028 2 21.975 17.549999999999997 36.325 24.15 3 22.575 19.1 27.35 30.975 4 26.775 26.474999999999998 20.674999999999997 26.075 5 27.224999999999998 31.574999999999996 23.150000000000002 18.05 6 22.475 32.324999999999996 24.375 20.825 7 16.925 25.25 39.65 18.175 8 19.225 23.35 30.3 27.125 9 22.400000000000002 20.849999999999998 31.674999999999997 25.074999999999996 10-14 23.150000000000002 27.205000000000002 24.445 25.2 15-19 22.95 24.740000000000002 26.44 25.869999999999997 20-24 22.91 26.085 25.53 25.474999999999998 25-29 22.585 25.535000000000004 25.729999999999997 26.150000000000002 30-34 22.759999999999998 25.55 25.845000000000002 25.845000000000002 35-39 22.5 26.205000000000002 25.47 25.825 40-44 22.7 25.990000000000002 26.045 25.264999999999997 45-49 23.655 25.36 26.75 24.235 50-54 23.125 24.535 25.415 26.924999999999997 55-59 22.470000000000002 24.85 27.21 25.47 60-64 22.985 25.205 26.135 25.674999999999997 65-69 23.0 26.715 25.11 25.174999999999997 70-74 22.314999999999998 26.795 25.11 25.779999999999998 75-79 22.869999999999997 26.02 24.64 26.47 80-84 23.48 25.055 25.564999999999998 25.900000000000002 85-89 23.095 25.669999999999998 25.615 25.619999999999997 90-94 24.07 24.825 25.540000000000003 25.564999999999998 95-99 23.49 24.92 25.75 25.840000000000003 100-104 23.53 26.590000000000003 25.19 24.69 105-109 23.86 25.345000000000002 25.230000000000004 25.564999999999998 110-114 22.75 25.71 25.94 25.6 115-119 23.52 24.654999999999998 25.72 26.105 120-124 23.799999999999997 24.805 25.130000000000003 26.265 125-129 23.94 25.495 24.975 25.590000000000003 130-134 23.56 26.650000000000002 24.675 25.115 135-139 23.74 25.82 24.39 26.05 140-144 23.916195809790487 25.891294564728234 24.74123706185309 25.45127256362818 145-149 23.544999999999998 25.97 25.2 25.285000000000004 150 23.3 25.374999999999996 24.55 26.775 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 8.0 1 6.5 2 5.5 3 4.5 4 2.5 5 2.0 6 1.0 7 0.0 8 0.5 9 1.5 10 1.0 11 0.0 12 0.0 13 0.0 14 0.5 15 0.5 16 0.5 17 1.0 18 0.5 19 0.0 20 0.0 21 0.0 22 0.0 23 0.5 24 0.5 25 0.0 26 0.5 27 1.5 28 4.5 29 5.5 30 8.5 31 11.5 32 13.5 33 19.5 34 24.5 35 41.5 36 59.0 37 68.0 38 80.5 39 99.5 40 133.0 41 159.5 42 175.5 43 181.0 44 179.5 45 187.0 46 201.5 47 198.5 48 179.0 49 179.0 50 160.0 51 129.0 52 124.5 53 116.5 54 94.0 55 81.5 56 90.5 57 95.0 58 93.5 59 98.5 60 90.5 61 87.0 62 85.0 63 65.5 64 64.0 65 58.0 66 47.0 67 40.5 68 32.5 69 30.5 70 24.0 71 17.5 72 10.0 73 7.0 74 6.5 75 4.0 76 1.5 77 1.0 78 0.5 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 4.875 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 0.005 145-149 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 94.77499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 98.20627802690582 93.075 2 1.371669744130836 2.6 3 0.1846478501714587 0.525 4 0.10551305724083357 0.4 5 0.052756528620416784 0.25 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.052756528620416784 0.75 >50 0.026378264310208392 2.4 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGC 96 2.4 TruSeq Adapter, Index 6 (100% over 50bp) TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 20 0.5 No Hit NATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGC 10 0.25 TruSeq Adapter, Index 6 (98% over 50bp) AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATG 5 0.125 TruSeq Adapter, Index 6 (100% over 49bp) GTCGAACTTGCCGGAGACGAAGTCGTAGTGGCCGCCCACGAGCTTGAGGG 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 0.125 0.0 0.0 0.0 0.0 2 0.125 0.0 0.0 0.0 0.0 3 0.125 0.0 0.0 0.0 0.0 4 0.125 0.0 0.0 0.0 0.0 5 0.125 0.0 0.0 0.0 0.0 6 0.125 0.0 0.0 0.0 0.0 7 0.125 0.0 0.0 0.0 0.0 8 0.125 0.0 0.0 0.0 0.0 9 0.125 0.0 0.0 0.0 0.0 10-11 0.125 0.0 0.0 0.0 0.0 12-13 0.125 0.0 0.0 0.0 0.0 14-15 0.125 0.0 0.0 0.0 0.0 16-17 0.125 0.0 0.0 0.0 0.0 18-19 0.125 0.0 0.0 0.0 0.0 20-21 0.125 0.0 0.0 0.0 0.0 22-23 0.125 0.0 0.0 0.0 0.0 24-25 0.125 0.0 0.0 0.0 0.0 26-27 0.125 0.0 0.0 0.0 0.0 28-29 0.125 0.0 0.0 0.0 0.0 30-31 0.125 0.0 0.0 0.0 0.0 32-33 0.125 0.0 0.0 0.0 0.0 34-35 0.125 0.0 0.0 0.0 0.0 36-37 0.125 0.0 0.0 0.0 0.0 38-39 0.125 0.0 0.0 0.0 0.0 40-41 0.125 0.0 0.0 0.0 0.0 42-43 0.125 0.0 0.0 0.0 0.0 44-45 0.125 0.0 0.0 0.0 0.0 46-47 0.125 0.0 0.0 0.0 0.0 48-49 0.125 0.0 0.0 0.0 0.0 50-51 0.125 0.0 0.0 0.0 0.0 52-53 0.125 0.0 0.0 0.0 0.0 54-55 0.125 0.0 0.0 0.0 0.0 56-57 0.125 0.0 0.0 0.0 0.0 58-59 0.15 0.0 0.0 0.0 0.0 60-61 0.175 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 0.175 0.0 0.0 0.0 0.0 68-69 0.2 0.0 0.0 0.0 0.0 70-71 0.2 0.0 0.0 0.0 0.0 72-73 0.2 0.0 0.0 0.0 0.0 74-75 0.2 0.0 0.0 0.0 0.0 76-77 0.21250000000000002 0.0 0.0 0.0 0.0 78-79 0.25 0.0 0.0 0.0 0.0 80-81 0.2625 0.0 0.0 0.0 0.0 82-83 0.3 0.0 0.0 0.0 0.0 84-85 0.3 0.0 0.0 0.0 0.0 86-87 0.3875 0.0 0.0 0.0 0.0 88-89 0.4 0.0 0.0 0.0 0.0 90-91 0.4375 0.0 0.0 0.0 0.0 92-93 0.475 0.0 0.0 0.0 0.0 94-95 0.5375000000000001 0.0 0.0 0.0 0.0 96-97 0.55 0.0 0.0 0.0 0.0 98-99 0.6 0.0 0.0 0.0 0.0 100-101 0.6375 0.0 0.0 0.0 0.0 102-103 0.7 0.0 0.0 0.0 0.0 104-105 0.8 0.0 0.0 0.0 0.0 106-107 0.85 0.0 0.0 0.0 0.0 108-109 0.95 0.0 0.0 0.0 0.0 110-111 0.9875 0.0 0.0 0.0 0.0 112-113 1.125 0.0 0.0 0.0 0.0 114-115 1.275 0.0 0.0 0.0 0.0 116-117 1.4 0.0 0.0 0.0 0.0 118-119 1.6625 0.0 0.0 0.0 0.0 120-121 1.875 0.0 0.0 0.0 0.0 122-123 1.9500000000000002 0.0 0.0 0.0 0.0 124-125 2.125 0.0 0.0 0.0 0.0 126-127 2.2750000000000004 0.0 0.0 0.0 0.0 128-129 2.45 0.0 0.0 0.0 0.0 130-131 2.625 0.0 0.0 0.0 0.0 132-133 2.95 0.0 0.0 0.0 0.0 134-135 3.1625 0.0 0.0 0.0 0.0 136-137 3.5625 0.0 0.0 0.0 0.0 138 3.875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAAAGG 10 0.005976293 151.5263 1 TTTTCGT 10 0.0069808904 143.95 6 GAAAAAC 10 0.0069808904 143.95 7 AGGAAAA 10 0.0069808904 143.95 5 TCATGCT 10 0.0069808904 143.95 8 AAAAACG 10 0.0069808904 143.95 8 TTTGTCT 10 0.0069808904 143.95 5 GGAAAAA 10 0.0069808904 143.95 6 TCGGAAG 30 1.4637406E-5 95.96667 3 CGGAAGA 30 1.4637406E-5 95.96667 4 ATCGGAA 30 1.4637406E-5 95.96667 2 GGAAGAG 30 1.4637406E-5 95.96667 5 GATCGGA 25 7.285412E-4 90.915794 1 AAGAGCA 35 3.146605E-5 82.25714 7 GAAGAGC 35 3.146605E-5 82.25714 6 GAGCACA 35 3.146605E-5 82.25714 9 AGAGCAC 35 3.146605E-5 82.25714 8 TATATAT 20 0.006149672 28.79 60-64 ATATATA 20 0.006149672 28.79 60-64 AAAAAAA 140 2.6320777E-9 14.3949995 65-69 >>END_MODULE SRR8096888 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8096888_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 49 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 28.7575 32.0 27.0 33.0 18.0 33.0 2 29.182 33.0 28.0 33.0 18.0 34.0 3 28.93275 33.0 28.0 33.0 18.0 34.0 4 29.01025 33.0 30.0 33.0 15.0 34.0 5 28.718 33.0 29.0 33.0 15.0 34.0 6 32.062 37.0 30.0 38.0 16.0 38.0 7 32.23075 37.0 29.0 38.0 16.0 38.0 8 32.33275 38.0 31.0 38.0 16.0 38.0 9 32.0415 38.0 29.0 38.0 16.0 38.0 10-14 31.8728 37.4 29.4 38.0 15.8 38.0 15-19 31.60595 37.0 29.0 38.0 15.0 38.0 20-24 31.473300000000002 37.0 29.0 38.0 15.4 38.0 25-29 31.030400000000004 37.0 28.4 38.0 15.0 38.0 30-34 30.73505 37.0 27.8 38.0 14.2 38.0 35-39 30.40365 37.0 27.0 38.0 14.0 38.0 40-44 30.21445 36.4 27.0 38.0 14.0 38.0 45-49 29.724350000000005 36.0 25.8 38.0 14.0 38.0 50-54 29.16965 36.0 24.4 38.0 11.6 38.0 55-59 28.6881 35.0 19.2 38.0 2.0 38.0 60-64 28.35065 34.4 16.0 38.0 2.0 38.0 65-69 27.854000000000003 34.0 16.0 38.0 2.0 38.0 70-74 27.36685 34.0 16.0 38.0 2.0 38.0 75-79 26.594600000000003 33.2 15.4 38.0 2.0 38.0 80-84 26.0217 32.6 15.0 37.8 2.0 38.0 85-89 25.3666 31.4 15.0 37.2 2.0 38.0 90-94 24.5582 30.0 14.8 37.0 2.0 38.0 95-99 23.794600000000003 28.8 13.6 37.0 2.0 38.0 100-104 22.91175 27.2 13.0 36.2 2.0 38.0 105-109 21.7923 24.6 6.4 35.4 2.0 38.0 110-114 20.88505 23.2 2.0 35.0 2.0 38.0 115-119 19.802200000000003 21.4 2.0 34.4 2.0 38.0 120-124 18.6235 15.0 2.0 34.0 2.0 38.0 125-129 17.1405 14.4 2.0 33.8 2.0 37.4 130-134 15.750250000000003 13.4 2.0 32.8 2.0 36.6 135-139 13.926049999999998 2.0 2.0 29.2 2.0 36.0 140-144 12.24705 2.0 2.0 25.4 2.0 35.0 145-149 9.93985 2.0 2.0 14.8 2.0 34.6 150 7.0715 2.0 2.0 2.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 181.0 3 46.0 4 25.0 5 31.0 6 32.0 7 27.0 8 36.0 9 24.0 10 39.0 11 46.0 12 48.0 13 48.0 14 53.0 15 75.0 16 68.0 17 76.0 18 97.0 19 99.0 20 94.0 21 98.0 22 108.0 23 126.0 24 117.0 25 154.0 26 174.0 27 175.0 28 169.0 29 233.0 30 231.0 31 246.0 32 242.0 33 249.0 34 235.0 35 191.0 36 92.0 37 15.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.851405622489956 17.645582329317268 9.161646586345382 35.34136546184739 2 26.999747665909663 26.141811758768608 29.195054251829422 17.663386323492304 3 23.12547336531179 24.79171926281242 27.69502650845746 24.387780863418328 4 26.958059626073776 30.44466902475998 17.38251642243557 25.21475492673067 5 28.535353535353536 33.156565656565654 19.62121212121212 18.68686868686869 6 25.11380880121396 33.66211431461811 20.460293373798685 20.763783510369247 7 22.073324905183313 19.317319848293298 33.72945638432364 24.87989886219975 8 22.629582806573957 24.197218710493047 25.082174462705435 28.09102402022756 9 25.720060636685194 22.081859525012632 26.124305204648813 26.07377463365336 10-14 27.27916266370026 25.003792283966224 22.086261819285028 25.630783233048493 15-19 25.93810053605745 25.13907150804086 23.778699302113885 25.1441286537878 20-24 26.68082094833687 26.72631685370539 23.036093418259025 23.556768779698718 25-29 26.05751250821246 26.86612422297468 22.79779653307727 24.278566735735584 30-34 26.772807682587818 25.610310841546625 23.472327520849127 24.144553955016427 35-39 25.799282792060207 25.910399515127025 23.546643769887368 24.7436739229254 40-44 26.44369221441924 25.701005405951598 23.558833931187795 24.29646844844137 45-49 25.682231655548815 25.555892460076812 22.761269456236104 26.00060642813827 50-54 25.992213964305577 26.05288437231407 23.454168562616918 24.500733100763437 55-59 25.624178712220765 26.44799353077934 23.819872637218236 24.107955119781664 60-64 24.610639158576053 27.5586569579288 23.442556634304207 24.38814724919094 65-69 25.26044300596743 26.727015272580157 23.252756144432084 24.75978557702033 70-74 25.74853327938499 27.53894396115719 22.344729921100544 24.36779283835727 75-79 24.73444613050076 27.415275670207386 23.434496712190185 24.415781487101672 80-84 24.768553650022763 27.277786209338796 23.46840694086103 24.485253199777407 85-89 25.357811156627726 27.492034592626307 23.07186567541597 24.078288575329996 90-94 25.33508674320975 27.17616711344899 23.41813767639472 24.07060846694654 95-99 25.72209014113005 27.411604026506147 22.939956497546664 23.926349334817136 100-104 25.388234103900047 27.887095958318582 22.616217309929688 24.108452627851687 105-109 24.67880627212949 27.637835103692467 23.050075872534144 24.633282751643907 110-114 24.539660056657222 27.99473897207608 22.75900445163901 24.70659651962768 115-119 24.811535542625855 28.257019984821653 22.241335694409308 24.690108778143184 120-124 24.705287123703517 28.762964836832783 22.691626612699213 23.840121426764483 125-129 24.926641707983404 28.665385004553272 22.149144996458563 24.258828291004754 130-134 24.855813012243246 29.312961651320453 22.290802387938886 23.54042294849742 135-139 23.8112100364225 29.593282072035613 22.35936867664913 24.236139214892756 140-144 24.356315443370935 30.375840963124084 20.967170823005716 24.300672770499265 145-149 23.900486420753953 31.28800162140251 21.62545601945683 23.186055938386705 150 22.584724329792614 32.59989883662114 20.8649468892261 23.950429944360142 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 25.0 1 20.5 2 8.5 3 0.5 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.5 10 1.0 11 0.5 12 0.0 13 0.0 14 1.0 15 1.5 16 0.5 17 0.0 18 0.5 19 1.0 20 2.0 21 2.5 22 1.5 23 2.0 24 2.0 25 1.0 26 2.5 27 7.5 28 9.5 29 9.5 30 12.5 31 18.5 32 18.5 33 22.0 34 27.5 35 30.5 36 46.5 37 63.0 38 67.0 39 76.5 40 108.0 41 129.5 42 135.5 43 148.5 44 152.0 45 150.0 46 170.5 47 173.0 48 158.0 49 161.0 50 157.0 51 148.0 52 131.0 53 104.5 54 100.5 55 116.0 56 111.0 57 100.5 58 101.5 59 113.5 60 121.0 61 103.5 62 94.0 63 86.0 64 73.5 65 74.5 66 62.5 67 50.5 68 51.0 69 42.0 70 31.5 71 22.5 72 15.0 73 10.5 74 8.5 75 7.0 76 3.5 77 0.5 78 0.0 79 0.5 80 1.0 81 0.5 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 0.4 2 0.9249999999999999 3 0.975 4 1.05 5 1.0 6 1.15 7 1.125 8 1.125 9 1.05 10-14 1.115 15-19 1.13 20-24 1.09 25-29 1.065 30-34 1.075 35-39 1.005 40-44 1.035 45-49 1.06 50-54 1.105 55-59 1.0699999999999998 60-64 1.1199999999999999 65-69 1.13 70-74 1.1400000000000001 75-79 1.15 80-84 1.165 85-89 1.135 90-94 1.145 95-99 1.155 100-104 1.155 105-109 1.15 110-114 1.16 115-119 1.175 120-124 1.175 125-129 1.17 130-134 1.17 135-139 1.16 140-144 1.155 145-149 1.32 150 1.15 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 97.82499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 98.87554306158958 96.72500000000001 2 0.8688985433171479 1.7000000000000002 3 0.1277791975466394 0.375 4 0.0 0.0 5 0.051111679018655765 0.25 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.025555839509327882 0.22499999999999998 >10 0.051111679018655765 0.7250000000000001 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 16 0.4 No Hit GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 13 0.325 Illumina Single End PCR Primer 1 (100% over 50bp) CNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 9 0.22499999999999998 No Hit GNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 5 0.125 No Hit ANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 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 0.075 0.0 0.0 0.0 0.0 2 0.075 0.0 0.0 0.0 0.0 3 0.075 0.0 0.0 0.0 0.0 4 0.075 0.0 0.0 0.0 0.0 5 0.075 0.0 0.0 0.0 0.0 6 0.075 0.0 0.0 0.0 0.0 7 0.075 0.0 0.0 0.0 0.0 8 0.075 0.0 0.0 0.0 0.0 9 0.075 0.0 0.0 0.0 0.0 10-11 0.075 0.0 0.0 0.0 0.0 12-13 0.075 0.0 0.0 0.0 0.0 14-15 0.075 0.0 0.0 0.0 0.0 16-17 0.075 0.0 0.0 0.0 0.0 18-19 0.075 0.0 0.0 0.0 0.0 20-21 0.075 0.0 0.0 0.0 0.0 22-23 0.075 0.0 0.0 0.0 0.0 24-25 0.075 0.0 0.0 0.0 0.0 26-27 0.075 0.0 0.0 0.0 0.0 28-29 0.075 0.0 0.0 0.0 0.0 30-31 0.075 0.0 0.0 0.0 0.0 32-33 0.075 0.0 0.0 0.0 0.0 34-35 0.075 0.0 0.0 0.0 0.0 36-37 0.075 0.0 0.0 0.0 0.0 38-39 0.075 0.0 0.0 0.0 0.0 40-41 0.075 0.0 0.0 0.0 0.0 42-43 0.075 0.0 0.0 0.0 0.0 44-45 0.075 0.0 0.0 0.0 0.0 46-47 0.075 0.0 0.0 0.0 0.0 48-49 0.075 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 0.075 0.0 0.0 0.0 0.0 56-57 0.0875 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.1375 0.0 0.0 0.0 0.0 82-83 0.175 0.0 0.0 0.0 0.0 84-85 0.175 0.0 0.0 0.0 0.0 86-87 0.2 0.0 0.0 0.0 0.0 88-89 0.2 0.0 0.0 0.0 0.0 90-91 0.2 0.0 0.0 0.0 0.0 92-93 0.21250000000000002 0.0 0.0 0.0 0.0 94-95 0.2625 0.0 0.0 0.0 0.0 96-97 0.275 0.0 0.0 0.0 0.0 98-99 0.275 0.0 0.0 0.0 0.0 100-101 0.275 0.0 0.0 0.0 0.0 102-103 0.275 0.0 0.0 0.0 0.0 104-105 0.275 0.0 0.0 0.0 0.0 106-107 0.275 0.0 0.0 0.0 0.0 108-109 0.275 0.0 0.0 0.0 0.0 110-111 0.2875 0.0 0.0 0.0 0.0 112-113 0.3375 0.0 0.0 0.0 0.0 114-115 0.3625 0.0 0.0 0.0 0.0 116-117 0.42500000000000004 0.0 0.0 0.0 0.0 118-119 0.5125 0.0 0.0 0.0 0.0 120-121 0.575 0.0 0.0 0.0 0.0 122-123 0.6 0.0 0.0 0.0 0.0 124-125 0.6625000000000001 0.0 0.0 0.0 0.0 126-127 0.675 0.0 0.0 0.0 0.0 128-129 0.7 0.0 0.0 0.0 0.0 130-131 0.7 0.0 0.0 0.0 0.0 132-133 0.7375 0.0 0.0 0.0 0.0 134-135 0.7625 0.0 0.0 0.0 0.0 136-137 0.825 0.0 0.0 0.0 0.0 138 0.875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGCTCCC 10 0.0069790767 143.96251 4 CTCCCCT 10 0.0069790767 143.96251 6 AACCCCT 10 0.0069790767 143.96251 5 GAATCAA 10 0.0069790767 143.96251 4 GCTCCCC 10 0.0069790767 143.96251 5 ATACACA 10 0.0069790767 143.96251 6 ATCGGAA 25 5.9118884E-6 115.16999 2 CGGAAGA 20 3.6916917E-4 107.97188 4 GATCGGA 30 1.4631087E-5 95.975 1 TCGGAAG 25 8.965498E-4 86.377495 3 CCAGATG 20 0.006147062 28.792501 110-114 >>END_MODULE Read 2503102 spots for SRR8096888.sra Written 2503102 spots for SRR8096888.sra Read 2503102 spots for SRR8096888.sra Written 2503102 spots for SRR8096888.sra Read 2503102 spots for SRR8096888.sra Written 2503102 spots for SRR8096888.sra Read 2503102 spots for SRR8096888.sra Written 2503102 spots for SRR8096888.sra Read 2503102 spots for SRR8096888.sra Written 2503102 spots for SRR8096888.sra Read 2503102 spots for SRR8096888.sra Written 2503102 spots for SRR8096888.sra Read 2503102 spots for SRR8096888.sra Written 2503102 spots for SRR8096888.sra Read 2503102 spots for SRR8096888.sra Written 2503102 spots for SRR8096888.sra Read 2503102 spots for SRR8096888.sra Written 2503102 spots for SRR8096888.sra Read 2503102 spots for SRR8096888.sra Written 2503102 spots for SRR8096888.sra Read 2503102 spots for SRR8096888.sra Written 2503102 spots for SRR8096888.sra Read 2503102 spots for SRR8096888.sra Written 2503102 spots for SRR8096888.sra Read 2503102 spots for SRR8096888.sra Written 2503102 spots for SRR8096888.sra Read 2503102 spots for SRR8096888.sra Written 2503102 spots for SRR8096888.sra Read 2503102 spots for SRR8096888.sra Written 2503102 spots for SRR8096888.sra Read 2503121 spots for SRR8096888.sra Written 2503121 spots for SRR8096888.sra Read 2503102 spots for SRR8096888.sra Written 2503102 spots for SRR8096888.sra Read 2503102 spots for SRR8096888.sra Written 2503102 spots for SRR8096888.sra Read 2503102 spots for SRR8096888.sra Written 2503102 spots for SRR8096888.sra Read 2503102 spots for SRR8096888.sra Written 2503102 spots for SRR8096888.sra SRR ids: ['SRR8096888.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_nkjhfz3f SRR8096888.sra spots: 50062059 blocks: [[1, 2503102], [2503103, 5006204], [5006205, 7509306], [7509307, 10012408], [10012409, 12515510], [12515511, 15018612], [15018613, 17521714], [17521715, 20024816], [20024817, 22527918], [22527919, 25031020], [25031021, 27534122], [27534123, 30037224], [30037225, 32540326], [32540327, 35043428], [35043429, 37546530], [37546531, 40049632], [40049633, 42552734], [42552735, 45055836], [45055837, 47558938], [47558939, 50062059]] SRR8096888 file size 16844911 SRR8096888 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 SRR8096888 SRR8096888_1.fastq SRR8096888_2.fastq Input file: SRR8096888_1.fastq Paired file: SRR8096888_2.fastq trimmed: SRR8096888-trimmed-pair1.fastq, SRR8096888-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 14:23:30 2024 >> started Sat Dec 7 14:24:31 2024 >> done (60.916s) 50062059 read pairs processed; of these: 266324 ( 0.53%) short read pairs filtered out after trimming by size control 2222272 ( 4.44%) empty read pairs filtered out after trimming by size control 47573463 (95.03%) read pairs available; of these: 28258964 (59.40%) trimmed read pairs available after processing 19314499 (40.60%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 158 0.00% 19 379 0.00% 20 182 0.00% 21 179 0.00% 22 315 0.00% 23 180 0.00% 24 237 0.00% 25 258 0.00% 26 253 0.00% 27 205 0.00% 28 197 0.00% 29 178 0.00% 30 240 0.00% 31 166 0.00% 32 277 0.00% 33 206 0.00% 34 319 0.00% 35 400 0.00% 36 310 0.00% 37 340 0.00% 38 400 0.00% 39 479 0.00% 40 676 0.00% 41 631 0.00% 42 685 0.00% 43 719 0.00% 44 897 0.00% 45 1191 0.00% 46 1334 0.00% 47 1204 0.00% 48 1277 0.00% 49 1353 0.00% 50 1461 0.00% 51 1725 0.00% 52 1890 0.00% 53 2276 0.00% 54 2145 0.00% 55 3024 0.01% 56 3530 0.01% 57 2890 0.01% 58 4647 0.01% 59 5734 0.01% 60 4543 0.01% 61 16189 0.03% 62 5658 0.01% 63 2428 0.01% 64 2508 0.01% 65 2733 0.01% 66 2992 0.01% 67 3438 0.01% 68 4169 0.01% 69 4930 0.01% 70 5004 0.01% 71 4595 0.01% 72 4719 0.01% 73 5224 0.01% 74 5428 0.01% 75 5976 0.01% 76 6555 0.01% 77 7184 0.02% 78 7787 0.02% 79 8615 0.02% 80 9326 0.02% 81 10690 0.02% 82 12447 0.03% 83 15946 0.03% 84 32041 0.07% 85 34088 0.07% 86 36269 0.08% 87 38603 0.08% 88 38861 0.08% 89 39849 0.08% 90 39265 0.08% 91 39168 0.08% 92 39206 0.08% 93 40112 0.08% 94 43426 0.09% 95 45393 0.10% 96 48171 0.10% 97 51749 0.11% 98 56102 0.12% 99 57966 0.12% 100 60684 0.13% 101 64500 0.14% 102 68170 0.14% 103 72373 0.15% 104 76461 0.16% 105 80100 0.17% 106 86699 0.18% 107 88711 0.19% 108 94814 0.20% 109 95870 0.20% 110 100985 0.21% 111 105055 0.22% 112 109881 0.23% 113 114678 0.24% 114 119335 0.25% 115 125476 0.26% 116 132209 0.28% 117 138119 0.29% 118 144801 0.30% 119 152816 0.32% 120 162870 0.34% 121 170949 0.36% 122 180134 0.38% 123 189312 0.40% 124 199098 0.42% 125 210405 0.44% 126 218574 0.46% 127 231921 0.49% 128 243967 0.51% 129 255523 0.54% 130 271124 0.57% 131 287793 0.60% 132 301925 0.63% 133 319537 0.67% 134 337470 0.71% 135 361742 0.76% 136 390322 0.82% 137 417902 0.88% 138 443857 0.93% 139 478049 1.00% 140 518229 1.09% 141 566525 1.19% 142 616706 1.30% 143 695271 1.46% 144 783431 1.65% 145 953984 2.01% 146 1215207 2.55% 147 1701868 3.58% 148 2917389 6.13% 149 9701643 20.39% 150 19314499 40.60% 47573463 reads passed initial QC criterion=sequence-density sequence-density=1.97 sequence-density-rank=1 fanout-score=2.69 fanout-score-rank=11 prefix-density=2.02 prefix-fanout=2.6 sequence=GGTGTTGTCGAAGCCGATGATGCGGACATAGGCGTC criterion=fanout-score sequence-density=0.12 sequence-density-rank=23 fanout-score=11.79 fanout-score-rank=1 prefix-density=0.56 prefix-fanout=2.6 sequence=GCCGGGAACGATTCCCTGCTCGACAAGGATGTCAACAATCTTCTTGCCATCAACAGTCGATTGGTAGAGGGTCTCCTCGAAGAGGATAGCACCAGAGATGTAATTTCCCAGGCCTGGTGGAGTGACAAGGAGGGTACGGTAAGCCTGGCGGTTAGCCTCAGTGTTCTCAAGGCCAATCGAGTCAAGTCTCTTTCCACAGGTAGCATTGGACTCATCCATGGCTAGGATGCCCCTTCCTGGTGATGCGATGGTTTTCGCGGTCTTGACAAGTTCATCAGCGTATGCGCTGGCACGGACAACCATGGAGACGGTCATCTGCTTGGGAGTGGCAGCCTGGCGGGTGGCGCCCCATTCGGACTTCTTGGGAAGGAAAGACGATTTGAGGATAGTAGCCGAGGCCATTGTTTCTGGCTCCAAAGGCAAGAGGATCAGGTGCTACCCTCTTCTTTGACACAAGCTTGCAAT criterion=sequence-density sequence-density=1.17 sequence-density-rank=1 fanout-score=2.64 fanout-score-rank=16 prefix-density=1.29 prefix-fanout=2.4 sequence=TGAAGCAGATCGAGTA criterion=fanout-score sequence-density=0.03 sequence-density-rank=24 fanout-score=31.58 fanout-score-rank=1 prefix-density=0.10 prefix-fanout=8.9 sequence=GCAGCAGCCATTACTTGATCATCTGAAAAATCTTAATCCAGATCAGACCAAGCAGAGCAGAGATGTCTGCTACCTTCTCCTCCACCGTCGGAGCTCCGGCTTCTACGCCAACCAGCTTCCTTGGGAAGAAGCTCAAGAAGCAGGTGACCTCGGCCGTGAACTACCATGGCAAGAGCACCAAGGCCAACAGATTCACAGTCATGGCCAAGGAGGTGGACGAGTCAAAGCAGACTGACCAGGACAGGTGGAAGGGCCTCGCCTACGATATCTCCGACGACCAGCAGGACATCACCAGGGGGAAGGGTATCGTTGACTCGCTCTTCCAGGCGCCCATGGGCGACGGTACCCACGTGGCCGTCCTCAGCTCCCAAGAGTACATCAGCCAGGGCCTAAGGAAGTACGACTTCGACAACA SRR8096888 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 14:25:15 Started mapping on | Dec 07 14:25:15 Finished on | Dec 07 14:30:52 Mapping speed, Million of reads per hour | 508.20 Number of input reads | 47573463 Average input read length | 287 UNIQUE READS: Uniquely mapped reads number | 45793696 Uniquely mapped reads % | 96.26% Average mapped length | 287.28 Number of splices: Total | 46191023 Number of splices: Annotated (sjdb) | 43765698 Number of splices: GT/AG | 45571242 Number of splices: GC/AG | 515185 Number of splices: AT/AC | 12294 Number of splices: Non-canonical | 92302 Mismatch rate per base, % | 0.51% Deletion rate per base | 0.02% Deletion average length | 2.27 Insertion rate per base | 0.02% Insertion average length | 2.29 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 656118 % of reads mapped to multiple loci | 1.38% Number of reads mapped to too many loci | 17412 % of reads mapped to too many loci | 0.04% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.07% % of reads unmapped: other | 0.26% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1402766 1402766 1402766 N_multimapping 656118 656118 656118 N_noFeature 1600974 44323560 1945685 N_ambiguous 1320930 4992 199163 UnstrandedReadsAssigned:42871792 PositiveStrandReadsAssigned:1465144 NegativeStrandReadsAssigned:43648848 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=150 echo kmer=145 SRR8096888 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: SRR8096888-trimmed-pair1.fastq SRR8096888-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 47,573,463 reads, 43,586,897 reads pseudoaligned [quant] estimated average fragment length: 279.282 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,215 rounds 52973 SRR8096888.ke.tsv 35125 SRR8096888.se.tsv 88098 total ==> SRR8096888.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 658.181 0 0 PNS24247 1044 765.718 106.562 4.27645 PNS24249 1928 1649.72 42.0716 0.783665 PNS24246 1044 765.718 106.562 4.27645 PNS24248 1044 765.718 106.562 4.27645 PNS24244 1471 1192.72 311.244 8.01889 PNS24243 293 80.8154 0 0 KQK14069 1603 1324.72 4919.69 114.121 KQK14071 474 216.131 96.0209 13.6521 ==> SRR8096888.se.tsv <== BRADI_1g14170v3 5937 BRADI_1g53295v3 1243 BRADI_1g59795v3 529 BRADI_1g07683v3 0 BRADI_1g00485v3 3 BRADI_1g20270v3 1094 BRADI_1g74790v3 78 BRADI_1g09890v3 0 BRADI_1g77505v3 527 BRADI_1g48960v3 0 SRR8096888 completed mapping pipeline successfully