Starting /dee2/code/volunteer_pipeline.sh SRR5487669 current disk space = 3050291556352 free memory = 1578222392 SRR5487669 SRAfilesize 64870cec1651b6e0f1c83e09d987e69e SRR5487669.sra SRR5487669.sra file validated SRR5487669 is paired end SRR5487669 is conventional basespace SRR5487669 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5487669_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.02325 34.0 33.0 34.0 32.0 34.0 2 33.26125 34.0 33.0 34.0 32.0 34.0 3 33.333 34.0 33.0 34.0 33.0 34.0 4 33.31375 34.0 33.0 34.0 33.0 34.0 5 33.3455 34.0 33.0 34.0 33.0 34.0 6 37.0385 38.0 38.0 38.0 36.0 38.0 7 37.30775 38.0 38.0 38.0 37.0 38.0 8 37.45375 38.0 38.0 38.0 37.0 38.0 9 37.434 38.0 38.0 38.0 37.0 38.0 10-14 37.42965 38.0 38.0 38.0 37.0 38.0 15-19 37.4337 38.0 38.0 38.0 37.0 38.0 20-24 37.41329999999999 38.0 38.0 38.0 37.4 38.0 25-29 37.43105 38.0 38.0 38.0 37.0 38.0 30-34 37.368399999999994 38.0 38.0 38.0 37.0 38.0 35-39 37.2723 38.0 38.0 38.0 37.0 38.0 40-44 37.209900000000005 38.0 38.0 38.0 36.8 38.0 45-49 37.17415 38.0 38.0 38.0 36.8 38.0 50-54 37.218599999999995 38.0 38.0 38.0 36.8 38.0 55-59 37.0535 38.0 38.0 38.0 36.0 38.0 60-64 37.09315 38.0 38.0 38.0 36.0 38.0 65-69 37.098299999999995 38.0 38.0 38.0 36.2 38.0 70-74 36.9247 38.0 38.0 38.0 35.6 38.0 75-79 36.7538 38.0 38.0 38.0 35.4 38.0 80-84 36.7808 38.0 38.0 38.0 35.2 38.0 85-89 36.76695 38.0 38.0 38.0 35.4 38.0 90-94 36.836999999999996 38.0 38.0 38.0 36.0 38.0 95-99 36.6605 38.0 38.0 38.0 34.8 38.0 100-104 36.5099 38.0 38.0 38.0 34.0 38.0 105-109 36.582750000000004 38.0 38.0 38.0 34.4 38.0 110-114 36.41760000000001 38.0 38.0 38.0 34.2 38.0 115-119 36.17605 38.0 38.0 38.0 34.0 38.0 120-124 36.03145000000001 38.0 37.8 38.0 33.6 38.0 125-129 35.8986 38.0 37.8 38.0 32.8 38.0 130-134 35.9089 38.0 37.6 38.0 32.8 38.0 135-139 35.74115 38.0 37.6 38.0 32.2 38.0 140-144 35.5651 38.0 36.4 38.0 31.8 38.0 145-149 35.206399999999995 38.0 36.0 38.0 32.0 38.0 150 29.91875 35.0 29.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 3 1.0 4 0.0 5 0.0 6 0.0 7 1.0 8 0.0 9 1.0 10 0.0 11 2.0 12 2.0 13 0.0 14 0.0 15 1.0 16 0.0 17 1.0 18 6.0 19 9.0 20 4.0 21 3.0 22 6.0 23 6.0 24 9.0 25 3.0 26 22.0 27 19.0 28 29.0 29 26.0 30 38.0 31 45.0 32 60.0 33 76.0 34 113.0 35 192.0 36 439.0 37 2886.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 47.25163893091276 12.203731719616743 7.8416540595057995 32.7029752899647 2 24.54340755566675 13.93545158869152 31.37353014761071 30.147610708031024 3 21.4 18.95 25.874999999999996 33.775 4 24.975 25.8 21.9 27.325 5 24.7 32.975 22.7 19.625 6 20.150000000000002 34.449999999999996 24.275 21.125 7 15.1 24.6 41.55 18.75 8 18.85 23.825 31.075000000000003 26.25 9 18.975 22.475 32.300000000000004 26.25 10-14 21.745 28.384999999999998 25.855 24.015 15-19 21.915000000000003 26.845000000000002 27.145000000000003 24.095 20-24 20.965 27.125 27.084999999999997 24.825 25-29 20.9 27.255000000000003 27.265 24.58 30-34 20.65 27.765 27.205000000000002 24.38 35-39 21.025 27.644999999999996 26.8 24.529999999999998 40-44 22.0 26.875 26.905 24.22 45-49 21.675 26.75 27.189999999999998 24.385 50-54 21.33 27.625 26.33 24.715 55-59 20.79 27.245 27.650000000000002 24.315 60-64 20.865000000000002 27.345000000000002 27.325 24.465 65-69 20.785 27.565 26.640000000000004 25.009999999999998 70-74 21.115000000000002 27.68 26.229999999999997 24.975 75-79 20.7 27.205000000000002 26.755000000000003 25.34 80-84 20.8 27.325 27.21 24.665 85-89 21.6 26.83 27.229999999999997 24.34 90-94 22.035 26.26 27.295 24.41 95-99 21.395 26.76 27.084999999999997 24.759999999999998 100-104 21.595 26.810000000000002 26.775 24.82 105-109 21.825 27.33 26.33 24.515 110-114 21.715 26.895000000000003 27.12 24.27 115-119 21.14 27.095000000000002 26.825 24.94 120-124 21.605 27.82 25.979999999999997 24.595 125-129 22.465 26.965 25.619999999999997 24.95 130-134 22.375 26.955000000000002 25.615 25.055 135-139 21.345 28.115000000000002 26.245 24.295 140-144 21.91 26.72 26.484999999999996 24.884999999999998 145-149 21.45 27.735 25.605 25.21 150 22.025 28.075 25.124999999999996 24.775 >>END_MODULE >>Per sequence GC content pass #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 0.5 16 0.5 17 0.0 18 0.5 19 0.5 20 0.0 21 1.0 22 1.5 23 0.5 24 1.0 25 3.0 26 6.5 27 7.5 28 9.0 29 17.0 30 23.0 31 33.0 32 40.0 33 45.5 34 50.5 35 56.0 36 85.0 37 113.0 38 120.5 39 132.5 40 152.0 41 164.0 42 162.5 43 167.0 44 192.5 45 197.0 46 198.0 47 212.5 48 206.5 49 209.0 50 197.0 51 158.5 52 149.5 53 141.5 54 115.0 55 93.0 56 77.5 57 67.5 58 64.5 59 65.0 60 54.0 61 39.0 62 39.5 63 38.0 64 24.0 65 15.0 66 10.0 67 6.5 68 6.0 69 6.5 70 4.0 71 2.0 72 2.0 73 5.0 74 6.0 75 2.5 76 1.0 77 0.5 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 0.8500000000000001 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 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 90.9 #Duplication Level Percentage of deduplicated Percentage of total 1 93.94939493949394 85.39999999999999 2 4.07040704070407 7.3999999999999995 3 1.155115511551155 3.15 4 0.33003300330033003 1.2 5 0.3025302530253025 1.375 6 0.055005500550055 0.3 7 0.0 0.0 8 0.0275027502750275 0.2 9 0.0275027502750275 0.22499999999999998 >10 0.08250825082508251 0.75 >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 GCCTTATGTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGA 10 0.25 No Hit GTCGGCAATCGGACGGCGGGCGCACGCGTCGCATCTAGCCCGGATTCTGA 10 0.25 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACTATAATATCTCGTATGC 10 0.25 TruSeq Adapter, Index 9 (97% over 36bp) GTTCGATTAGTCTTTCGCCCCTATACCCAAGTCAGACGAACGATTTGCAC 9 0.22499999999999998 No Hit CCAGAACCCAAAAACTTTGATTTCTCATAAGGTGCTGGCGGAGTCCTAAA 8 0.2 No Hit GTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCT 6 0.15 No Hit GGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCG 6 0.15 No Hit GGGAAGCTATACTATATAGGTGGCTATCTATCCCTACCAAGGCTTATATT 5 0.125 No Hit GCCGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTT 5 0.125 No Hit GTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCA 5 0.125 No Hit GTCGGAAGATCCTGAATAAATCCTACTGTATCTGAAAGAAGAACACTGTA 5 0.125 No Hit GTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGACACCTGCG 5 0.125 No Hit CGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCAT 5 0.125 No Hit CACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGCTT 5 0.125 No Hit GGAAGCTATACTATATAGGTGGCTATCTATCCCTACCAAGGCTTATATTG 5 0.125 No Hit GTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCAT 5 0.125 No Hit CCGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTC 5 0.125 No Hit GCCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGC 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #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 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.037500000000000006 0.0 0.0 0.0 0.0 80-81 0.05 0.0 0.0 0.0 0.0 82-83 0.0625 0.0 0.0 0.0 0.0 84-85 0.1 0.0 0.0 0.0 0.0 86-87 0.2125 0.0 0.0 0.0 0.0 88-89 0.2625 0.0 0.0 0.0 0.0 90-91 0.325 0.0 0.0 0.0 0.0 92-93 0.3625 0.0 0.0 0.0 0.0 94-95 0.475 0.0 0.0 0.0 0.0 96-97 0.6625 0.0 0.0 0.0 0.0 98-99 0.8875 0.0 0.0 0.0 0.0 100-101 1.025 0.0 0.0 0.0 0.0 102-103 1.2625 0.0 0.0 0.0 0.0 104-105 1.4249999999999998 0.0 0.0 0.0 0.0 106-107 1.65 0.0 0.0 0.0 0.0 108-109 2.0125 0.0 0.0 0.0 0.0 110-111 2.2249999999999996 0.0 0.0 0.0 0.0 112-113 2.55 0.0 0.0 0.0 0.0 114-115 2.9000000000000004 0.0 0.0 0.0 0.0 116-117 3.3125 0.0 0.0 0.0 0.0 118-119 3.8375000000000004 0.0 0.0 0.0 0.0 120-121 4.3 0.0 0.0 0.0 0.0 122-123 4.6625 0.0 0.0 0.0 0.0 124-125 5.1375 0.0 0.0 0.0 0.0 126-127 5.612500000000001 0.0 0.0 0.0 0.0 128-129 6.2125 0.0 0.0 0.0 0.0 130-131 6.7375 0.0 0.0 0.0 0.0 132-133 7.175000000000001 0.0 0.0 0.0 0.0 134-135 7.725 0.0 0.0 0.0 0.0 136-137 8.35 0.0 0.0 0.0 0.0 138 8.8 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACACACC 10 0.0069754543 143.9875 8 >>END_MODULE SRR5487669 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5487669_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 46 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.586 33.0 33.0 34.0 32.0 34.0 2 32.58375 33.0 33.0 34.0 32.0 34.0 3 32.4645 34.0 33.0 34.0 31.0 34.0 4 32.51525 34.0 33.0 34.0 32.0 34.0 5 32.65675 34.0 33.0 34.0 32.0 34.0 6 36.743 38.0 38.0 38.0 35.0 38.0 7 36.4785 38.0 38.0 38.0 35.0 38.0 8 36.6725 38.0 38.0 38.0 35.0 38.0 9 36.69475 38.0 38.0 38.0 35.0 38.0 10-14 36.7558 38.0 38.0 38.0 36.0 38.0 15-19 36.79809999999999 38.0 38.0 38.0 36.0 38.0 20-24 36.835750000000004 38.0 38.0 38.0 36.0 38.0 25-29 36.7464 38.0 38.0 38.0 36.0 38.0 30-34 36.42925 38.0 38.0 38.0 35.2 38.0 35-39 35.3454 38.0 37.8 38.0 29.4 38.0 40-44 35.2793 38.0 38.0 38.0 29.4 38.0 45-49 35.722249999999995 38.0 38.0 38.0 31.6 38.0 50-54 36.140950000000004 38.0 38.0 38.0 33.8 38.0 55-59 36.616600000000005 38.0 38.0 38.0 35.8 38.0 60-64 36.5963 38.0 38.0 38.0 35.8 38.0 65-69 36.5042 38.0 38.0 38.0 35.4 38.0 70-74 36.4321 38.0 38.0 38.0 35.0 38.0 75-79 36.134699999999995 38.0 38.0 38.0 34.4 38.0 80-84 35.4483 38.0 38.0 38.0 30.6 38.0 85-89 34.324200000000005 38.0 38.0 38.0 22.4 38.0 90-94 34.3627 38.0 38.0 38.0 24.2 38.0 95-99 35.157799999999995 38.0 38.0 38.0 27.0 38.0 100-104 36.021350000000005 38.0 38.0 38.0 34.0 38.0 105-109 35.83235 38.0 38.0 38.0 33.4 38.0 110-114 35.832100000000004 38.0 38.0 38.0 33.6 38.0 115-119 35.75675 38.0 38.0 38.0 33.2 38.0 120-124 35.53245 38.0 38.0 38.0 32.2 38.0 125-129 35.256299999999996 38.0 37.6 38.0 30.4 38.0 130-134 34.173500000000004 38.0 36.4 38.0 21.2 38.0 135-139 32.994749999999996 38.0 35.4 38.0 9.6 38.0 140-144 31.209299999999995 38.0 33.6 38.0 2.0 38.0 145-149 30.880000000000003 38.0 32.6 38.0 2.0 38.0 150 24.6785 33.0 2.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 13.0 3 9.0 4 5.0 5 6.0 6 4.0 7 3.0 8 1.0 9 3.0 10 3.0 11 5.0 12 3.0 13 5.0 14 3.0 15 6.0 16 7.0 17 6.0 18 6.0 19 9.0 20 11.0 21 23.0 22 18.0 23 18.0 24 27.0 25 30.0 26 60.0 27 62.0 28 43.0 29 37.0 30 71.0 31 61.0 32 89.0 33 110.0 34 126.0 35 211.0 36 401.0 37 2505.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 43.625 21.975 10.95 23.45 2 29.15620291310899 25.08789552988448 28.227021597187342 17.528879959819186 3 21.87814702920443 26.560926485397786 30.991943605236656 20.568982880161126 4 25.41311967951928 32.67401101652479 23.635453179769655 18.27741612418628 5 26.152304609218437 34.76953907815631 21.392785571142284 17.685370741482966 6 22.95 36.175000000000004 22.2 18.675 7 22.770780856423173 21.03274559193955 36.49874055415617 19.697732997481108 8 23.375 24.5 26.85 25.275 9 22.95 24.6 28.95 23.5 10-14 25.165 27.560000000000002 25.88 21.395 15-19 25.085 26.97 26.68 21.265 20-24 24.58 27.42 26.545 21.455 25-29 25.28005601120224 27.18043608721744 26.05521104220844 21.484296859371874 30-34 25.12965107497105 26.917073661950557 26.22224459996979 21.731030663108605 35-39 24.26713459950454 27.441164327002475 26.228323699421964 22.063377374071017 40-44 24.61276332094176 26.925857083849646 26.693515076414702 21.767864518793886 45-49 24.73678830624553 27.00603086987632 26.944699989778186 21.31248083409997 50-54 24.1481705168856 26.704917207710505 26.946499572197897 22.200412703206 55-59 24.55 26.775 26.815 21.86 60-64 24.735 27.175 26.805 21.285 65-69 23.71 27.075 26.745 22.470000000000002 70-74 24.13 27.12 26.605 22.145 75-79 24.584084986971337 27.305071156544397 26.428141912206854 21.68270194427741 80-84 24.989777141688815 27.105908812103863 26.257411572275608 21.64690247393171 85-89 24.025768296546627 27.484422853522016 26.306896187559403 22.18291266237195 90-94 24.336515262771425 27.39431448652051 26.329591943774254 21.93957830693381 95-99 24.175879906684248 27.502789329546605 26.640632924231667 21.680697839537476 100-104 24.385 27.76 26.905 20.95 105-109 24.785 27.365000000000002 26.85 21.0 110-114 24.67 28.01 25.955000000000002 21.365000000000002 115-119 25.36 27.639999999999997 25.929999999999996 21.07 120-124 25.605 27.21 26.045 21.14 125-129 25.34788267093803 28.52137351086195 25.427970767844627 20.70277305035539 130-134 25.934818144666938 27.094401307723743 25.796894156109524 21.173886391499796 135-139 25.757021076303538 27.352125934836046 26.065582344019667 20.825270644840753 140-144 26.91821131950938 26.923711567020515 26.22518013310599 19.932896980364117 145-149 26.141748685101284 27.094724782586056 25.798052387647765 20.965474144664896 150 27.61856454476287 26.883083946233832 24.575196550849608 20.923154958153688 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.5 4 0.5 5 0.5 6 0.5 7 0.0 8 0.0 9 0.0 10 0.0 11 0.5 12 0.5 13 0.0 14 0.0 15 0.5 16 0.5 17 0.0 18 0.5 19 1.5 20 1.0 21 0.5 22 1.5 23 2.0 24 4.0 25 5.5 26 7.5 27 11.0 28 13.5 29 18.5 30 20.5 31 26.5 32 41.5 33 44.0 34 61.0 35 80.5 36 87.5 37 107.0 38 115.0 39 123.5 40 155.5 41 165.0 42 161.0 43 180.5 44 211.5 45 219.5 46 218.5 47 215.5 48 218.0 49 199.0 50 166.0 51 135.0 52 124.5 53 135.5 54 111.0 55 88.5 56 72.5 57 67.5 58 65.5 59 62.0 60 51.5 61 40.0 62 42.5 63 36.5 64 18.0 65 7.0 66 6.0 67 6.5 68 4.5 69 4.0 70 7.5 71 6.5 72 3.0 73 3.5 74 4.0 75 2.5 76 0.5 77 0.5 78 2.5 79 2.0 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 warn #Base N-Count 1 0.0 2 0.44999999999999996 3 0.7000000000000001 4 0.15 5 0.2 6 0.0 7 0.75 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.02 30-34 0.695 35-39 3.1199999999999997 40-44 3.16 45-49 2.17 50-54 0.655 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.22 80-84 2.18 85-89 5.3100000000000005 90-94 4.67 95-99 1.41 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.11 130-134 2.12 135-139 4.3950000000000005 140-144 9.095 145-149 3.9849999999999994 150 1.425 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 92.05 #Duplication Level Percentage of deduplicated Percentage of total 1 94.56816947311243 87.05000000000001 2 3.9652362846279194 7.3 3 0.7061379684953829 1.95 4 0.29875067897881585 1.0999999999999999 5 0.19011406844106463 0.8750000000000001 6 0.10863661053775121 0.6 7 0.08147745790331341 0.525 8 0.08147745790331341 0.6 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 GGAGTCTGACATGTGTGCGAGTCAACGGGCGAGTAAACCCGTAAGGCGCA 8 0.2 No Hit GGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTC 8 0.2 No Hit AGGAGTCTGACATGTGTGCGAGTCAACGGGCGAGTAAACCCGTAAGGCGC 8 0.2 No Hit GGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTT 7 0.17500000000000002 No Hit GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 7 0.17500000000000002 Illumina Single End PCR Primer 1 (100% over 50bp) GTCTGACATGTGTGCGAGTCAACGGGCGAGTAAACCCGTAAGGCGCAAGG 7 0.17500000000000002 No Hit CATTAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAAT 6 0.15 No Hit GTCTCTTTCAGAAGGCATTGGTATCTTTTCCCCACTTCCAAGCATTTTTT 6 0.15 No Hit CCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATGG 6 0.15 No Hit ACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGAT 6 0.15 No Hit GGACATTAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCC 5 0.125 No Hit AATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGA 5 0.125 No Hit GTTACTTTGAAGAAATTAGAGTGCTCAAAGCAAGCCTACGCTCTGGATAC 5 0.125 No Hit ATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAG 5 0.125 No Hit GTGCGAGTCAACGGGCGAGTAAACCCGTAAGGCGCAAGGAAGCTGACTGG 5 0.125 No Hit GGCGGGACTACCCGCTGAGTTTAAGCATATCAATAAGCGGAGGAAAAGAA 5 0.125 No Hit AAGGAGTCTGACATGTGTGCGAGTCAACGGGCGAGTAAACCCGTAAGGCG 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #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 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.037500000000000006 0.0 0.0 0.0 0.0 80-81 0.05 0.0 0.0 0.0 0.0 82-83 0.05 0.0 0.0 0.0 0.0 84-85 0.07500000000000001 0.0 0.0 0.0 0.0 86-87 0.1875 0.0 0.0 0.0 0.0 88-89 0.25 0.0 0.0 0.0 0.0 90-91 0.325 0.0 0.0 0.0 0.0 92-93 0.3625 0.0 0.0 0.0 0.0 94-95 0.48750000000000004 0.0 0.0 0.0 0.0 96-97 0.6875 0.0 0.0 0.0 0.0 98-99 0.9375 0.0 0.0 0.0 0.0 100-101 1.05 0.0 0.0 0.0 0.0 102-103 1.25 0.0 0.0 0.0 0.0 104-105 1.4 0.0 0.0 0.0 0.0 106-107 1.625 0.0 0.0 0.0 0.0 108-109 1.9874999999999998 0.0 0.0 0.0 0.0 110-111 2.2375 0.0 0.0 0.0 0.0 112-113 2.5625 0.0 0.0 0.0 0.0 114-115 2.8875 0.0 0.0 0.0 0.0 116-117 3.2375 0.0 0.0 0.0 0.0 118-119 3.725 0.0 0.0 0.0 0.0 120-121 4.175 0.0 0.0 0.0 0.0 122-123 4.4875 0.0 0.0 0.0 0.0 124-125 4.9875 0.0 0.0 0.0 0.0 126-127 5.45 0.0 0.0 0.0 0.0 128-129 5.987500000000001 0.0 0.0 0.0 0.0 130-131 6.4125 0.0 0.0 0.0 0.0 132-133 6.75 0.0 0.0 0.0 0.0 134-135 7.2625 0.0 0.0 0.0 0.0 136-137 7.824999999999999 0.0 0.0 0.0 0.0 138 8.275 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATTAGGG 10 0.0072563514 142.07594 2 AATTAGG 10 0.0072563514 142.07594 1 CTCAGAA 10 0.0072563514 142.07594 5 TTAGGGC 10 0.0072563514 142.07594 3 TAGGGCT 10 0.0072563514 142.07594 4 TTGCTCA 10 0.0072563514 142.07594 2 >>END_MODULE Read 1035860 spots for SRR5487669.sra Written 1035860 spots for SRR5487669.sra Read 1035860 spots for SRR5487669.sra Written 1035860 spots for SRR5487669.sra Read 1035860 spots for SRR5487669.sra Written 1035860 spots for SRR5487669.sra Read 1035860 spots for SRR5487669.sra Written 1035860 spots for SRR5487669.sra Read 1035860 spots for SRR5487669.sra Written 1035860 spots for SRR5487669.sra Read 1035860 spots for SRR5487669.sra Written 1035860 spots for SRR5487669.sra Read 1035860 spots for SRR5487669.sra Written 1035860 spots for SRR5487669.sra Read 1035860 spots for SRR5487669.sra Written 1035860 spots for SRR5487669.sra Read 1035860 spots for SRR5487669.sra Written 1035860 spots for SRR5487669.sra Read 1035860 spots for SRR5487669.sra Written 1035860 spots for SRR5487669.sra Read 1035860 spots for SRR5487669.sra Written 1035860 spots for SRR5487669.sra Read 1035860 spots for SRR5487669.sra Written 1035860 spots for SRR5487669.sra Read 1035860 spots for SRR5487669.sra Written 1035860 spots for SRR5487669.sra Read 1035860 spots for SRR5487669.sra Written 1035860 spots for SRR5487669.sra Read 1035860 spots for SRR5487669.sra Written 1035860 spots for SRR5487669.sra Read 1035860 spots for SRR5487669.sra Written 1035860 spots for SRR5487669.sra Read 1035873 spots for SRR5487669.sra Written 1035873 spots for SRR5487669.sra Read 1035860 spots for SRR5487669.sra Written 1035860 spots for SRR5487669.sra Read 1035860 spots for SRR5487669.sra Written 1035860 spots for SRR5487669.sra Read 1035860 spots for SRR5487669.sra Written 1035860 spots for SRR5487669.sra SRR ids: ['SRR5487669.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_vljj9v3_ SRR5487669.sra spots: 20717213 blocks: [[1, 1035860], [1035861, 2071720], [2071721, 3107580], [3107581, 4143440], [4143441, 5179300], [5179301, 6215160], [6215161, 7251020], [7251021, 8286880], [8286881, 9322740], [9322741, 10358600], [10358601, 11394460], [11394461, 12430320], [12430321, 13466180], [13466181, 14502040], [14502041, 15537900], [15537901, 16573760], [16573761, 17609620], [17609621, 18645480], [18645481, 19681340], [19681341, 20717213]] SRR5487669 file size 6958220 SRR5487669 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 SRR5487669 SRR5487669_1.fastq SRR5487669_2.fastq Input file: SRR5487669_1.fastq Paired file: SRR5487669_2.fastq trimmed: SRR5487669-trimmed-pair1.fastq, SRR5487669-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 Wed Feb 12 06:13:22 2025 >> started Wed Feb 12 06:13:49 2025 >> done (26.941s) 20717213 read pairs processed; of these: 42814 ( 0.21%) short read pairs filtered out after trimming by size control 86624 ( 0.42%) empty read pairs filtered out after trimming by size control 20587775 (99.38%) read pairs available; of these: 7783126 (37.80%) trimmed read pairs available after processing 12804649 (62.20%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 6 0.00% 19 9 0.00% 20 5 0.00% 21 11 0.00% 22 10 0.00% 23 8 0.00% 24 6 0.00% 25 12 0.00% 26 13 0.00% 27 16 0.00% 28 15 0.00% 29 9 0.00% 30 15 0.00% 31 23 0.00% 32 18 0.00% 33 19 0.00% 34 20 0.00% 35 28 0.00% 36 24 0.00% 37 30 0.00% 38 25 0.00% 39 31 0.00% 40 44 0.00% 41 49 0.00% 42 41 0.00% 43 49 0.00% 44 63 0.00% 45 101 0.00% 46 91 0.00% 47 119 0.00% 48 113 0.00% 49 151 0.00% 50 186 0.00% 51 182 0.00% 52 210 0.00% 53 203 0.00% 54 228 0.00% 55 251 0.00% 56 251 0.00% 57 312 0.00% 58 308 0.00% 59 318 0.00% 60 368 0.00% 61 451 0.00% 62 504 0.00% 63 557 0.00% 64 637 0.00% 65 822 0.00% 66 854 0.00% 67 1052 0.01% 68 1569 0.01% 69 4815 0.02% 70 7147 0.03% 71 3628 0.02% 72 2338 0.01% 73 2199 0.01% 74 2184 0.01% 75 2453 0.01% 76 2491 0.01% 77 2633 0.01% 78 3004 0.01% 79 3352 0.02% 80 3782 0.02% 81 4343 0.02% 82 5038 0.02% 83 5850 0.03% 84 9270 0.05% 85 9963 0.05% 86 10362 0.05% 87 10738 0.05% 88 11388 0.06% 89 11604 0.06% 90 12536 0.06% 91 13402 0.07% 92 14531 0.07% 93 16239 0.08% 94 17433 0.08% 95 19049 0.09% 96 19858 0.10% 97 20852 0.10% 98 21015 0.10% 99 22071 0.11% 100 23288 0.11% 101 24496 0.12% 102 25859 0.13% 103 27914 0.14% 104 32409 0.16% 105 31969 0.16% 106 33483 0.16% 107 33809 0.16% 108 34537 0.17% 109 35316 0.17% 110 36450 0.18% 111 38199 0.19% 112 41568 0.20% 113 43977 0.21% 114 46132 0.22% 115 48540 0.24% 116 50471 0.25% 117 51376 0.25% 118 50848 0.25% 119 50933 0.25% 120 52379 0.25% 121 53688 0.26% 122 55978 0.27% 123 58610 0.28% 124 61964 0.30% 125 64999 0.32% 126 66962 0.33% 127 67845 0.33% 128 69020 0.34% 129 69590 0.34% 130 71750 0.35% 131 71801 0.35% 132 74571 0.36% 133 77921 0.38% 134 82554 0.40% 135 85802 0.42% 136 89066 0.43% 137 92342 0.45% 138 96323 0.47% 139 100401 0.49% 140 106200 0.52% 141 112393 0.55% 142 121082 0.59% 143 134714 0.65% 144 151297 0.73% 145 172913 0.84% 146 215638 1.05% 147 295918 1.44% 148 526645 2.56% 149 3415181 16.59% 150 12804649 62.20% 20587775 reads passed initial QC criterion=sequence-density sequence-density=0.40 sequence-density-rank=1 fanout-score=2.42 fanout-score-rank=29 prefix-density=0.80 prefix-fanout=1.2 sequence=CGACGGTCTAAACCCAGCTCACGTTCCCTATTGGTGGGTGAACAATCCAACACTTGGTGAATTCTGCTTCACAATGATAGGAAGAGCCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCACAAGCCAGTTATCCCTGTGGTAACTTTTCTGACACCTCTAGCTTCAAATTCCGAAGGTCTAAAGGATCGATAGGCCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGCTTTTACCCTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGACACCTGCGTTATCTTTTAACAGATGTGCCGCCCCAGCCAAACTCCCCACCTGACAATGTCTTCCGCCCGGATCGGCCGCCGAAGCGGCCTTGGGTCCAAAAAGAGGGGCAGCGCCCCGCCTCCGATTCACGGAATAAGTAAAATAACGTTAAAAGTAGTGGTATTTCACCTTCGCCGAAGCTCCCACTTATCCTACAC criterion=fanout-score sequence-density=0.10 sequence-density-rank=25 fanout-score=21.91 fanout-score-rank=1 prefix-density=1.55 prefix-fanout=1.4 sequence=CCATCTTTCGGCTAACCTAGCCTCCTCCGTCCCTCGGGACCAACAAGGGGTAGTACAGGAATATTCGCCTGTTGTCCATCGACTACGCCTTTCGGCCTGATCTTAGGCCCTGACTCACCCTCCGTGGACGAACCTTGCGGAGGAACCCTTAGGTTTTCGGGGCATTGGATTCTCACCAATGTTTGCGTTACTCAAGCCGACATTCTCGCTTCCGCTTCGTCCACCCCCGCTCGCGCGGGTGCTTCCCTCTAAGCGGAACGCTCCCCTACCGATGCATTTTTACATCCCACAGCTTCGGCAGATCGCTTAGCCCCGTTCATCTTCGGCGCAAGAGCGCTCGATCAGTGAGCTATTACGCACTCTTTCAAGGGTGGCTGCTTCTAGGCAAACCTCCTGGCTGTCTCTGCACCCCTACCTCCTTTATCACTGAGCGGTCATTTAGGGGCCTTAGCTGGTGATCCGGGCTGTTTCCCTCTCGACGATGAAGCTTATCCCCCACCGTCTCACTGGC criterion=sequence-density sequence-density=0.71 sequence-density-rank=1 fanout-score=2.55 fanout-score-rank=30 prefix-density=0.72 prefix-fanout=2.5 sequence=TTAGACCGTCGTGAGACAGGTTAGTTTTACCCTACTGATGACAGTGTCGCAATAGTAATCCAACCTAGTACGAGAGGAACCGTTGATTCGCACAATTGGTCATCGCGCTTGGTTGAAAAGCCAGTGGCGCGAAGCTACCGTGCGTTGGATTATGACTGAACGCCTCTAAGTCAGAATCCGGGCTAGATGCGACGCGTGCGCCCGCCGTCCGATTGCCGACCTGCAGTAGGGGCCTCTTGGCCCCGGAGGCACGTGCCGTTGGCCAAGCCCTCGCGGTGAAAGAGCCGCGCGGGCCGCCTTGAAGTACAATTCCCACCGAGCGGCGGGTAGAATCCTTTGCAGACGACTTAAATACGCGACGGGGTATTGTAA criterion=fanout-score sequence-density=0.08 sequence-density-rank=20 fanout-score=25.79 fanout-score-rank=1 prefix-density=1.00 prefix-fanout=2.2 sequence=GGAAGAGCTAGAATTCTAACCTTGTGTCAGGACCTACGGGCCAAGGGACAGTCTCAGGTAGACAGTTTCTATGGGGCGTAGGCCTCCCAAAAGGTAACGGAGGCGTGCAAAGGTTTCCTCGGGCCGGACGGAGATTGGCCCTCGAGTGCAAAGGCAGAAGGGAGCTTGACTGCAAGACCCACCCGTCGAGCAGGGACGAAAGTCGGCCTTAGTGATCCGACGGTGCCGAGTGGAAGGGCCGTCGCTCAACGGATAAAAGTTACTCTAGGGATAACAGGCTGATCTTCCCCAAGAGCTCACATCGACGGGAAGGTTTGGCACCTCGATGTCGGC SRR5487669 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 12 06:14:54 Started mapping on | Feb 12 06:14:54 Finished on | Feb 12 06:24:09 Mapping speed, Million of reads per hour | 133.54 Number of input reads | 20587775 Average input read length | 291 UNIQUE READS: Uniquely mapped reads number | 12568206 Uniquely mapped reads % | 61.05% Average mapped length | 291.14 Number of splices: Total | 10883770 Number of splices: Annotated (sjdb) | 10699696 Number of splices: GT/AG | 10672557 Number of splices: GC/AG | 179685 Number of splices: AT/AC | 8116 Number of splices: Non-canonical | 23412 Mismatch rate per base, % | 0.26% Deletion rate per base | 0.02% Deletion average length | 2.18 Insertion rate per base | 0.02% Insertion average length | 1.93 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 572097 % of reads mapped to multiple loci | 2.78% Number of reads mapped to too many loci | 3701376 % of reads mapped to too many loci | 17.98% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 15.65% % of reads unmapped: other | 2.54% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 7473584 7473584 7473584 N_multimapping 572097 572097 572097 N_noFeature 725060 12307777 817319 N_ambiguous 238535 1427 69317 UnstrandedReadsAssigned:11604611 PositiveStrandReadsAssigned:259002 NegativeStrandReadsAssigned:11681570 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=149 echo kmer=145 SRR5487669 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: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR5487669-trimmed-pair1.fastq SRR5487669-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 20,587,775 reads, 14,574,159 reads pseudoaligned [quant] estimated average fragment length: 223.887 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,061 rounds 52401 SRR5487669.ke.tsv 34699 SRR5487669.se.tsv 87100 total ==> SRR5487669.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1795.11 344 11.1938 Potri.005G024800.1.v4.1 1035 812.113 224 16.1117 Potri.004G059700.1.v4.1 961 738.131 20 1.58273 Potri.007G009000.2.v4.1 1416 1193.11 1 0.0489585 Potri.003G141000.2.v4.1 2943 2720.11 267 5.73369 Potri.016G087400.1.v4.1 270 84.0844 543 377.22 Potri.015G069301.1.v4.1 564 343.411 0 0 Potri.010G195200.1.v4.1 1773 1550.11 21 0.791345 Potri.012G127500.1.v4.1 977 754.119 1773 137.334 ==> SRR5487669.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 74 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 209 Potri.001G212900.v4.1 3 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 114 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 7 SRR5487669 completed mapping pipeline successfully