Starting /dee2/code/volunteer_pipeline.sh ERR1942991 current disk space = 1523611467776 free memory = 1563691268 ERR1942991 SRAfilesize 597841233211fe6aeffd65a4775fde01 ERR1942991.sra ERR1942991.sra file validated ERR1942991 is single end ERR1942991 is conventional basespace ERR1942991 read1 length is 25-257 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR1942991_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 25-257 %GC 60 >>END_MODULE >>Per base sequence quality warn #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 25.00975 26.0 23.0 28.0 20.0 29.0 2 24.47125 26.0 22.0 27.0 19.0 29.0 3 24.11375 25.0 22.0 27.0 17.0 29.0 4 24.82375 26.0 23.0 28.0 20.0 29.0 5 23.98675 25.0 22.0 27.0 15.0 29.0 6 24.198 26.0 22.0 28.0 15.0 29.0 7 23.081 24.0 21.0 27.0 15.0 28.0 8 24.479 26.0 23.0 28.0 19.0 29.0 9 24.021 25.0 22.0 27.0 17.0 29.0 10-14 24.30165 25.4 22.4 27.2 18.2 28.6 15-19 24.253999999999998 25.6 22.2 27.8 18.0 28.8 20-24 24.229949999999995 25.6 22.4 27.0 18.6 28.0 25-29 23.82921951522733 25.2 21.8 27.2 16.4 28.2 30-34 23.82301465531415 24.8 21.8 27.2 17.4 28.2 35-39 24.02192851833122 25.2 22.2 27.0 17.6 28.0 40-44 23.957705659588978 25.4 22.0 27.0 15.8 28.0 45-49 23.699643298073983 24.8 21.6 27.0 15.6 28.0 50-54 23.74509580134788 24.8 21.4 27.4 15.4 28.2 55-59 23.848273580109172 25.0 21.8 27.0 16.4 28.0 60-64 23.236117969230854 24.2 21.0 27.0 14.4 28.0 65-69 22.819069111884737 23.8 20.2 27.0 14.0 28.0 70-74 21.525282913379787 23.0 18.0 26.8 11.8 28.0 75-79 22.43361136650403 23.4 20.0 26.8 14.0 28.0 80-84 21.77121893481683 23.0 18.8 26.6 12.8 28.0 85-89 21.608312905639423 22.8 18.6 26.0 13.2 28.0 90-94 21.262219053273316 22.2 18.4 25.2 13.0 27.2 95-99 21.96499934158719 23.0 19.4 26.2 13.4 27.8 100-104 21.873184174241068 23.0 19.0 26.0 13.2 27.6 105-109 21.63481624101804 22.8 19.0 25.8 13.4 27.4 110-114 21.840101284980083 22.8 19.2 26.0 13.0 27.8 115-119 21.66501757816838 22.8 19.0 26.0 13.0 27.6 120-124 21.64631947328472 23.0 19.0 25.8 13.0 27.4 125-129 21.555536743191286 23.0 19.0 26.0 13.0 27.6 130-134 21.350685966642658 22.8 18.8 25.8 12.6 27.2 135-139 21.758653391945337 22.8 19.6 26.0 13.6 27.0 140-144 21.573508899414946 22.8 19.2 25.8 13.6 27.0 145-149 21.58721947515885 22.8 19.2 25.6 13.4 27.0 150-154 21.62983266438831 22.8 19.4 25.2 13.6 27.0 155-159 20.91335303880336 22.0 17.6 25.0 13.0 27.0 160-164 20.84397894789952 22.0 18.0 24.6 13.0 27.0 165-169 21.3283113297716 22.2 19.0 25.0 14.0 27.0 170-174 21.263494055360777 22.0 18.6 25.0 13.8 27.0 175-179 20.872453544845506 21.8 17.8 25.0 13.0 27.0 180-184 20.843751325939404 22.0 18.4 24.6 13.2 27.0 185-189 21.31681184722403 22.6 18.8 25.0 13.2 27.0 190-194 20.894305572704575 21.8 18.4 24.8 13.2 27.0 195-199 20.5983117952976 21.8 17.2 24.8 12.8 26.8 200-204 19.959763928321774 20.8 16.6 23.8 12.4 26.0 205-209 20.900254618346235 21.8 18.2 24.6 13.2 26.2 210-214 19.841472334724678 20.4 16.2 23.6 12.0 25.4 215-219 19.56047059559757 20.2 15.0 23.6 12.6 25.6 220-224 20.27377213096026 20.666666666666668 16.0 24.0 13.0 26.0 225-229 18.773778462998102 NaN NaN NaN NaN NaN 230-234 17.891779091744024 NaN NaN NaN NaN NaN 235-239 17.649062575132724 NaN NaN NaN NaN NaN 240-244 17.64516178266178 NaN NaN NaN NaN NaN 245-249 20.066666666666666 NaN NaN NaN NaN NaN 250-254 17.4 NaN NaN NaN NaN NaN 255-257 20.0 NaN NaN NaN NaN NaN >>END_MODULE >>Per sequence quality scores warn #Quality Count 15 2.0 16 8.0 17 41.0 18 118.0 19 253.0 20 419.0 21 512.0 22 584.0 23 588.0 24 507.0 25 428.0 26 409.0 27 130.0 28 1.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 18.675 42.35 26.224999999999998 12.75 2 35.199999999999996 32.475 4.6 27.725 3 15.950000000000001 21.525 8.924999999999999 53.6 4 32.475 35.025 11.525 20.974999999999998 5 15.925 36.075 22.725 25.275 6 26.974999999999998 11.725 7.775 53.525 7 24.0 29.75 11.0 35.25 8 13.450000000000001 14.249999999999998 36.825 35.475 9 16.1 32.375 7.6499999999999995 43.875 10-14 28.155 22.31 16.04 33.495000000000005 15-19 37.775 16.88 11.42 33.925 20-24 31.03 20.560000000000002 18.52 29.89 25-29 33.20142263186896 21.755247207333568 13.810549516605722 31.232780644191756 30-34 28.373266078184113 21.109709962168978 13.851197982345523 36.66582597730139 35-39 31.473112273396637 24.297973899355103 14.319809069212411 29.90910475803585 40-44 25.965488907148725 28.435702547247327 14.158792111750204 31.44001643385374 45-49 22.388996391402124 20.10878092149992 21.447623032268186 36.054599654829765 50-54 30.44990103247205 17.091959557053443 18.64334242764671 33.814796982827794 55-59 22.93756967670011 21.103678929765888 18.528428093645484 37.43032329988852 60-64 30.487875455755542 19.098327449505177 22.217720932924358 28.196076161814922 65-69 28.316250074926575 12.851405622489958 26.25427081460169 32.578073487981776 70-74 31.335115183912432 10.01018200330915 28.4077892325315 30.246913580246915 75-79 23.739270386266096 18.81035407725322 19.869903433476395 37.58047210300429 80-84 23.987359954036197 22.9316288422867 19.548980178109737 33.53203102556736 85-89 23.185214313802597 22.272906016515925 20.46401887534408 34.0778607943374 90-94 15.355967434609388 31.31820543911311 16.09215312662394 37.23367399965356 95-99 18.927070005483458 21.705355510875528 26.576494242368852 32.79108024127216 100-104 18.493887530562347 21.124694376528115 20.420537897310513 39.960880195599024 105-109 24.458717497151145 19.434372733865118 20.93649642598156 35.170413343002174 110-114 26.4257481648786 18.452851496329757 20.70016939582157 34.42123094297007 115-119 24.99693063228975 18.809085328422345 22.848373235113566 33.34561080417434 120-124 28.751196826699495 17.23430447271235 20.093010532074956 33.9214881685132 125-129 31.020597800836303 11.15068917453926 23.664240359299985 34.16447266532445 130-134 29.743589743589745 10.76923076923077 20.86021505376344 38.62696443341604 135-139 24.22560429722471 22.739480752014323 18.81826320501343 34.21665174574754 140-144 29.54107211723872 18.742768993443885 20.24681835711531 31.469340532202082 145-149 26.27986348122867 17.34591447500502 18.00843204175868 38.36579000200763 150-154 26.139690506064404 20.17984107068172 17.14763697197825 36.53283145127561 155-159 28.024058810425483 19.826241924704835 19.558921808866117 32.590777456003565 160-164 29.633136094674555 18.224852071005916 13.562130177514792 38.57988165680473 165-169 32.49756572541382 15.96884128529698 17.989289191820838 33.54430379746836 170-174 26.521626521626523 21.678321678321677 17.715617715617714 34.084434084434086 175-179 27.0979020979021 14.801864801864802 22.31934731934732 35.78088578088578 180-184 28.106600557793616 14.657576696622248 20.235512860241712 37.000309885342425 185-189 26.762002042900917 18.692543411644536 16.343207354443308 38.20224719101123 190-194 22.3760092272203 20.26143790849673 19.76163014225298 37.60092272202999 195-199 26.533742331288344 17.94478527607362 22.341513292433536 33.1799591002045 200-204 27.496382054992765 14.327062228654125 25.180897250361795 32.99565846599132 205-209 26.845637583892618 26.174496644295303 14.381591562799617 32.59827420901246 210-214 24.555160142348754 24.31791221826809 22.894424673784105 28.23250296559905 215-219 22.49637155297533 18.722786647314948 25.544267053701013 33.236574746008706 220-224 27.184466019417474 18.83495145631068 22.330097087378643 31.650485436893206 225-229 19.46107784431138 23.652694610778443 23.952095808383234 32.93413173652694 230-234 18.466898954703833 18.466898954703833 26.132404181184672 36.933797909407666 235-239 24.285714285714285 15.714285714285714 34.285714285714285 25.71428571428571 240-244 40.0 25.71428571428571 5.714285714285714 28.57142857142857 245-249 26.666666666666668 13.333333333333334 0.0 60.0 250-254 20.0 60.0 20.0 0.0 255-257 33.33333333333333 66.66666666666666 0.0 0.0 >>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 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.5 30 1.0 31 0.5 32 0.0 33 0.0 34 5.0 35 7.5 36 4.5 37 4.5 38 7.666666666666666 39 8.833333333333332 40 3.0 41 1.1666666666666665 42 1.6666666666666665 43 15.166666666666673 44 19.000000000000004 45 28.333333333333336 46 62.5 47 136.0 48 115.5 49 27.5 50 22.0 51 37.0 52 34.5 53 30.5 54 80.0 55 125.5 56 106.0 57 86.0 58 89.0 59 152.0 60 320.0 61 400.0 62 432.49999999999983 63 519.6666666666679 64 437.0000000000009 65 319.3333333333333 66 293.16666666666663 67 224.3333333333333 68 157.5 69 128.5 70 102.0 71 62.0 72 24.5 73 27.0 74 37.5 75 41.5 76 44.5 77 35.0 78 13.5 79 3.0 80 0.5 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 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-154 0.0 155-159 0.0 160-164 0.0 165-169 0.0 170-174 0.0 175-179 0.0 180-184 0.0 185-189 0.0 190-194 0.0 195-199 0.0 200-204 0.0 205-209 0.0 210-214 0.0 215-219 0.0 220-224 0.0 225-229 0.0 230-234 0.0 235-239 0.0 240-244 0.0 245-249 0.0 250-254 0.0 255-257 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 25-29 24.0 30-34 30.0 35-39 27.0 40-44 63.0 45-49 69.0 50-54 125.0 55-59 151.0 60-64 145.0 65-69 121.0 70-74 216.0 75-79 143.0 80-84 291.0 85-89 247.0 90-94 79.0 95-99 165.0 100-104 113.0 105-109 166.0 110-114 135.0 115-119 181.0 120-124 164.0 125-129 109.0 130-134 67.0 135-139 107.0 140-144 45.0 145-149 47.0 150-154 47.0 155-159 60.0 160-164 35.0 165-169 21.0 170-174 106.0 175-179 32.0 180-184 71.0 185-189 39.0 190-194 118.0 195-199 131.0 200-204 84.0 205-209 40.0 210-214 39.0 215-219 28.0 220-224 39.0 225-229 21.0 230-234 7.0 235-239 26.0 240-244 20.0 245-249 5.0 250-254 0.0 255-258 1.0 >>END_MODULE >>Sequence Duplication Levels fail #Total Deduplicated Percentage 29.2 #Duplication Level Percentage of deduplicated Percentage of total 1 81.93493150684932 23.925 2 6.335616438356165 3.6999999999999997 3 2.73972602739726 2.4 4 1.4554794520547945 1.7000000000000002 5 0.684931506849315 1.0 6 0.8561643835616438 1.5 7 0.3424657534246575 0.7000000000000001 8 0.3424657534246575 0.8 9 0.08561643835616438 0.22499999999999998 >10 4.280821917808219 29.175 >50 0.684931506849315 13.475000000000001 >100 0.2568493150684931 21.4 >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 ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCAT 328 8.200000000000001 No Hit TGCGTCCTCTGCTGGGGGCTGTGACGTTGCCCATGAGACTGCGATTCTCG 286 7.1499999999999995 No Hit AACGACTCCAGCCCCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAAGA 242 6.05 No Hit TAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATCCGGCTG 97 2.4250000000000003 No Hit GGAACGACCAAGACGACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCA 86 2.15 No Hit AACGACCAAGACGACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGT 64 1.6 No Hit CAGCAGGTCAACATCTCCACGGGGGTCGTCAATGCCACCGTCGACAACAC 64 1.6 No Hit AAGACGACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACAC 60 1.5 No Hit AGACGGGCGGGCTCACGGTGTTCGCGCCCACGGACAACGCGTTCACGAGC 58 1.4500000000000002 No Hit AGTACCCGCTCAACGTCACCGCCACCGGCCAGCAGGTCAACATCTCCACG 57 1.425 No Hit GAGCCCTTCACCAAGTTCTTCGGGTGCTCCATTCACAACTGCGACAAGCA 53 1.325 No Hit GCTAGCGAAAGCCGGGCAGTTCAACACGTTCATCCGGCTGCTGGCAGTTC 45 1.125 No Hit TAACAGGCGCCCACGGACAACGCGTTCACGAGCCTGGCTTCCGGCACGCTCAACTCGCTTTCGG 44 1.0999999999999999 No Hit CCAAATCGACAACCAGCTCAACAGCTCCCAGACGGGCGGGCTCACGGTGT 43 1.075 No Hit CAGCAGGTCAACATCTCCACGGGGGTCGTCAATGCCACCGTCACCGGCGACCAGCTCGTGGTCTACCAGGT 42 1.05 No Hit ACCGGCAGCCGGAACGACCAAGACGACCAACATAACAGGCGTGCTAGCGA 41 1.0250000000000001 No Hit CACCGGCCAGCAGGTCAACATCTCCACGGGGGTCGTCAATGCCACCGTCG 41 1.0250000000000001 No Hit CCAACGACTCCAGCCCCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAAGACGACCAACATAACAGGC 40 1.0 No Hit AACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATCCG 40 1.0 No Hit TGCTGGGGGCTGTGACGTTGCCCATGAGACTGCGATTCTCGGTCTACACG 38 0.95 No Hit GTTCCACGGGCGTCGCCGCCCAAATCGACAACCAGCTCAACAGCTCCCAG 38 0.95 No Hit TGCTGCGTTCCACGGCGTCGCCGCCCAAATCGACAACCAGCTCAACAGCT 32 0.8 No Hit TGCTGCGTTCCACGGGCGTCGCCGCCCAAATCGACAACCAGCTCAACAGC 31 0.775 No Hit GGCACCGGCAGCCGGAACGACCAAGACGACCAACATAACAGGCGTGCTAG 31 0.775 No Hit CAGCTTCAACGTCACTCCAGCCCCAGCGGCTCCGGCACAACCAGCTCAAC 30 0.75 No Hit TCATTTCTAGTGCTGCTCGTGATCTCAGCGGCGATCACGGCGTCGGCGCA 29 0.7250000000000001 No Hit GAACGACCAAGACGACCAACATAACAGGCGTGCTAGCGAAAGCCCGGCTG 27 0.675 No Hit GACACGGATTCCACCGCGTCCCGGGCAGCCGGAGGTGGTGGGGGTGGCGG 27 0.675 No Hit GTTCCACGGGCGTCGCCGCCCCAAATCGACAACCAGCTCAACAGCTCCCA 26 0.65 No Hit CGGAACGACCAAGACGACCAACATAACAGGCGTGCTAGCGAAAGCCGGGC 25 0.625 No Hit ACGACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTT 23 0.575 No Hit ACGACTCCAGCCCCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAAGAC 23 0.575 No Hit GCACCGGCAGCCGGAACGACCAAGACGACCAACATAACAGGCGTGCTAGC 23 0.575 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATCCGG 23 0.575 No Hit AGACGGGCGGGCTCACGGTGTTCGCGCCCACGGACAACGCGTTCACGAGCCTGGCTTCCG 21 0.525 No Hit CATTGGCGTCCTGCGTCCTCTGCTGGGGGCTGTGACGTTGCCCATGAGAC 20 0.5 No Hit ACGCTCAACTCGCTTTCGGACAGCCAGAAGAACTCGCTGGTGCAGTTCCA 19 0.475 No Hit ATCACGGCGTCGGCGCAGGGCCCAACGGCGGCGCCAACGACTCCAGCCCCAGCGGC 19 0.475 No Hit TAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATCCGGCTGCTGCGTTCCACGGGCGTCGCCG 19 0.475 No Hit CCGTCAATGCCACCGTCGACAACACGCTCTTCACCGGCGACCAGCTCGTGGTCTA 18 0.44999999999999996 No Hit AGCTCAACAGCTCCCAGACGGGCGGGCTCACGGTGTTCGCGCCCACGGAC 18 0.44999999999999996 No Hit AAGAAAACATCTCATCATCCGTCGGCATCCTCCTATGGAAGCAAATCTAA 18 0.44999999999999996 No Hit GAAAAAAGGAGCGTGAGAGCCAAATGGGGACCGTTACTACCGGCCCGTTC 18 0.44999999999999996 No Hit AGTTCGACACCGTGAGCAACCCGCTCAGGACGCAGGCCGGGAGCAGCTCCCCGGGGGAGTACCCGCTCAAC 17 0.42500000000000004 No Hit ACCACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATC 17 0.42500000000000004 No Hit CAGAAGAACTCGCTGGTGCAGTTCCACGTGCTGTCCACGGCGGTGCCCAT 15 0.375 No Hit AAGACGCCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACG 15 0.375 No Hit GGGTGGCGGCGTCGTCGCGGTGGCCATGGCATTGGCGTCCTGCGTCCTCT 15 0.375 No Hit AGCTCAACAGCTCCCAGACGGGCGGGCGTCACGGTGTTCGCGCCCACGGA 14 0.35000000000000003 No Hit ATTGGCGTCCTGCGTCCTCTGCTGGGGGCTGTGACGTTGCCCATGAGACT 14 0.35000000000000003 No Hit AGGTCAACATCTCCACGGGGGTCGTCAATGCCACCGTCGACAACACGCTCTTCACC 14 0.35000000000000003 No Hit TGCGTCCTCTGCTGGGGCTGTGACGTTGCCCATGAGACTGCGATTCTCGG 13 0.325 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATCCG 13 0.325 No Hit AGTACCGCTCAACGTCACCGCCACCGGCCAGCAGGTCAACATCTCCACGG 12 0.3 No Hit CAGACGGGCGGGCTCACGGTGTTCGCGCCCACGGACAACGCGTTCACGAGCCTGGCTTCC 12 0.3 No Hit CGTTCCACGGGCGTCGCCGCCCCAAATCGACAACCAGCTCAACAGCTCCC 12 0.3 No Hit ATGTCGCAGTTCGACACCGTGAGCAACCCGCTCAGGACGCAGGCCGGGAG 11 0.27499999999999997 No Hit AACGACTCCAGCCCCCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAAG 11 0.27499999999999997 No Hit GGCTGCTGCGTTCCACGGCGTCGCCGCCCAAATCGACAACCAGCTCAACA 10 0.25 No Hit GTGCCCATGTCGCAGTTCGACACCGTGAGCAACCCGCTCAGGACGCAGGCC 10 0.25 No Hit AAAAAAGGAGCGTGAGAGCCAAATGAATCGAAAGATTCATGTTTGGTTCG 10 0.25 No Hit GACACGGATTCCACCGCGTCCCGGGCAGCCGGAGGTGGTGGGGGTGGGCG 9 0.22499999999999998 No Hit GGCAGTTCAACACGTTCATCCGGCTGCTGCGTTCCACGGGCGGCGCCAAC 8 0.2 No Hit CGTTCCACGGCGTCGCCGCCCCAAATCGACAACCAGCTCAACAGCTCCCA 8 0.2 No Hit AATGGAGCCATGCAGAGATCATTTCTAGTGCTGCTCGTGATCTCAGCGGC 8 0.2 No Hit ACCAAGACGACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAA 8 0.2 No Hit AGGTCAACATCTCCACGGGGGTCGTCAATGCCACCGTCGACAACACGCTC 7 0.17500000000000002 No Hit GCAGTTCAACACGTTCATCCGGCTGCTGCGTTCCACGGGCGTCGCCGCCC 7 0.17500000000000002 No Hit GTTCCACGGGCGTCGCCGCCCCCAAATCGACAACCAGCTCAACAGCTCCC 7 0.17500000000000002 No Hit CAGCAGGTCAACATCTCCACGGGGTCGTCAATGCCACCGTCGACAACACG 7 0.17500000000000002 No Hit AGCTCAACAGCTCCCAGACGGGCGGCGTCACGGTGTTCGCGCCCACGGAC 6 0.15 No Hit ACCGGCAGCCGGAACGACCAAGACGCCAACATAACAGGCGTGCTAGCGAA 6 0.15 No Hit TGCGTCCTCTGCTGGGGGCTGTGACGTTGCCCATGAGACTGCGAATTCTC 6 0.15 No Hit GCAGTTCAACACGTTCATCCGGCTGCTGCGTTCCACGGCGTCGCCGCC 6 0.15 No Hit AATGGAAGCCATGCAGAGATCATTTCTAGTGCTGCTCGTGATCTCAGCGG 6 0.15 No Hit TGCTGCGTTCCACGGCGTCGCCGCCCAATCGACAACCAGCTCAACAGCTC 6 0.15 No Hit TGCGTCCCCTGCTGGGGGCTGTGACGTTGCCCATGAGACTGCGATTCTCG 6 0.15 No Hit TGCGTCCTCTGCTGGGGGCTGTGACGTTGCCCATGAGAGCTGCGATTCTC 6 0.15 No Hit ACCGGCAGCCGGAACGACCAAGACGACCACATAACAGGCGTGCTAGCGAA 6 0.15 No Hit GGAACGACCAAGACGCCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAG 6 0.15 No Hit GCAGTTCAACACGTTCATCCGGCTGCTGCGTTCCACGGCGTCGCCGCCCA 5 0.125 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATCCGGCTGCTGCGTTCCACGGCGTCG 5 0.125 No Hit GGAACGACCAAGACGACCAACATAACAGGCGTGCTAGCGAAAGCC 5 0.125 No Hit TGCGTCCTCTGCTGGGGGCTGTGACGTTGCCCCATGAGACTGCGATTCTC 5 0.125 No Hit AACGACTCCAGCCCCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAGAC 5 0.125 No Hit TGCTGCGTTCCACGGGCGTCGCCGCCCAATCGACAACCAGCTCAACAGCT 5 0.125 No Hit TGCGTCCTCTGCTGGGGGCTGTGACGTTGCCCATGAGACTGCGATTCTCGGTCTACACGTCGAGTTT 5 0.125 No Hit CGTTCCACGGCGTCGCCGCCCAAATCGACAACCAGCTCAACAGCTCCCAG 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 10-14 0.0 0.0 0.0 0.0 0.0 15-19 0.0 0.0 0.0 0.0 0.0 20-24 0.0 0.0 0.0 0.0 0.0 25-29 0.0 0.0 0.0 0.0 0.0 30-34 0.0 0.0 0.0 0.0 0.0 35-39 0.0 0.0 0.0 0.0 0.0 40-44 0.0 0.0 0.0 0.0 0.0 45-49 0.0 0.0 0.0 0.0 0.0 50-54 0.0 0.0 0.0 0.0 0.0 55-59 0.0 0.0 0.0 0.0 0.0 60-64 0.0 0.0 0.0 0.0 0.0 65-69 0.0 0.0 0.0 0.0 0.0 70-74 0.0 0.0 0.0 0.0 0.0 75-79 0.0 0.0 0.0 0.0 0.0 80-84 0.0 0.0 0.0 0.0 0.0 85-89 0.0 0.0 0.0 0.0 0.0 90-94 0.0 0.0 0.0 0.0 0.0 95-99 0.0 0.0 0.0 0.0 0.0 100-104 0.0 0.0 0.0 0.0 0.0 105-109 0.0 0.0 0.0 0.0 0.0 110-114 0.0 0.0 0.0 0.0 0.0 115-119 0.0 0.0 0.0 0.0 0.0 120-124 0.0 0.0 0.0 0.0 0.0 125-129 0.0 0.0 0.0 0.0 0.0 130-134 0.0 0.0 0.0 0.0 0.0 135-139 0.0 0.0 0.0 0.0 0.0 140-144 0.0 0.0 0.0 0.0 0.0 145-149 0.0 0.0 0.0 0.0 0.0 150-154 0.0 0.0 0.0 0.0 0.0 155-159 0.0 0.0 0.0 0.0 0.0 160-164 0.0 0.0 0.0 0.0 0.0 165-169 0.0 0.0 0.0 0.0 0.0 170-174 0.0 0.0 0.0 0.0 0.0 175-179 0.0 0.0 0.0 0.0 0.0 180-184 0.0 0.0 0.0 0.0 0.0 185-189 0.0 0.0 0.0 0.0 0.0 190-194 0.0 0.0 0.0 0.0 0.0 195-199 0.0 0.0 0.0 0.0 0.0 200-204 0.0 0.0 0.0 0.0 0.0 205-209 0.0 0.0 0.0 0.0 0.0 210-214 0.0 0.0 0.0 0.0 0.0 215-219 0.0 0.0 0.0 0.0 0.0 220-224 0.0 0.0 0.0 0.0 0.0 225-229 0.0 0.0 0.0 0.0 0.0 230-234 0.0 0.0 0.0 0.0 0.0 235-239 0.0 0.0 0.0 0.0 0.0 240-244 0.0 0.0 0.0 0.0 0.0 245 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACAAAAA 5 0.0 8336.0 220 AACAAAA 5 0.002357221 1667.2 215-219 AAACAAA 5 0.002357221 1667.2 215-219 TAAAAAA 5 0.002357221 1667.2 210-214 AAAACAA 5 0.002357221 1667.2 215-219 AAAAACA 5 0.002357221 1667.2 215-219 AAAAAAC 5 0.002357221 1667.2 215-219 AAAAAAA 20 0.0 1667.2 210-214 GCTGCTA 5 0.0035355487 1389.3334 205-209 GCTAAAA 5 0.0035355487 1389.3334 205-209 TGCTAAA 5 0.0035355487 1389.3334 205-209 CTAAAAA 5 0.0035355487 1389.3334 205-209 CTGCTAA 5 0.0035355487 1389.3334 205-209 GACAGCC 25 0.005894467 833.6 205-209 TATATAT 10 0.005881052 151.56364 180-184 GCTTTCG 55 1.1662055E-4 133.73262 195-199 CTTTCGG 60 1.6496329E-4 122.588234 195-199 CTCTGCT 70 0.0 96.75714 7 TCCTCTG 70 0.0 96.75714 5 TGCGTCC 70 0.0 96.75714 1 >>END_MODULE Read 889368 spots for ERR1942991.sra Written 889368 spots for ERR1942991.sra Read 889368 spots for ERR1942991.sra Written 889368 spots for ERR1942991.sra Read 889368 spots for ERR1942991.sra Written 889368 spots for ERR1942991.sra Read 889379 spots for ERR1942991.sra Written 889379 spots for ERR1942991.sra Read 889368 spots for ERR1942991.sra Written 889368 spots for ERR1942991.sra Read 889368 spots for ERR1942991.sra Written 889368 spots for ERR1942991.sra Read 889368 spots for ERR1942991.sra Written 889368 spots for ERR1942991.sra Read 889368 spots for ERR1942991.sra Written 889368 spots for ERR1942991.sra Read 889368 spots for ERR1942991.sra Written 889368 spots for ERR1942991.sra Read 889368 spots for ERR1942991.sra Written 889368 spots for ERR1942991.sra Read 889368 spots for ERR1942991.sra Written 889368 spots for ERR1942991.sra Read 889368 spots for ERR1942991.sra Written 889368 spots for ERR1942991.sra Read 889368 spots for ERR1942991.sra Written 889368 spots for ERR1942991.sra Read 889368 spots for ERR1942991.sra Written 889368 spots for ERR1942991.sra Read 889368 spots for ERR1942991.sra Written 889368 spots for ERR1942991.sra Read 889368 spots for ERR1942991.sra Written 889368 spots for ERR1942991.sra Read 889368 spots for ERR1942991.sra Written 889368 spots for ERR1942991.sra Read 889368 spots for ERR1942991.sra Written 889368 spots for ERR1942991.sra Read 889368 spots for ERR1942991.sra Written 889368 spots for ERR1942991.sra Read 889368 spots for ERR1942991.sra Written 889368 spots for ERR1942991.sra SRR ids: ['ERR1942991.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_dn21cvje ERR1942991.sra spots: 17787371 blocks: [[1, 889368], [889369, 1778736], [1778737, 2668104], [2668105, 3557472], [3557473, 4446840], [4446841, 5336208], [5336209, 6225576], [6225577, 7114944], [7114945, 8004312], [8004313, 8893680], [8893681, 9783048], [9783049, 10672416], [10672417, 11561784], [11561785, 12451152], [12451153, 13340520], [13340521, 14229888], [14229889, 15119256], [15119257, 16008624], [16008625, 16897992], [16897993, 17787371]] ERR1942991 file size 4896567 ERR1942991 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 ERR1942991 ERR1942991_1.fastq Input file: ERR1942991_1.fastq trimmed: ERR1942991-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- 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 -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Tue Dec 10 00:44:57 2024 >> started Tue Dec 10 00:45:07 2024 >> done (10.345s) 17787371 reads processed; of these: 216 ( 0.00%) short reads filtered out after trimming by size control 27 ( 0.00%) empty reads filtered out after trimming by size control 17787128 (100.00%) reads available; of these: 953099 ( 5.36%) trimmed reads available after processing 16834029 (94.64%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 251 0.00% 19 353 0.00% 20 593 0.00% 21 925 0.01% 22 1708 0.01% 23 1960 0.01% 24 4933 0.03% 25 26026 0.15% 26 27140 0.15% 27 27916 0.16% 28 28326 0.16% 29 28884 0.16% 30 28931 0.16% 31 29148 0.16% 32 29771 0.17% 33 29229 0.16% 34 30261 0.17% 35 31017 0.17% 36 32232 0.18% 37 32996 0.19% 38 33638 0.19% 39 34336 0.19% 40 35788 0.20% 41 36810 0.21% 42 37147 0.21% 43 37819 0.21% 44 38964 0.22% 45 40193 0.23% 46 42333 0.24% 47 43196 0.24% 48 44951 0.25% 49 46139 0.26% 50 47014 0.26% 51 49805 0.28% 52 49688 0.28% 53 52549 0.30% 54 54328 0.31% 55 55803 0.31% 56 59213 0.33% 57 63379 0.36% 58 63944 0.36% 59 64496 0.36% 60 69338 0.39% 61 70853 0.40% 62 72990 0.41% 63 77568 0.44% 64 76293 0.43% 65 78642 0.44% 66 78316 0.44% 67 83631 0.47% 68 86204 0.48% 69 88001 0.49% 70 90969 0.51% 71 93355 0.52% 72 94688 0.53% 73 96155 0.54% 74 102820 0.58% 75 106153 0.60% 76 105467 0.59% 77 113856 0.64% 78 108501 0.61% 79 113136 0.64% 80 112519 0.63% 81 115628 0.65% 82 118588 0.67% 83 118879 0.67% 84 122725 0.69% 85 129470 0.73% 86 131320 0.74% 87 129726 0.73% 88 132042 0.74% 89 135278 0.76% 90 150629 0.85% 91 137583 0.77% 92 139314 0.78% 93 141286 0.79% 94 143115 0.80% 95 151869 0.85% 96 154127 0.87% 97 152864 0.86% 98 159047 0.89% 99 152153 0.86% 100 154922 0.87% 101 160687 0.90% 102 159184 0.89% 103 154112 0.87% 104 159152 0.89% 105 161706 0.91% 106 158745 0.89% 107 157476 0.89% 108 157286 0.88% 109 167302 0.94% 110 168707 0.95% 111 170998 0.96% 112 164562 0.93% 113 158767 0.89% 114 164917 0.93% 115 163876 0.92% 116 160589 0.90% 117 167826 0.94% 118 167814 0.94% 119 167510 0.94% 120 165100 0.93% 121 161398 0.91% 122 162544 0.91% 123 160107 0.90% 124 158367 0.89% 125 156795 0.88% 126 157062 0.88% 127 154031 0.87% 128 153663 0.86% 129 158754 0.89% 130 155833 0.88% 131 148762 0.84% 132 148686 0.84% 133 146381 0.82% 134 141775 0.80% 135 140508 0.79% 136 141455 0.80% 137 142110 0.80% 138 144248 0.81% 139 139511 0.78% 140 136624 0.77% 141 136347 0.77% 142 129912 0.73% 143 129365 0.73% 144 131249 0.74% 145 132895 0.75% 146 134915 0.76% 147 122717 0.69% 148 124340 0.70% 149 123448 0.69% 150 119444 0.67% 151 118235 0.66% 152 110607 0.62% 153 117213 0.66% 154 120034 0.67% 155 109781 0.62% 156 106635 0.60% 157 106310 0.60% 158 100086 0.56% 159 102727 0.58% 160 99586 0.56% 161 97165 0.55% 162 99282 0.56% 163 98262 0.55% 164 95431 0.54% 165 91213 0.51% 166 86611 0.49% 167 86426 0.49% 168 85164 0.48% 169 80953 0.46% 170 78048 0.44% 171 78614 0.44% 172 75955 0.43% 173 73595 0.41% 174 70799 0.40% 175 67944 0.38% 176 67665 0.38% 177 66742 0.38% 178 65804 0.37% 179 63192 0.36% 180 61477 0.35% 181 57553 0.32% 182 55334 0.31% 183 53211 0.30% 184 51855 0.29% 185 50320 0.28% 186 49506 0.28% 187 47609 0.27% 188 45521 0.26% 189 42604 0.24% 190 41167 0.23% 191 40296 0.23% 192 40049 0.23% 193 38828 0.22% 194 38359 0.22% 195 36596 0.21% 196 34831 0.20% 197 34326 0.19% 198 32813 0.18% 199 31165 0.18% 200 29743 0.17% 201 28880 0.16% 202 28356 0.16% 203 27752 0.16% 204 26143 0.15% 205 24458 0.14% 206 23204 0.13% 207 22943 0.13% 208 22003 0.12% 209 20507 0.12% 210 20049 0.11% 211 19156 0.11% 212 18290 0.10% 213 17842 0.10% 214 17555 0.10% 215 16708 0.09% 216 15773 0.09% 217 15002 0.08% 218 14398 0.08% 219 12850 0.07% 220 12288 0.07% 221 11610 0.07% 222 10982 0.06% 223 10564 0.06% 224 9994 0.06% 225 9345 0.05% 226 8955 0.05% 227 8395 0.05% 228 7781 0.04% 229 7321 0.04% 230 7009 0.04% 231 6592 0.04% 232 6340 0.04% 233 5751 0.03% 234 5429 0.03% 235 5242 0.03% 236 5080 0.03% 237 4651 0.03% 238 4445 0.02% 239 4095 0.02% 240 3738 0.02% 241 3524 0.02% 242 3155 0.02% 243 3028 0.02% 244 2698 0.02% 245 2525 0.01% 246 2348 0.01% 247 2175 0.01% 248 2032 0.01% 249 1879 0.01% 250 1704 0.01% 251 1535 0.01% 252 1471 0.01% 253 1270 0.01% 254 1245 0.01% 255 1153 0.01% 256 1076 0.01% 257 917 0.01% 258 834 0.00% 259 755 0.00% 260 746 0.00% 261 662 0.00% 262 612 0.00% 263 527 0.00% 264 486 0.00% 265 465 0.00% 266 422 0.00% 267 352 0.00% 268 360 0.00% 269 302 0.00% 270 281 0.00% 271 252 0.00% 272 233 0.00% 273 186 0.00% 274 190 0.00% 275 162 0.00% 276 129 0.00% 277 118 0.00% 278 102 0.00% 279 103 0.00% 280 79 0.00% 281 75 0.00% 282 61 0.00% 283 44 0.00% 284 45 0.00% 285 37 0.00% 286 37 0.00% 287 32 0.00% 288 23 0.00% 289 23 0.00% 290 19 0.00% 291 11 0.00% 292 21 0.00% 293 18 0.00% 294 10 0.00% 295 10 0.00% 296 13 0.00% 297 5 0.00% 298 8 0.00% 299 7 0.00% 300 8 0.00% 301 3 0.00% 302 6 0.00% 303 4 0.00% 304 3 0.00% 305 7 0.00% 306 1 0.00% 307 1 0.00% 308 6 0.00% 309 1 0.00% 310 3 0.00% 311 3 0.00% 312 3 0.00% 313 1 0.00% 314 3 0.00% 315 1 0.00% 316 3 0.00% 317 2 0.00% 318 1 0.00% 319 4 0.00% 320 0 0.00% 321 2 0.00% 322 1 0.00% 323 1 0.00% 324 0 0.00% 325 1 0.00% 326 0 0.00% 327 1 0.00% 328 1 0.00% 329 1 0.00% 330 2 0.00% 331 1 0.00% 332 1 0.00% 333 0 0.00% 334 0 0.00% 335 1 0.00% 336 1 0.00% 337 0 0.00% 338 2 0.00% 339 1 0.00% 340 0 0.00% 341 0 0.00% 342 1 0.00% 343 0 0.00% 344 1 0.00% 345 1 0.00% 346 0 0.00% 347 0 0.00% 348 2 0.00% 349 1 0.00% 350 1 0.00% 351 0 0.00% 352 0 0.00% 353 0 0.00% 354 3 0.00% 355 2 0.00% 356 2 0.00% 357 0 0.00% 358 0 0.00% 359 0 0.00% 360 1 0.00% 361 0 0.00% 362 2 0.00% 363 0 0.00% 364 0 0.00% 365 1 0.00% 366 0 0.00% 367 2 0.00% 368 1 0.00% 369 1 0.00% 17787128 reads passed initial QC criterion=sequence-density sequence-density=1.05 sequence-density-rank=1 fanout-score=1.00 fanout-score-rank=39 prefix-density=0.01 prefix-fanout=1.0 sequence=TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGAGACAACCTGGCGAACTG criterion=fanout-score sequence-density=0.07 sequence-density-rank=22 fanout-score=50.90 fanout-score-rank=1 prefix-density=0.47 prefix-fanout=8.0 sequence=CTGCTGCTGGAAGTGAGTTTCACTGCTGCTGGATGTATCTCTGATTAATGAGTTGCTGCTCTTTAGAAGGAAGAAGGGGTTTGATATCGCCGCGGACACGCTGCATTGGCGTCTAGTGAGTGGTATTTTGGTGTGGCAGACAGAGTTACGTGCTGAGTTTATACTAGTCGGGTCTTTTGTTATCTTTTGTGGTTTTCCTTCGTTTTCGAGTCTAAAACTGCAATAGCTGTGCAGTTTGCTCTATCAGTCGTCCTGTTATTTTTTAGTATGCTGAAACTGCATCAGTAATACCATATGTGATATTCGTACCCTGTTA Started job on | Dec 10 00:45:22 Started mapping on | Dec 10 00:45:22 Finished on | Dec 10 00:46:01 Mapping speed, Million of reads per hour | 1641.89 Number of input reads | 17787128 Average input read length | 119 UNIQUE READS: Uniquely mapped reads number | 15202902 Uniquely mapped reads % | 85.47% Average mapped length | 117.89 Number of splices: Total | 4853212 Number of splices: Annotated (sjdb) | 4415954 Number of splices: GT/AG | 4622609 Number of splices: GC/AG | 60507 Number of splices: AT/AC | 3333 Number of splices: Non-canonical | 166763 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.25% Deletion average length | 1.18 Insertion rate per base | 0.21% Insertion average length | 1.16 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 765873 % of reads mapped to multiple loci | 4.31% Number of reads mapped to too many loci | 243505 % of reads mapped to too many loci | 1.37% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 8.26% % of reads unmapped: other | 0.59% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1818353 1818353 1818353 N_multimapping 765873 765873 765873 N_noFeature 605394 712403 14768408 N_ambiguous 373205 52932 1451 UnstrandedReadsAssigned:14224303 PositiveStrandReadsAssigned:14437567 NegativeStrandReadsAssigned:433043 Dataset is classified positive stranded MeadianReadLen=119 20thPercentileLength=84 echo kmer=79 ERR1942991 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=31 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [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 single-end mode [quant] will process file 1: ERR1942991-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 17,787,128 reads, 14,917,530 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,193 rounds 52973 ERR1942991.ke.tsv 35125 ERR1942991.se.tsv 88098 total ==> ERR1942991.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 99.1932 10.3024 PNS24249 1928 1829 75.4204 4.04729 PNS24246 1044 945 99.1932 10.3024 PNS24248 1044 945 99.1932 10.3024 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 5526.72 360.669 KQK14071 474 375 2.90039 0.759128 ==> ERR1942991.se.tsv <== BRADI_1g14170v3 5610 BRADI_1g53295v3 114 BRADI_1g59795v3 344 BRADI_1g07683v3 1 BRADI_1g00485v3 0 BRADI_1g20270v3 763 BRADI_1g74790v3 600 BRADI_1g09890v3 0 BRADI_1g77505v3 546 BRADI_1g48960v3 0 ERR1942991 completed mapping pipeline successfully