Starting /dee2/code/volunteer_pipeline.sh SRR7169637 current disk space = 3051867017216 free memory = 1412932044 SRR7169637 SRAfilesize 1b8539aa1be16928e41f93f63ef1e60a SRR7169637.sra SRR7169637.sra file validated SRR7169637 is paired end SRR7169637 is conventional basespace SRR7169637 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7169637_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.6275 34.0 33.0 34.0 32.0 34.0 2 33.232 34.0 33.0 34.0 32.0 34.0 3 33.28175 34.0 33.0 34.0 32.0 34.0 4 33.283 34.0 33.0 34.0 33.0 34.0 5 33.3025 34.0 33.0 34.0 33.0 34.0 6 36.8445 38.0 37.0 38.0 35.0 38.0 7 37.16625 38.0 38.0 38.0 36.0 38.0 8 37.18625 38.0 38.0 38.0 36.0 38.0 9 37.34075 38.0 38.0 38.0 37.0 38.0 10-14 37.3311 38.0 38.0 38.0 37.0 38.0 15-19 37.28254999999999 38.0 38.0 38.0 36.8 38.0 20-24 37.251850000000005 38.0 38.0 38.0 36.8 38.0 25-29 37.2252 38.0 38.0 38.0 36.6 38.0 30-34 37.1262 38.0 38.0 38.0 36.0 38.0 35-39 37.03515 38.0 38.0 38.0 36.0 38.0 40-44 36.82875 38.0 38.0 38.0 35.4 38.0 45-49 36.7435 38.0 38.0 38.0 35.0 38.0 50-54 36.62625 38.0 38.0 38.0 34.2 38.0 55-59 36.587450000000004 38.0 38.0 38.0 34.0 38.0 60-64 36.539 38.0 38.0 38.0 34.0 38.0 65-69 36.4051 38.0 37.4 38.0 34.0 38.0 70-74 36.3833 38.0 38.0 38.0 34.0 38.0 75-79 36.21849999999999 38.0 37.2 38.0 33.2 38.0 80-84 36.1374 38.0 37.0 38.0 33.0 38.0 85-89 35.886 38.0 37.0 38.0 31.8 38.0 90-94 35.7299 38.0 37.0 38.0 30.6 38.0 95-99 35.5883 38.0 37.0 38.0 30.0 38.0 100-104 35.215 38.0 36.0 38.0 28.8 38.0 105-109 35.061899999999994 38.0 36.0 38.0 28.2 38.0 110-114 34.9042 38.0 35.8 38.0 27.8 38.0 115-119 34.4994 38.0 35.0 38.0 25.2 38.0 120-124 34.3496 38.0 35.0 38.0 25.2 38.0 125-129 33.972249999999995 38.0 34.0 38.0 23.0 38.0 130-134 33.68965000000001 38.0 34.0 38.0 22.2 38.0 135-139 33.36455 38.0 34.0 38.0 17.4 38.0 140-144 32.62455 38.0 33.2 38.0 14.4 38.0 145-149 31.800349999999998 37.6 33.0 38.0 11.2 38.0 150-151 28.063000000000002 35.0 17.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 4 1.0 5 0.0 6 0.0 7 1.0 8 1.0 9 0.0 10 0.0 11 0.0 12 2.0 13 1.0 14 1.0 15 4.0 16 7.0 17 5.0 18 10.0 19 7.0 20 13.0 21 10.0 22 12.0 23 15.0 24 25.0 25 20.0 26 34.0 27 32.0 28 37.0 29 54.0 30 62.0 31 89.0 32 100.0 33 149.0 34 221.0 35 355.0 36 893.0 37 1839.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.051543761163565 12.350089308497065 9.39015054860934 36.20821638173003 2 24.099999999999998 14.075 30.25 31.574999999999996 3 19.375 20.225 25.4 35.0 4 22.275 27.675 23.825 26.224999999999998 5 22.1 32.800000000000004 23.05 22.05 6 19.6 35.225 24.275 20.9 7 13.55 27.725 40.849999999999994 17.875 8 17.875 26.174999999999997 31.574999999999996 24.375 9 15.875 25.0 34.949999999999996 24.175 10-14 20.365 29.705 27.284999999999997 22.645 15-19 19.814999999999998 29.244999999999997 26.97 23.97 20-24 19.96 28.34 28.1 23.599999999999998 25-29 19.93 29.09 27.1 23.880000000000003 30-34 19.655 28.73 27.91 23.705000000000002 35-39 19.98 28.439999999999998 27.91 23.669999999999998 40-44 20.45 28.285 27.315 23.95 45-49 20.46 28.7 26.905 23.935000000000002 50-54 20.19 28.485 27.42 23.905 55-59 19.580000000000002 29.4 27.169999999999998 23.849999999999998 60-64 19.735 28.384999999999998 27.33 24.55 65-69 20.3 28.965000000000003 27.365000000000002 23.369999999999997 70-74 20.02 28.494999999999997 27.36 24.125 75-79 20.29 28.62 26.68 24.41 80-84 19.919999999999998 27.755000000000003 27.825 24.5 85-89 20.41 28.785 27.015 23.79 90-94 20.51 28.49 27.150000000000002 23.849999999999998 95-99 20.325 29.03 27.36 23.285 100-104 20.833541802171414 28.878771201280834 26.77240206133987 23.515284935207887 105-109 20.945 27.515 27.85 23.69 110-114 20.15616397217078 28.54997747635017 27.328695129886384 23.96516342159267 115-119 20.509229153118905 28.84798159171627 27.43234455504977 23.21044470011505 120-124 20.75745447268361 28.762257354412647 27.276365819491694 23.203922353412047 125-129 20.9 28.26 26.75 24.09 130-134 20.935467733866933 28.649324662331168 26.768384192096047 23.646823411705853 135-139 20.51 28.29 27.634999999999998 23.565 140-144 20.745 27.715 27.305 24.235 145-149 20.43 28.310000000000002 27.405 23.855 150-151 19.975 28.499999999999996 26.950000000000003 24.575 >>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 0.0 16 0.0 17 0.0 18 0.5 19 0.5 20 0.0 21 1.5 22 1.5 23 0.5 24 2.0 25 4.0 26 5.0 27 7.0 28 12.0 29 18.0 30 16.5 31 15.5 32 27.5 33 38.5 34 48.5 35 63.5 36 82.5 37 100.0 38 120.0 39 149.5 40 177.0 41 218.0 42 238.0 43 251.5 44 280.0 45 283.0 46 281.0 47 276.0 48 240.5 49 205.0 50 171.5 51 142.0 52 128.0 53 104.5 54 82.0 55 54.5 56 40.5 57 33.0 58 21.0 59 15.5 60 11.0 61 8.5 62 6.0 63 5.5 64 3.5 65 0.5 66 2.0 67 2.0 68 0.5 69 1.0 70 0.5 71 0.5 72 1.0 73 0.5 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 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 2.025 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 0.065 105-109 0.0 110-114 0.105 115-119 0.045 120-124 0.06 125-129 0.0 130-134 0.05 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.75 #Duplication Level Percentage of deduplicated Percentage of total 1 99.74937343358395 99.5 2 0.2506265664160401 0.5 3 0.0 0.0 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences pass >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0125 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 0.025 0.0 0.0 0.0 0.0 80-81 0.037500000000000006 0.0 0.0 0.0 0.0 82-83 0.05 0.0 0.0 0.0 0.0 84-85 0.05 0.0 0.0 0.0 0.0 86-87 0.0625 0.0 0.0 0.0 0.0 88-89 0.0875 0.0 0.0 0.0 0.0 90-91 0.1 0.0 0.0 0.0 0.0 92-93 0.1125 0.0 0.0 0.0 0.0 94-95 0.125 0.0 0.0 0.0 0.0 96-97 0.15 0.0 0.0 0.0 0.0 98-99 0.175 0.0 0.0 0.0 0.0 100-101 0.225 0.0 0.0 0.0 0.0 102-103 0.25 0.0 0.0 0.0 0.0 104-105 0.2875 0.0 0.0 0.0 0.0 106-107 0.475 0.0 0.0 0.0 0.0 108-109 0.5625 0.0 0.0 0.0 0.0 110-111 0.6 0.0 0.0 0.0 0.0 112-113 0.6375 0.0 0.0 0.0 0.0 114-115 0.75 0.0 0.0 0.0 0.0 116-117 0.975 0.0 0.0 0.0 0.0 118-119 1.125 0.0 0.0 0.0 0.0 120-121 1.2625 0.0 0.0 0.0 0.0 122-123 1.4125 0.0 0.0 0.0 0.0 124-125 1.675 0.0 0.0 0.0 0.0 126-127 1.925 0.0 0.0 0.0 0.0 128-129 2.1375 0.0 0.0 0.0 0.0 130-131 2.3875 0.0 0.0 0.0 0.0 132-133 2.5999999999999996 0.0 0.0 0.0 0.0 134-135 2.8499999999999996 0.0 0.0 0.0 0.0 136-137 3.0999999999999996 0.0 0.0 0.0 0.0 138-139 3.3875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATAAAGA 10 0.006830828 145.0 6 TAAAGAC 10 0.006830828 145.0 7 >>END_MODULE SRR7169637 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7169637_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.46625 33.0 33.0 34.0 32.0 34.0 2 32.694 33.0 33.0 34.0 32.0 34.0 3 32.75 33.0 33.0 34.0 32.0 34.0 4 32.76325 33.0 33.0 34.0 32.0 34.0 5 32.64275 34.0 33.0 34.0 32.0 34.0 6 36.78825 38.0 38.0 38.0 36.0 38.0 7 36.80625 38.0 38.0 38.0 36.0 38.0 8 36.78725 38.0 38.0 38.0 35.0 38.0 9 36.8125 38.0 38.0 38.0 36.0 38.0 10-14 36.6741 38.0 38.0 38.0 35.6 38.0 15-19 36.71124999999999 38.0 38.0 38.0 36.0 38.0 20-24 36.710899999999995 38.0 38.0 38.0 36.0 38.0 25-29 36.722 38.0 38.0 38.0 36.0 38.0 30-34 36.750350000000005 38.0 38.0 38.0 36.0 38.0 35-39 36.566199999999995 38.0 38.0 38.0 35.2 38.0 40-44 36.58245 38.0 38.0 38.0 35.6 38.0 45-49 36.499550000000006 38.0 38.0 38.0 35.2 38.0 50-54 36.3768 38.0 38.0 38.0 34.8 38.0 55-59 35.9433 38.0 38.0 38.0 34.0 38.0 60-64 35.71835 38.0 38.0 38.0 33.2 38.0 65-69 35.58655 38.0 38.0 38.0 33.0 38.0 70-74 35.531600000000005 38.0 38.0 38.0 33.0 38.0 75-79 35.31635 38.0 38.0 38.0 30.8 38.0 80-84 35.37045 38.0 38.0 38.0 31.2 38.0 85-89 35.48775 38.0 38.0 38.0 31.0 38.0 90-94 35.447700000000005 38.0 37.8 38.0 31.4 38.0 95-99 35.31735 38.0 37.8 38.0 30.2 38.0 100-104 35.12415 38.0 37.0 38.0 28.8 38.0 105-109 35.1347 38.0 37.0 38.0 30.0 38.0 110-114 34.907149999999994 38.0 37.0 38.0 28.2 38.0 115-119 34.6257 38.0 36.2 38.0 26.2 38.0 120-124 34.46585 38.0 36.0 38.0 25.8 38.0 125-129 34.267 38.0 35.8 38.0 23.8 38.0 130-134 33.796049999999994 38.0 35.0 38.0 19.0 38.0 135-139 33.2291 38.0 35.0 38.0 14.6 38.0 140-144 32.9134 38.0 35.0 38.0 13.8 38.0 145-149 31.983399999999996 38.0 33.6 38.0 6.4 38.0 150-151 28.149 36.0 17.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 11.0 3 11.0 4 3.0 5 2.0 6 3.0 7 4.0 8 1.0 9 4.0 10 5.0 11 9.0 12 8.0 13 24.0 14 21.0 15 5.0 16 2.0 17 3.0 18 8.0 19 10.0 20 14.0 21 10.0 22 11.0 23 19.0 24 24.0 25 25.0 26 47.0 27 38.0 28 43.0 29 51.0 30 46.0 31 61.0 32 74.0 33 95.0 34 147.0 35 210.0 36 523.0 37 2428.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.30856138589003 23.92668842580969 13.90911373336681 24.855636454933467 2 29.625 26.150000000000002 27.224999999999998 17.0 3 21.475 28.425 30.875000000000004 19.225 4 22.175 34.050000000000004 24.349999999999998 19.425 5 24.95 36.025 21.175 17.849999999999998 6 20.075000000000003 38.375 23.275000000000002 18.275 7 20.200000000000003 21.45 38.25 20.1 8 22.275 25.95 27.450000000000003 24.325 9 21.349999999999998 25.424999999999997 31.05 22.175 10-14 23.016111277894527 28.68507955568898 26.24337035925148 22.055438807165014 15-19 23.73636272645381 28.035231708537683 27.790011009908916 20.43839455509959 20-24 23.01 27.644999999999996 27.810000000000002 21.535 25-29 22.5 28.610000000000003 27.93 20.96 30-34 22.770000000000003 27.925 27.705000000000002 21.6 35-39 22.82 27.87 27.96 21.349999999999998 40-44 23.27 28.000000000000004 27.744999999999997 20.985 45-49 23.215 27.785 27.800000000000004 21.2 50-54 22.99075748442837 28.03395619851316 28.24994976893711 20.72533654812136 55-59 23.87280012172237 28.26494902875691 27.483897144596032 20.378353704924685 60-64 23.308155557823824 27.743186689803 28.182096560171484 20.766561192201692 65-69 23.359271014641138 28.079246442100953 27.853998157059483 20.707484386198423 70-74 23.630031752535082 27.445457338932705 28.234149339342412 20.690361569189797 75-79 23.94792147214106 27.192577784612233 28.57142857142857 20.288072171818136 80-84 23.061599754826847 27.576871999182757 28.389008070282973 20.972520175707427 85-89 23.151909017059303 27.503046303818035 28.122461413484974 21.22258326563769 90-94 23.470421393841168 28.074351701782817 27.805915721231766 20.64931118314425 95-99 23.725212464589234 27.726628895184135 27.90368271954674 20.644475920679888 100-104 23.40145690004047 27.86321327397815 27.554633751517603 21.180696074463782 105-109 23.765478898155166 27.824109173616375 28.102097548647965 20.30831437958049 110-114 23.65298187143362 27.69277382214816 28.162399636418723 20.491844669999494 115-119 23.36811331216291 27.773577297242802 28.685921669438986 20.1723877211553 120-124 24.243951612903224 28.180443548387096 26.794354838709676 20.78125 125-129 23.97509869419982 27.27502783682559 28.292337281101325 20.457536187873266 130-134 24.541435902647223 27.64595294954525 27.590061480615823 20.222549667191707 135-139 24.063952597435765 27.00618072227614 28.11462430403024 20.815242376257853 140-144 24.32570755924049 27.944111776447105 27.575617994779673 20.15456266953273 145-149 24.930733709594662 27.880964597229347 26.885582349923038 20.30271934325295 150-151 24.378622021893108 27.778493238892466 27.70122343850612 20.141661300708307 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.5 5 0.5 6 0.0 7 0.0 8 0.0 9 0.5 10 0.5 11 0.0 12 0.0 13 1.0 14 1.0 15 0.0 16 0.0 17 0.5 18 1.5 19 4.0 20 4.5 21 2.0 22 7.0 23 10.0 24 7.5 25 10.0 26 9.0 27 6.5 28 11.0 29 14.5 30 15.0 31 19.0 32 25.0 33 32.5 34 39.0 35 51.0 36 73.0 37 97.0 38 127.5 39 171.0 40 203.5 41 232.0 42 253.5 43 270.5 44 292.0 45 282.0 46 274.5 47 270.0 48 229.0 49 188.5 50 163.0 51 137.5 52 116.0 53 88.5 54 67.0 55 49.5 56 32.0 57 27.0 58 21.0 59 13.5 60 8.5 61 8.0 62 10.0 63 9.0 64 5.5 65 2.5 66 1.0 67 0.0 68 0.5 69 0.5 70 0.5 71 0.5 72 0.5 73 0.5 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 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 0.42500000000000004 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 0.06999999999999999 15-19 0.09 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 0.45999999999999996 55-59 1.415 60-64 2.03 65-69 2.33 70-74 2.37 75-79 2.455 80-84 2.11 85-89 1.52 90-94 1.28 95-99 1.16 100-104 1.16 105-109 1.075 110-114 0.985 115-119 0.8049999999999999 120-124 0.8 125-129 1.21 130-134 1.595 135-139 2.1149999999999998 140-144 2.305 145-149 2.55 150-151 2.9375 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.675 #Duplication Level Percentage of deduplicated Percentage of total 1 99.67394030599448 99.35000000000001 2 0.32605969400551793 0.65 3 0.0 0.0 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences pass >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0125 0.0 0.0 0.0 0.0 82-83 0.025 0.0 0.0 0.0 0.0 84-85 0.025 0.0 0.0 0.0 0.0 86-87 0.037500000000000006 0.0 0.0 0.0 0.0 88-89 0.0625 0.0 0.0 0.0 0.0 90-91 0.075 0.0 0.0 0.0 0.0 92-93 0.0875 0.0 0.0 0.0 0.0 94-95 0.1 0.0 0.0 0.0 0.0 96-97 0.125 0.0 0.0 0.0 0.0 98-99 0.15 0.0 0.0 0.0 0.0 100-101 0.2 0.0 0.0 0.0 0.0 102-103 0.225 0.0 0.0 0.0 0.0 104-105 0.2625 0.0 0.0 0.0 0.0 106-107 0.44999999999999996 0.0 0.0 0.0 0.0 108-109 0.5375000000000001 0.0 0.0 0.0 0.0 110-111 0.575 0.0 0.0 0.0 0.0 112-113 0.6375 0.0 0.0 0.0 0.0 114-115 0.75 0.0 0.0 0.0 0.0 116-117 0.975 0.0 0.0 0.0 0.0 118-119 1.0875 0.0 0.0 0.0 0.0 120-121 1.1875 0.0 0.0 0.0 0.0 122-123 1.3375 0.0 0.0 0.0 0.0 124-125 1.6 0.0 0.0 0.0 0.0 126-127 1.875 0.0 0.0 0.0 0.0 128-129 2.0875 0.0 0.0 0.0 0.0 130-131 2.3125 0.0 0.0 0.0 0.0 132-133 2.5 0.0 0.0 0.0 0.0 134-135 2.75 0.0 0.0 0.0 0.0 136-137 2.9875 0.0 0.0 0.0 0.0 138-139 3.2625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATTGAAA 10 0.006830828 145.0 4 TTGAAAG 10 0.006830828 145.0 5 TGAAAGA 10 0.006830828 145.0 6 >>END_MODULE Read 866050 spots for SRR7169637.sra Written 866050 spots for SRR7169637.sra Read 866050 spots for SRR7169637.sra Written 866050 spots for SRR7169637.sra Read 866050 spots for SRR7169637.sra Written 866050 spots for SRR7169637.sra Read 866050 spots for SRR7169637.sra Written 866050 spots for SRR7169637.sra Read 866050 spots for SRR7169637.sra Written 866050 spots for SRR7169637.sra Read 866050 spots for SRR7169637.sra Written 866050 spots for SRR7169637.sra Read 866050 spots for SRR7169637.sra Written 866050 spots for SRR7169637.sra Read 866050 spots for SRR7169637.sra Written 866050 spots for SRR7169637.sra Read 866050 spots for SRR7169637.sra Written 866050 spots for SRR7169637.sra Read 866050 spots for SRR7169637.sra Written 866050 spots for SRR7169637.sra Read 866050 spots for SRR7169637.sra Written 866050 spots for SRR7169637.sra Read 866050 spots for SRR7169637.sra Written 866050 spots for SRR7169637.sra Read 866050 spots for SRR7169637.sra Written 866050 spots for SRR7169637.sra Read 866050 spots for SRR7169637.sra Written 866050 spots for SRR7169637.sra Read 866050 spots for SRR7169637.sra Written 866050 spots for SRR7169637.sra Read 866050 spots for SRR7169637.sra Written 866050 spots for SRR7169637.sra Read 866050 spots for SRR7169637.sra Written 866050 spots for SRR7169637.sra Read 866050 spots for SRR7169637.sra Written 866050 spots for SRR7169637.sra Read 866067 spots for SRR7169637.sra Written 866067 spots for SRR7169637.sra Read 866050 spots for SRR7169637.sra Written 866050 spots for SRR7169637.sra SRR ids: ['SRR7169637.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_p04usq3t SRR7169637.sra spots: 17321017 blocks: [[1, 866050], [866051, 1732100], [1732101, 2598150], [2598151, 3464200], [3464201, 4330250], [4330251, 5196300], [5196301, 6062350], [6062351, 6928400], [6928401, 7794450], [7794451, 8660500], [8660501, 9526550], [9526551, 10392600], [10392601, 11258650], [11258651, 12124700], [12124701, 12990750], [12990751, 13856800], [13856801, 14722850], [14722851, 15588900], [15588901, 16454950], [16454951, 17321017]] SRR7169637 file size 5847823 SRR7169637 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 SRR7169637 SRR7169637_1.fastq SRR7169637_2.fastq Input file: SRR7169637_1.fastq Paired file: SRR7169637_2.fastq trimmed: SRR7169637-trimmed-pair1.fastq, SRR7169637-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 Tue Feb 11 11:24:36 2025 >> started Tue Feb 11 11:25:07 2025 >> done (30.403s) 17321017 read pairs processed; of these: 29695 ( 0.17%) short read pairs filtered out after trimming by size control 20295 ( 0.12%) empty read pairs filtered out after trimming by size control 17271027 (99.71%) read pairs available; of these: 9985893 (57.82%) trimmed read pairs available after processing 7285134 (42.18%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 8 0.00% 20 3 0.00% 21 8 0.00% 22 6 0.00% 23 5 0.00% 24 7 0.00% 25 3 0.00% 26 10 0.00% 27 9 0.00% 28 10 0.00% 29 9 0.00% 30 18 0.00% 31 14 0.00% 32 20 0.00% 33 12 0.00% 34 18 0.00% 35 15 0.00% 36 22 0.00% 37 20 0.00% 38 30 0.00% 39 23 0.00% 40 33 0.00% 41 28 0.00% 42 32 0.00% 43 35 0.00% 44 41 0.00% 45 53 0.00% 46 56 0.00% 47 60 0.00% 48 64 0.00% 49 86 0.00% 50 84 0.00% 51 104 0.00% 52 116 0.00% 53 116 0.00% 54 134 0.00% 55 165 0.00% 56 150 0.00% 57 184 0.00% 58 209 0.00% 59 231 0.00% 60 221 0.00% 61 300 0.00% 62 311 0.00% 63 385 0.00% 64 371 0.00% 65 441 0.00% 66 508 0.00% 67 678 0.00% 68 927 0.01% 69 1337 0.01% 70 1196 0.01% 71 958 0.01% 72 1059 0.01% 73 1179 0.01% 74 1399 0.01% 75 1729 0.01% 76 1568 0.01% 77 1327 0.01% 78 1757 0.01% 79 2712 0.02% 80 4205 0.02% 81 2006 0.01% 82 2338 0.01% 83 2790 0.02% 84 4048 0.02% 85 4873 0.03% 86 5384 0.03% 87 5601 0.03% 88 5298 0.03% 89 5673 0.03% 90 5953 0.03% 91 6402 0.04% 92 6851 0.04% 93 7438 0.04% 94 7968 0.05% 95 8461 0.05% 96 9267 0.05% 97 10178 0.06% 98 11158 0.06% 99 13968 0.08% 100 17010 0.10% 101 14351 0.08% 102 12514 0.07% 103 13072 0.08% 104 13815 0.08% 105 14513 0.08% 106 15460 0.09% 107 15867 0.09% 108 16731 0.10% 109 17627 0.10% 110 18442 0.11% 111 19617 0.11% 112 20827 0.12% 113 21962 0.13% 114 23663 0.14% 115 24474 0.14% 116 26342 0.15% 117 27562 0.16% 118 28935 0.17% 119 30023 0.17% 120 31825 0.18% 121 33762 0.20% 122 36042 0.21% 123 38208 0.22% 124 41012 0.24% 125 42937 0.25% 126 45827 0.27% 127 48009 0.28% 128 51145 0.30% 129 53607 0.31% 130 57185 0.33% 131 60610 0.35% 132 65603 0.38% 133 70573 0.41% 134 76284 0.44% 135 82597 0.48% 136 89514 0.52% 137 96939 0.56% 138 106676 0.62% 139 118632 0.69% 140 130366 0.75% 141 141456 0.82% 142 161098 0.93% 143 182838 1.06% 144 216798 1.26% 145 261998 1.52% 146 333346 1.93% 147 451809 2.62% 148 681741 3.95% 149 1284903 7.44% 150 4347270 25.17% 151 7285134 42.18% 17271027 reads passed initial QC criterion=sequence-density sequence-density=0.22 sequence-density-rank=1 fanout-score=2.77 fanout-score-rank=32 prefix-density=0.24 prefix-fanout=2.4 sequence=CTGGCCATTCAATGTGACATCCTCTTGAGTGGCTTTCAAAAGCCTGATAAAAACGCTGAACTGACCACCTTTTTCTAGGACTTTGGTGACATTGGTTGGACCGGGTGGTGCTGGGGCTGCAGCTGGTGACTGAGCTAGGGTTGGAGGGCAATGAAGAA criterion=fanout-score sequence-density=0.02 sequence-density-rank=39 fanout-score=83.05 fanout-score-rank=1 prefix-density=0.26 prefix-fanout=6.3 sequence=TCTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACT criterion=sequence-density sequence-density=0.27 sequence-density-rank=1 fanout-score=2.69 fanout-score-rank=30 prefix-density=0.30 prefix-fanout=2.4 sequence=TTGTGATTTTGATC criterion=fanout-score sequence-density=0.13 sequence-density-rank=9 fanout-score=45.58 fanout-score-rank=1 prefix-density=0.49 prefix-fanout=12.4 sequence=TGTTGGTGGTGG SRR7169637 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 11:26:03 Started mapping on | Feb 11 11:26:03 Finished on | Feb 11 11:28:24 Mapping speed, Million of reads per hour | 440.96 Number of input reads | 17271027 Average input read length | 294 UNIQUE READS: Uniquely mapped reads number | 16278824 Uniquely mapped reads % | 94.26% Average mapped length | 293.44 Number of splices: Total | 15353803 Number of splices: Annotated (sjdb) | 15096807 Number of splices: GT/AG | 15135355 Number of splices: GC/AG | 173818 Number of splices: AT/AC | 12612 Number of splices: Non-canonical | 32018 Mismatch rate per base, % | 0.45% Deletion rate per base | 0.03% Deletion average length | 2.60 Insertion rate per base | 0.02% Insertion average length | 2.35 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 291572 % of reads mapped to multiple loci | 1.69% Number of reads mapped to too many loci | 147297 % of reads mapped to too many loci | 0.85% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.98% % of reads unmapped: other | 0.23% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 729358 729358 729358 N_multimapping 291572 291572 291572 N_noFeature 384493 16099809 466353 N_ambiguous 165561 936 67722 UnstrandedReadsAssigned:15728770 PositiveStrandReadsAssigned:178079 NegativeStrandReadsAssigned:15744749 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=149 echo kmer=145 SRR7169637 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: SRR7169637-trimmed-pair1.fastq SRR7169637-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 17,271,027 reads, 15,757,292 reads pseudoaligned [quant] estimated average fragment length: 256.148 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,074 rounds 52401 SRR7169637.ke.tsv 34699 SRR7169637.se.tsv 87100 total ==> SRR7169637.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1762.85 359 12.8438 Potri.005G024800.1.v4.1 1035 779.852 23 1.86008 Potri.004G059700.1.v4.1 961 705.879 7 0.625436 Potri.007G009000.2.v4.1 1416 1160.85 0 0 Potri.003G141000.2.v4.1 2943 2687.85 273.055 6.40708 Potri.016G087400.1.v4.1 270 73.1829 1662 1432.31 Potri.015G069301.1.v4.1 564 315.064 0 0 Potri.010G195200.1.v4.1 1773 1517.85 28 1.16344 Potri.012G127500.1.v4.1 977 721.859 6092 532.259 ==> SRR7169637.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1256 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 238 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 18 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 1 SRR7169637 completed mapping pipeline successfully