Starting /dee2/code/volunteer_pipeline.sh SRR7168866 current disk space = 3091332825088 free memory = 1578286080 SRR7168866 SRAfilesize 0ef2a7f52bd3e0da01752a4d6255a242 SRR7168866.sra SRR7168866.sra file validated SRR7168866 is paired end SRR7168866 is conventional basespace SRR7168866 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7168866_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 32.36725 34.0 34.0 34.0 33.0 34.0 2 33.38575 34.0 34.0 34.0 33.0 34.0 3 33.4945 34.0 34.0 34.0 33.0 34.0 4 33.558 34.0 34.0 34.0 33.0 34.0 5 33.574 34.0 34.0 34.0 33.0 34.0 6 37.365 38.0 38.0 38.0 37.0 38.0 7 37.48175 38.0 38.0 38.0 37.0 38.0 8 37.6035 38.0 38.0 38.0 38.0 38.0 9 37.668 38.0 38.0 38.0 38.0 38.0 10-14 37.642950000000006 38.0 38.0 38.0 38.0 38.0 15-19 37.6555 38.0 38.0 38.0 38.0 38.0 20-24 37.61299999999999 38.0 38.0 38.0 38.0 38.0 25-29 37.55045 38.0 38.0 38.0 38.0 38.0 30-34 37.5526 38.0 38.0 38.0 38.0 38.0 35-39 37.52835 38.0 38.0 38.0 38.0 38.0 40-44 37.441900000000004 38.0 38.0 38.0 38.0 38.0 45-49 37.456599999999995 38.0 38.0 38.0 38.0 38.0 50-54 37.44775 38.0 38.0 38.0 37.8 38.0 55-59 37.396950000000004 38.0 38.0 38.0 37.0 38.0 60-64 37.353449999999995 38.0 38.0 38.0 37.0 38.0 65-69 37.291700000000006 38.0 38.0 38.0 37.0 38.0 70-74 37.1695 38.0 38.0 38.0 37.0 38.0 75-79 36.921350000000004 38.0 38.0 38.0 36.4 38.0 80-84 36.855549999999994 38.0 38.0 38.0 36.2 38.0 85-89 36.71985 38.0 38.0 38.0 36.0 38.0 90-94 36.660849999999996 38.0 38.0 38.0 35.6 38.0 95-99 36.58305 38.0 38.0 38.0 35.2 38.0 100-104 36.424249999999994 38.0 38.0 38.0 34.6 38.0 105-109 36.3346 38.0 38.0 38.0 34.4 38.0 110-114 36.270399999999995 38.0 38.0 38.0 34.0 38.0 115-119 35.99059999999999 38.0 37.8 38.0 33.8 38.0 120-124 35.7598 38.0 37.4 38.0 33.0 38.0 125-129 35.50750000000001 38.0 37.0 38.0 31.2 38.0 130-134 35.26225 38.0 36.0 38.0 30.4 38.0 135-139 34.8591 38.0 35.8 38.0 29.2 38.0 140-144 34.3805 38.0 35.0 38.0 27.2 38.0 145-149 33.6374 38.0 33.0 38.0 21.6 38.0 150-151 29.083125000000003 34.5 24.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 8 1.0 9 2.0 10 1.0 11 1.0 12 1.0 13 1.0 14 0.0 15 2.0 16 0.0 17 3.0 18 10.0 19 23.0 20 4.0 21 6.0 22 6.0 23 6.0 24 4.0 25 9.0 26 17.0 27 20.0 28 24.0 29 22.0 30 29.0 31 41.0 32 51.0 33 75.0 34 105.0 35 197.0 36 559.0 37 2780.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.65349623082921 13.309072004159084 12.425266441382895 35.6121653236288 2 22.875 17.575 32.275 27.275 3 20.474999999999998 21.425 24.8 33.300000000000004 4 21.975 30.349999999999998 21.375 26.3 5 22.936468234117058 34.092046023011505 23.311655827913956 19.65982991495748 6 18.5 35.525 25.124999999999996 20.849999999999998 7 14.799999999999999 25.174999999999997 41.25 18.775 8 17.849999999999998 25.6 30.925000000000004 25.624999999999996 9 17.849999999999998 25.1 33.45 23.599999999999998 10-14 19.715 29.765000000000004 26.634999999999998 23.885 15-19 19.595000000000002 27.92 28.155 24.33 20-24 19.515 29.065 27.785 23.635 25-29 19.885 28.470000000000002 27.584999999999997 24.060000000000002 30-34 19.73493373343336 28.802200550137535 28.072018004501125 23.390847711927982 35-39 20.386019300965046 28.261413070653536 27.341367068353417 24.011200560028 40-44 20.305 28.51 27.515 23.669999999999998 45-49 19.78 28.060000000000002 28.27 23.89 50-54 20.77 27.955000000000002 27.0 24.275 55-59 19.595000000000002 27.775 28.225 24.404999999999998 60-64 20.485 28.044999999999998 27.62 23.849999999999998 65-69 19.875 28.345 27.389999999999997 24.39 70-74 19.965 29.2 27.61 23.225 75-79 19.675 28.08 27.42 24.825 80-84 20.215 28.215 27.43 24.14 85-89 20.74 28.67 26.87 23.72 90-94 20.605 28.32 26.625 24.45 95-99 20.625 28.26 27.515 23.599999999999998 100-104 20.615 28.110000000000003 26.634999999999998 24.64 105-109 20.94 28.095 26.26 24.705 110-114 20.825 28.175 26.895000000000003 24.104999999999997 115-119 20.495 28.525 26.755000000000003 24.224999999999998 120-124 21.29 28.025 26.39 24.295 125-129 20.7 28.1 26.345000000000002 24.855 130-134 21.315 27.615000000000002 26.445 24.625 135-139 21.415 28.02 26.384999999999998 24.18 140-144 21.15 27.925 26.284999999999997 24.64 145-149 21.315 28.17 25.94 24.575 150-151 21.777331492406176 27.676666248274127 25.8692104932848 24.676791766034896 >>END_MODULE >>Per sequence GC content warn #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 0.5 12 0.5 13 0.0 14 0.5 15 0.5 16 0.0 17 0.0 18 0.0 19 0.0 20 0.5 21 0.5 22 1.0 23 1.5 24 1.5 25 4.0 26 7.5 27 8.5 28 11.5 29 16.0 30 21.0 31 26.0 32 31.0 33 43.5 34 57.5 35 72.0 36 90.0 37 104.0 38 123.0 39 152.5 40 189.5 41 217.5 42 218.5 43 231.5 44 249.0 45 239.0 46 256.0 47 264.0 48 242.5 49 221.0 50 188.0 51 135.5 52 108.0 53 110.5 54 81.0 55 65.0 56 55.0 57 39.0 58 32.5 59 24.0 60 20.0 61 14.0 62 6.5 63 3.5 64 3.0 65 2.5 66 2.5 67 1.0 68 0.5 69 2.0 70 2.0 71 0.5 72 0.0 73 0.0 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 3.8249999999999997 2 0.0 3 0.0 4 0.0 5 0.05 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 0.025 35-39 0.005 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 0.0 150-151 0.41250000000000003 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 98.75 #Duplication Level Percentage of deduplicated Percentage of total 1 99.41772151898735 98.175 2 0.4810126582278481 0.95 3 0.05063291139240507 0.15 4 0.0 0.0 5 0.025316455696202535 0.125 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.025316455696202535 0.6 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGCGCTATCTCGTATGC 24 0.6 TruSeq Adapter, Index 1 (97% over 36bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACAGCGCTATCTCGTATGCC 5 0.125 TruSeq Adapter, Index 1 (97% over 35bp) >>END_MODULE >>Adapter Content fail #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 0.075 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.075 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.0875 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.2 0.0 0.0 0.0 0.0 82-83 0.21250000000000002 0.0 0.0 0.0 0.0 84-85 0.225 0.0 0.0 0.0 0.0 86-87 0.32499999999999996 0.0 0.0 0.0 0.0 88-89 0.5 0.0 0.0 0.0 0.0 90-91 0.6625 0.0 0.0 0.0 0.0 92-93 0.7875 0.0 0.0 0.0 0.0 94-95 0.975 0.0 0.0 0.0 0.0 96-97 1.15 0.0 0.0 0.0 0.0 98-99 1.3 0.0 0.0 0.0 0.0 100-101 1.575 0.0 0.0 0.0 0.0 102-103 1.8 0.0 0.0 0.0 0.0 104-105 2.0999999999999996 0.0 0.0 0.0 0.0 106-107 2.525 0.0 0.0 0.0 0.0 108-109 2.925 0.0 0.0 0.0 0.0 110-111 3.25 0.0 0.0 0.0 0.0 112-113 3.725 0.0 0.0 0.0 0.0 114-115 4.15 0.0 0.0 0.0 0.0 116-117 4.5375 0.0 0.0 0.0 0.0 118-119 5.05 0.0 0.0 0.0 0.0 120-121 5.4 0.0 0.0 0.0 0.0 122-123 5.875 0.0 0.0 0.0 0.0 124-125 6.45 0.0 0.0 0.0 0.0 126-127 6.9 0.0 0.0 0.0 0.0 128-129 7.65 0.0 0.0 0.0 0.0 130-131 8.3625 0.0 0.0 0.0 0.0 132-133 9.1125 0.0 0.0 0.0 0.0 134-135 9.6875 0.0 0.0 0.0 0.0 136-137 10.45 0.0 0.0 0.0 0.0 138-139 11.274999999999999 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTCACTT 10 0.0068378756 144.95 4 GCGCTAT 45 6.566359E-4 19.326666 140-144 AGCGCTA 45 6.566359E-4 19.326666 140-144 CGCTATC 40 0.0076702754 18.11875 140-144 GTCACAG 50 0.0013329011 17.394 135-139 TCCAGTC 50 0.0013329011 17.394 130-134 TCACAGC 55 0.0025218718 15.812727 135-139 CTCCAGT 60 0.0045021977 14.495001 130-134 CTGAACT 65 0.007655029 13.379999 125-129 AAAAAAA 65 0.007655029 13.379999 70-74 AGATCGG 65 0.007655029 13.379999 105-109 >>END_MODULE SRR7168866 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7168866_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.07625 33.0 33.0 34.0 32.0 34.0 2 33.133 34.0 33.0 34.0 33.0 34.0 3 33.09575 34.0 33.0 34.0 33.0 34.0 4 33.146 34.0 33.0 34.0 33.0 34.0 5 33.16875 34.0 33.0 34.0 33.0 34.0 6 37.2165 38.0 38.0 38.0 37.0 38.0 7 37.24575 38.0 38.0 38.0 37.0 38.0 8 37.1915 38.0 38.0 38.0 38.0 38.0 9 37.222 38.0 38.0 38.0 38.0 38.0 10-14 37.17405000000001 38.0 38.0 38.0 37.4 38.0 15-19 37.143950000000004 38.0 38.0 38.0 37.8 38.0 20-24 37.141299999999994 38.0 38.0 38.0 37.4 38.0 25-29 37.1114 38.0 38.0 38.0 37.6 38.0 30-34 37.11705 38.0 38.0 38.0 37.4 38.0 35-39 37.110350000000004 38.0 38.0 38.0 37.8 38.0 40-44 37.1222 38.0 38.0 38.0 37.8 38.0 45-49 37.037749999999996 38.0 38.0 38.0 37.2 38.0 50-54 36.977500000000006 38.0 38.0 38.0 37.0 38.0 55-59 37.00275 38.0 38.0 38.0 37.0 38.0 60-64 36.993849999999995 38.0 38.0 38.0 37.0 38.0 65-69 36.87175 38.0 38.0 38.0 36.8 38.0 70-74 36.6269 38.0 38.0 38.0 36.6 38.0 75-79 36.579150000000006 38.0 38.0 38.0 36.2 38.0 80-84 36.46535 38.0 38.0 38.0 36.0 38.0 85-89 36.385000000000005 38.0 38.0 38.0 36.0 38.0 90-94 36.29665000000001 38.0 38.0 38.0 35.2 38.0 95-99 36.2678 38.0 38.0 38.0 34.8 38.0 100-104 36.13755 38.0 38.0 38.0 34.4 38.0 105-109 36.0886 38.0 38.0 38.0 34.0 38.0 110-114 35.975 38.0 38.0 38.0 34.0 38.0 115-119 35.74145 38.0 38.0 38.0 33.6 38.0 120-124 35.59335 38.0 38.0 38.0 33.0 38.0 125-129 35.28675 38.0 37.0 38.0 30.6 38.0 130-134 35.051100000000005 38.0 36.6 38.0 30.0 38.0 135-139 34.50035 38.0 36.0 38.0 27.6 38.0 140-144 33.96419999999999 38.0 34.6 38.0 23.8 38.0 145-149 33.19295 38.0 33.2 38.0 16.8 38.0 150-151 28.06825 34.5 17.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 9.0 3 13.0 4 3.0 5 2.0 6 3.0 7 1.0 8 2.0 9 2.0 10 0.0 11 2.0 12 6.0 13 6.0 14 3.0 15 1.0 16 5.0 17 29.0 18 7.0 19 0.0 20 5.0 21 13.0 22 9.0 23 8.0 24 13.0 25 14.0 26 14.0 27 17.0 28 18.0 29 27.0 30 24.0 31 37.0 32 42.0 33 58.0 34 95.0 35 213.0 36 470.0 37 2829.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.175000000000004 20.05 18.075 24.7 2 26.275 26.375 29.525000000000002 17.825 3 22.75 29.125 29.549999999999997 18.575 4 25.85 31.125000000000004 23.474999999999998 19.55 5 26.575 34.675 21.349999999999998 17.4 6 21.75763645468202 35.92889334001001 23.685528292438658 18.627941912869304 7 19.474342928660825 20.926157697121404 38.97371714643304 20.625782227784732 8 23.523523523523522 24.64964964964965 26.351351351351347 25.475475475475474 9 22.2972972972973 26.001001001001 28.153153153153156 23.54854854854855 10-14 24.608299544476147 28.622916353806875 25.429243630174703 21.33954047154227 15-19 24.37546933667084 27.414267834793492 27.229036295369212 20.98122653316646 20-24 24.37290341961648 28.03785109898363 27.016472237520656 20.572773243879237 25-29 23.879625456912525 28.311051023984778 26.84392368934956 20.965399829753142 30-34 23.741799789673994 28.168661425209073 26.836596724923634 21.2529420601933 35-39 24.05450082652908 27.12017231878976 27.691228773230474 21.134098081450684 40-44 24.31674842326559 27.159875863449795 27.48523375713285 21.03814195615177 45-49 24.119471683009806 27.61656994196518 27.036221733039824 21.22773664198519 50-54 24.67597457839163 27.918730921283093 27.108041835560226 20.29725266476505 55-59 23.788546255506606 27.09751702042451 28.02863436123348 21.085302362835403 60-64 23.67867867867868 28.48848848848849 27.227227227227228 20.605605605605607 65-69 23.713456147376853 28.429114937925508 27.162595114136966 20.694833800560673 70-74 24.449228920488682 28.494892849989984 26.722411375926296 20.333466853595034 75-79 24.298083179020068 27.68129723237075 27.115759971973375 20.904859616635804 80-84 24.348827890202365 28.005409737527547 27.419354838709676 20.22640753356041 85-89 24.77211259140539 27.942502253831513 26.87568867074026 20.409696484022838 90-94 24.48693562919211 27.755531084192615 27.129842827109822 20.62769045950546 95-99 24.08843095083279 28.059820937328066 27.199519831941178 20.65222827989796 100-104 24.187256176853055 28.79863959187756 26.587976392917877 20.426127838351505 105-109 24.584750850510307 28.116870122073244 27.146287772663598 20.15209125475285 110-114 25.15131809314191 28.117652943824723 26.927117202741236 19.80391176029213 115-119 25.29408820143165 27.97216799319217 26.981028182409773 19.75271562296641 120-124 24.70205307961943 28.14221331997997 27.59639459188783 19.55933900851277 125-129 24.981222773020882 27.625056331680938 26.98913424465475 20.404586650643434 130-134 25.716002403364712 28.31964750650911 26.50210294412177 19.462247146004405 135-139 25.830997196635963 27.863436123348016 26.47677212655186 19.828794553464157 140-144 25.949272099654806 27.92535894742108 26.599629796388015 19.525739156536094 145-149 26.1874968717153 28.249662145252515 26.45277541418489 19.11006556884729 150-151 26.0625 27.700000000000003 27.150000000000002 19.0875 >>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 1.0 6 1.0 7 0.0 8 0.5 9 1.0 10 0.5 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.5 17 0.5 18 0.5 19 0.5 20 1.0 21 1.5 22 0.5 23 0.5 24 1.0 25 2.0 26 2.5 27 1.5 28 2.5 29 5.0 30 8.0 31 11.5 32 15.5 33 21.5 34 29.0 35 48.0 36 74.0 37 89.0 38 104.5 39 140.0 40 191.0 41 225.0 42 242.5 43 266.5 44 273.0 45 259.0 46 280.5 47 279.5 48 229.0 49 210.0 50 191.0 51 157.0 52 138.5 53 120.5 54 96.0 55 73.5 56 50.5 57 39.5 58 32.0 59 18.0 60 17.5 61 15.0 62 9.0 63 8.5 64 4.0 65 1.0 66 1.5 67 1.5 68 0.5 69 0.5 70 1.0 71 0.5 72 0.5 73 1.0 74 0.5 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 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.15 7 0.125 8 0.1 9 0.1 10-14 0.11499999999999999 15-19 0.125 20-24 0.135 25-29 0.145 30-34 0.155 35-39 0.185 40-44 0.11 45-49 0.06 50-54 0.08499999999999999 55-59 0.12 60-64 0.1 65-69 0.12 70-74 0.13999999999999999 75-79 0.095 80-84 0.18 85-89 0.16999999999999998 90-94 0.11 95-99 0.034999999999999996 100-104 0.03 105-109 0.06 110-114 0.045 115-119 0.11499999999999999 120-124 0.15 125-129 0.145 130-134 0.13999999999999999 135-139 0.12 140-144 0.055 145-149 0.105 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 98.45 #Duplication Level Percentage of deduplicated Percentage of total 1 99.13661757237176 97.6 2 0.7618080243778568 1.5 3 0.07618080243778569 0.22499999999999998 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 0.025393600812595223 0.675 >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 GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 27 0.675 Illumina Single End PCR Primer 1 (100% over 50bp) >>END_MODULE >>Adapter Content fail #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 0.075 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.075 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.0875 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.2 0.0 0.0 0.0 0.0 82-83 0.21250000000000002 0.0 0.0 0.0 0.0 84-85 0.225 0.0 0.0 0.0 0.0 86-87 0.32499999999999996 0.0 0.0 0.0 0.0 88-89 0.48750000000000004 0.0 0.0 0.0 0.0 90-91 0.6375 0.0 0.0 0.0 0.0 92-93 0.7749999999999999 0.0 0.0 0.0 0.0 94-95 1.0 0.0 0.0 0.0 0.0 96-97 1.1875 0.0 0.0 0.0 0.0 98-99 1.35 0.0 0.0 0.0 0.0 100-101 1.5875 0.0 0.0 0.0 0.0 102-103 1.825 0.0 0.0 0.0 0.0 104-105 2.1375 0.0 0.0 0.0 0.0 106-107 2.6 0.0 0.0 0.0 0.0 108-109 3.0 0.0 0.0 0.0 0.0 110-111 3.3499999999999996 0.0 0.0 0.0 0.0 112-113 3.8 0.0 0.0 0.0 0.0 114-115 4.237500000000001 0.0 0.0 0.0 0.0 116-117 4.6625 0.0 0.0 0.0 0.0 118-119 5.112500000000001 0.0 0.0 0.0 0.0 120-121 5.475 0.0 0.0 0.0 0.0 122-123 5.925 0.0 0.0 0.0 0.0 124-125 6.5375 0.0 0.0 0.0 0.0 126-127 6.9875 0.0 0.0 0.0 0.0 128-129 7.725 0.0 0.0 0.0 0.0 130-131 8.5 0.0 0.0 0.0 0.0 132-133 9.2625 0.0 0.0 0.0 0.0 134-135 9.875 0.0 0.0 0.0 0.0 136-137 10.6375 0.0 0.0 0.0 0.0 138-139 11.475000000000001 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATCTCGG 40 0.0076550315 18.125 140-144 GATCTCG 40 0.0076550315 18.125 140-144 AAGAGTG 50 0.0013298223 17.4 130-134 GTGTAGA 55 0.0025160722 15.818182 135-139 TGTAGAT 55 0.0025160722 15.818182 135-139 TAGGGAA 60 0.004491891 14.500001 125-129 TCGTGTA 65 0.0076375785 13.384615 120-124 CGTGTAG 65 0.0076375785 13.384615 120-124 AAAGAGT 65 0.0076375785 13.384615 130-134 >>END_MODULE Read 492499 spots for SRR7168866.sra Written 492499 spots for SRR7168866.sra Read 492499 spots for SRR7168866.sra Written 492499 spots for SRR7168866.sra Read 492506 spots for SRR7168866.sra Written 492506 spots for SRR7168866.sra Read 492499 spots for SRR7168866.sra Written 492499 spots for SRR7168866.sra Read 492499 spots for SRR7168866.sra Written 492499 spots for SRR7168866.sra Read 492499 spots for SRR7168866.sra Written 492499 spots for SRR7168866.sra Read 492499 spots for SRR7168866.sra Written 492499 spots for SRR7168866.sra Read 492499 spots for SRR7168866.sra Written 492499 spots for SRR7168866.sra Read 492499 spots for SRR7168866.sra Written 492499 spots for SRR7168866.sra Read 492499 spots for SRR7168866.sra Written 492499 spots for SRR7168866.sra Read 492499 spots for SRR7168866.sra Written 492499 spots for SRR7168866.sra Read 492499 spots for SRR7168866.sra Written 492499 spots for SRR7168866.sra Read 492499 spots for SRR7168866.sra Written 492499 spots for SRR7168866.sra Read 492499 spots for SRR7168866.sra Written 492499 spots for SRR7168866.sra Read 492499 spots for SRR7168866.sra Written 492499 spots for SRR7168866.sra Read 492499 spots for SRR7168866.sra Written 492499 spots for SRR7168866.sra Read 492499 spots for SRR7168866.sra Written 492499 spots for SRR7168866.sra Read 492499 spots for SRR7168866.sra Written 492499 spots for SRR7168866.sra Read 492499 spots for SRR7168866.sra Written 492499 spots for SRR7168866.sra Read 492499 spots for SRR7168866.sra Written 492499 spots for SRR7168866.sra SRR ids: ['SRR7168866.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_cwb0bksb SRR7168866.sra spots: 9849987 blocks: [[1, 492499], [492500, 984998], [984999, 1477497], [1477498, 1969996], [1969997, 2462495], [2462496, 2954994], [2954995, 3447493], [3447494, 3939992], [3939993, 4432491], [4432492, 4924990], [4924991, 5417489], [5417490, 5909988], [5909989, 6402487], [6402488, 6894986], [6894987, 7387485], [7387486, 7879984], [7879985, 8372483], [8372484, 8864982], [8864983, 9357481], [9357482, 9849987]] SRR7168866 file size 3316430 SRR7168866 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 SRR7168866 SRR7168866_1.fastq SRR7168866_2.fastq Input file: SRR7168866_1.fastq Paired file: SRR7168866_2.fastq trimmed: SRR7168866-trimmed-pair1.fastq, SRR7168866-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 Feb 15 12:02:15 2025 >> started Sat Feb 15 12:13:36 2025 >> done (681.242s) 9849987 read pairs processed; of these: 22661 ( 0.23%) short read pairs filtered out after trimming by size control 81065 ( 0.82%) empty read pairs filtered out after trimming by size control 9746261 (98.95%) read pairs available; of these: 5240652 (53.77%) trimmed read pairs available after processing 4505609 (46.23%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 6 0.00% 19 6 0.00% 20 5 0.00% 21 5 0.00% 22 9 0.00% 23 5 0.00% 24 9 0.00% 25 5 0.00% 26 4 0.00% 27 10 0.00% 28 12 0.00% 29 4 0.00% 30 5 0.00% 31 14 0.00% 32 6 0.00% 33 4 0.00% 34 14 0.00% 35 12 0.00% 36 16 0.00% 37 16 0.00% 38 15 0.00% 39 16 0.00% 40 23 0.00% 41 26 0.00% 42 33 0.00% 43 32 0.00% 44 43 0.00% 45 39 0.00% 46 54 0.00% 47 51 0.00% 48 50 0.00% 49 73 0.00% 50 59 0.00% 51 94 0.00% 52 79 0.00% 53 92 0.00% 54 112 0.00% 55 135 0.00% 56 125 0.00% 57 150 0.00% 58 158 0.00% 59 224 0.00% 60 197 0.00% 61 310 0.00% 62 288 0.00% 63 320 0.00% 64 383 0.00% 65 457 0.00% 66 459 0.00% 67 612 0.01% 68 847 0.01% 69 3365 0.03% 70 3542 0.04% 71 1604 0.02% 72 1305 0.01% 73 1440 0.01% 74 1511 0.02% 75 1607 0.02% 76 1792 0.02% 77 1788 0.02% 78 1974 0.02% 79 2294 0.02% 80 2613 0.03% 81 2873 0.03% 82 3346 0.03% 83 3812 0.04% 84 4850 0.05% 85 5686 0.06% 86 6008 0.06% 87 6549 0.07% 88 7188 0.07% 89 7523 0.08% 90 8039 0.08% 91 8579 0.09% 92 9064 0.09% 93 10117 0.10% 94 10978 0.11% 95 11796 0.12% 96 12299 0.13% 97 12665 0.13% 98 13087 0.13% 99 13473 0.14% 100 14499 0.15% 101 15444 0.16% 102 16355 0.17% 103 17578 0.18% 104 18671 0.19% 105 19892 0.20% 106 20606 0.21% 107 21209 0.22% 108 21551 0.22% 109 22505 0.23% 110 23251 0.24% 111 24237 0.25% 112 25157 0.26% 113 26527 0.27% 114 27516 0.28% 115 29129 0.30% 116 29972 0.31% 117 30635 0.31% 118 31435 0.32% 119 31405 0.32% 120 32379 0.33% 121 32987 0.34% 122 33801 0.35% 123 35621 0.37% 124 37256 0.38% 125 38364 0.39% 126 39544 0.41% 127 40914 0.42% 128 41541 0.43% 129 42371 0.43% 130 43430 0.45% 131 44369 0.46% 132 45656 0.47% 133 47599 0.49% 134 49012 0.50% 135 51453 0.53% 136 53231 0.55% 137 55656 0.57% 138 57692 0.59% 139 59615 0.61% 140 61727 0.63% 141 64988 0.67% 142 69360 0.71% 143 75598 0.78% 144 85227 0.87% 145 97741 1.00% 146 117354 1.20% 147 150606 1.55% 148 225881 2.32% 149 445030 4.57% 150 2308585 23.69% 151 4505609 46.23% 9746261 reads passed initial QC criterion=sequence-density sequence-density=0.53 sequence-density-rank=1 fanout-score=2.06 fanout-score-rank=27 prefix-density=0.55 prefix-fanout=2.0 sequence=ATACGGATAAAGG criterion=fanout-score sequence-density=0.24 sequence-density-rank=11 fanout-score=17.08 fanout-score-rank=1 prefix-density=0.51 prefix-fanout=7.9 sequence=CCATTCTTGAGTTCCTTCACCTTCAACTC criterion=sequence-density sequence-density=0.53 sequence-density-rank=1 fanout-score=1.94 fanout-score-rank=32 prefix-density=0.53 prefix-fanout=1.9 sequence=CCAGGGTACTATGATGGACGCTACTGGACTATGTGGAAACTACCCATGTTTGGATGCACTGAGGCATCTCAGGTGCTGATTGAGCTCGAGGAGGCGAAGAAAGCTTACCCTAACTCCTTTATCCGTATCATTGGATTCGACAACACTCGTCAAGTGCAGTGCATCAGTTTTATCGCCTCCAAGCCGAAGGGTGTCTAGGTTCCAAGATTTGATGAGTCCCTAGCTAT criterion=fanout-score sequence-density=0.05 sequence-density-rank=31 fanout-score=31.10 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=9.4 sequence=TGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAG SRR7168866 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 15 13:57:34 Started mapping on | Feb 15 13:57:51 Finished on | Feb 15 16:48:30 Mapping speed, Million of reads per hour | 3.43 Number of input reads | 9746261 Average input read length | 290 UNIQUE READS: Uniquely mapped reads number | 8823891 Uniquely mapped reads % | 90.54% Average mapped length | 289.93 Number of splices: Total | 7812515 Number of splices: Annotated (sjdb) | 7613302 Number of splices: GT/AG | 7653678 Number of splices: GC/AG | 131300 Number of splices: AT/AC | 5113 Number of splices: Non-canonical | 22424 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.03% Deletion average length | 2.72 Insertion rate per base | 0.02% Insertion average length | 2.06 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 261513 % of reads mapped to multiple loci | 2.68% Number of reads mapped to too many loci | 52000 % of reads mapped to too many loci | 0.53% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.12% % of reads unmapped: other | 0.12% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 675621 675621 675621 N_multimapping 261513 261513 261513 N_noFeature 286932 8652939 372680 N_ambiguous 147793 804 62075 UnstrandedReadsAssigned:8389166 PositiveStrandReadsAssigned:170148 NegativeStrandReadsAssigned:8389136 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=146 echo kmer=141 SRR7168866 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: SRR7168866-trimmed-pair1.fastq SRR7168866-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 9,746,261 reads, 8,459,463 reads pseudoaligned [quant] estimated average fragment length: 212.526 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,059 rounds 52401 SRR7168866.ke.tsv 34699 SRR7168866.se.tsv 87100 total ==> SRR7168866.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1806.47 214 13.5561 Potri.005G024800.1.v4.1 1035 823.474 132 18.3433 Potri.004G059700.1.v4.1 961 749.474 7 1.0688 Potri.007G009000.2.v4.1 1416 1204.47 0 0 Potri.003G141000.2.v4.1 2943 2731.47 296 12.4007 Potri.016G087400.1.v4.1 270 91.139 502 630.308 Potri.015G069301.1.v4.1 564 354.085 0 0 Potri.010G195200.1.v4.1 1773 1561.47 4 0.293142 Potri.012G127500.1.v4.1 977 765.474 308 46.044 ==> SRR7168866.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 53 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 201 Potri.001G212900.v4.1 255 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 5 SRR7168866 completed mapping pipeline successfully