Starting /dee2/code/volunteer_pipeline.sh SRR12919404 current disk space = 3050723053568 free memory = 1576712252 SRR12919404 SRAfilesize cf810e9aed51197e7167df46beda7018 SRR12919404.sra SRR12919404.sra file validated SRR12919404 is paired end SRR12919404 is conventional basespace SRR12919404 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12919404_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 36.547 37.0 37.0 37.0 37.0 37.0 2 36.24375 37.0 37.0 37.0 37.0 37.0 3 36.5085 37.0 37.0 37.0 37.0 37.0 4 36.553 37.0 37.0 37.0 37.0 37.0 5 36.645 37.0 37.0 37.0 37.0 37.0 6 36.639 37.0 37.0 37.0 37.0 37.0 7 36.558 37.0 37.0 37.0 37.0 37.0 8 36.6445 37.0 37.0 37.0 37.0 37.0 9 36.6285 37.0 37.0 37.0 37.0 37.0 10-14 36.6205 37.0 37.0 37.0 37.0 37.0 15-19 36.6047 37.0 37.0 37.0 37.0 37.0 20-24 36.54129999999999 37.0 37.0 37.0 37.0 37.0 25-29 36.5289 37.0 37.0 37.0 37.0 37.0 30-34 36.47090000000001 37.0 37.0 37.0 37.0 37.0 35-39 36.4801 37.0 37.0 37.0 37.0 37.0 40-44 36.4474 37.0 37.0 37.0 37.0 37.0 45-49 36.3894 37.0 37.0 37.0 37.0 37.0 50-54 36.382000000000005 37.0 37.0 37.0 37.0 37.0 55-59 36.32769999999999 37.0 37.0 37.0 37.0 37.0 60-64 36.27569999999999 37.0 37.0 37.0 37.0 37.0 65-69 36.2354 37.0 37.0 37.0 37.0 37.0 70-74 36.2566 37.0 37.0 37.0 37.0 37.0 75-79 36.2067 37.0 37.0 37.0 37.0 37.0 80-84 36.2053 37.0 37.0 37.0 37.0 37.0 85-89 36.12349999999999 37.0 37.0 37.0 37.0 37.0 90-94 36.0255 37.0 37.0 37.0 37.0 37.0 95-99 36.0283 37.0 37.0 37.0 37.0 37.0 100-104 36.035399999999996 37.0 37.0 37.0 37.0 37.0 105-109 35.974900000000005 37.0 37.0 37.0 37.0 37.0 110-114 35.8718 37.0 37.0 37.0 37.0 37.0 115-119 35.86899999999999 37.0 37.0 37.0 37.0 37.0 120-124 35.863 37.0 37.0 37.0 37.0 37.0 125-129 35.7781 37.0 37.0 37.0 37.0 37.0 130-134 35.634 37.0 37.0 37.0 37.0 37.0 135-139 35.5472 37.0 37.0 37.0 37.0 37.0 140-144 35.328 37.0 37.0 37.0 37.0 37.0 145-149 35.2241 37.0 37.0 37.0 32.2 37.0 150-151 34.917 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 1.0 19 1.0 20 2.0 21 1.0 22 1.0 23 2.0 24 1.0 25 8.0 26 8.0 27 14.0 28 16.0 29 18.0 30 22.0 31 43.0 32 63.0 33 95.0 34 131.0 35 343.0 36 2890.0 37 340.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.975 14.025000000000002 8.35 35.65 2 20.68792367562139 14.762741652021088 34.44639718804921 30.102937484308313 3 18.0 20.724999999999998 29.725 31.55 4 21.6 28.375 24.075 25.95 5 20.974999999999998 33.550000000000004 26.025 19.45 6 21.275 34.825 25.575 18.325 7 14.299999999999999 27.725 41.55 16.425 8 17.9 26.8 31.2 24.099999999999998 9 18.525 25.75 32.85 22.875 10-14 19.98 31.345 26.284999999999997 22.39 15-19 19.98 29.955 27.16 22.905 20-24 19.82 30.115 27.560000000000002 22.505 25-29 19.52 30.2 27.794999999999998 22.485 30-34 19.67 30.845 27.025 22.46 35-39 19.78 30.425 26.884999999999998 22.91 40-44 20.7 30.545 26.119999999999997 22.634999999999998 45-49 20.68 29.580000000000002 26.555 23.185 50-54 20.49 30.325000000000003 26.685 22.5 55-59 20.375 29.685 26.784999999999997 23.155 60-64 19.99 29.909999999999997 27.33 22.770000000000003 65-69 19.919999999999998 30.509999999999998 26.52 23.05 70-74 20.630000000000003 29.759999999999998 26.790000000000003 22.82 75-79 20.315 30.04 26.169999999999998 23.474999999999998 80-84 21.17 29.459999999999997 26.345000000000002 23.025000000000002 85-89 20.835 29.085 26.96 23.119999999999997 90-94 20.655 29.69 26.46 23.195 95-99 20.3 29.609999999999996 26.895000000000003 23.195 100-104 21.115000000000002 29.78 25.755 23.35 105-109 21.044999999999998 29.84 26.22 22.895 110-114 21.315 29.125 25.990000000000002 23.57 115-119 21.975 29.080000000000002 25.619999999999997 23.325000000000003 120-124 21.87 28.78 25.115 24.235 125-129 21.465 29.28 25.285000000000004 23.97 130-134 21.6 28.665000000000003 25.6 24.135 135-139 21.8 28.794999999999998 25.595000000000002 23.810000000000002 140-144 22.455 28.605000000000004 25.135 23.805 145-149 22.42 28.715000000000003 24.959999999999997 23.905 150-151 22.875 28.287499999999998 24.2875 24.55 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.5 3 0.5 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 1.0 13 0.5 14 1.0 15 1.5 16 0.5 17 1.5 18 2.0 19 1.5 20 1.5 21 1.0 22 0.5 23 0.0 24 2.5 25 6.0 26 7.5 27 10.0 28 12.0 29 23.0 30 35.0 31 44.5 32 61.5 33 82.0 34 98.5 35 110.5 36 130.0 37 153.0 38 175.0 39 185.0 40 199.5 41 196.5 42 187.0 43 197.5 44 207.0 45 200.0 46 192.0 47 195.5 48 193.0 49 182.0 50 145.0 51 117.5 52 114.5 53 111.5 54 85.5 55 63.5 56 53.5 57 41.5 58 36.5 59 29.5 60 23.0 61 19.5 62 17.5 63 12.0 64 7.5 65 5.0 66 3.0 67 3.5 68 3.0 69 1.5 70 1.0 71 1.5 72 2.0 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 0.42500000000000004 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 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 87.85 #Duplication Level Percentage of deduplicated Percentage of total 1 89.35685828116107 78.5 2 8.537279453614115 15.0 3 1.5367103016505406 4.05 4 0.28457598178713717 1.0 5 0.14228799089356858 0.625 6 0.08537279453614115 0.44999999999999996 7 0.028457598178713718 0.17500000000000002 8 0.028457598178713718 0.2 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 GCCTTATGTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGA 8 0.2 No Hit GGGAAGCTATACTATATAGGTGGCTATCTATCCCTACCAAGGCTTATATT 7 0.17500000000000002 No Hit GCATGACGAGGCAGTTTCCAGAAACGTGTATCACATCTAGGCATGGAATC 6 0.15 No Hit GTGTGCTAGCCCGTCGAGACTGAAAAGCTATAACCCGCAGACCCGAGCGA 6 0.15 No Hit CCCATTTTTAGTTATAATGATGCCTTATGTGATAGATGCCTCTTTAAAAT 6 0.15 No Hit TTTTTTTTAAGGGTAAAACGCAAGCACCGGCTGTCGAGTTGTACGGCCGT 5 0.125 No Hit GGGCATCCTTTTTTATCATACAACTCAAAAGACTCACAAGACTCACGATC 5 0.125 No Hit CTTTAAAATATCTAAGTGCTGGGGTTATGAGTAGGGATGAGCATAAACCA 5 0.125 No Hit CTTATGTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGAGT 5 0.125 No Hit GGACAACTGATGGACCCACGTTGCGAGTCCAGTAAATCAGGACGGGGATA 5 0.125 No Hit >>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 0.0 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 0.0125 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.07500000000000001 0.0 0.0 0.0 0.0 70-71 0.125 0.0 0.0 0.0 0.0 72-73 0.175 0.0 0.0 0.0 0.0 74-75 0.2 0.0 0.0 0.0 0.0 76-77 0.25 0.0 0.0 0.0 0.0 78-79 0.3 0.0 0.0 0.0 0.0 80-81 0.32499999999999996 0.0 0.0 0.0 0.0 82-83 0.44999999999999996 0.0 0.0 0.0 0.0 84-85 0.7 0.0 0.0 0.0 0.0 86-87 0.7875000000000001 0.0 0.0 0.0 0.0 88-89 0.9125 0.0 0.0 0.0 0.0 90-91 1.0625 0.0 0.0 0.0 0.0 92-93 1.1749999999999998 0.0 0.0 0.0 0.0 94-95 1.4125 0.0 0.0 0.0 0.0 96-97 1.7875 0.0 0.0 0.0 0.0 98-99 2.1500000000000004 0.0 0.0 0.0 0.0 100-101 2.45 0.0 0.0 0.0 0.0 102-103 2.8125 0.0 0.0 0.0 0.0 104-105 3.0999999999999996 0.0 0.0 0.0 0.0 106-107 3.4 0.0 0.0 0.0 0.0 108-109 4.025 0.0 0.0 0.0 0.0 110-111 4.675 0.0 0.0 0.0 0.0 112-113 5.25 0.0 0.0 0.0 0.0 114-115 5.8625 0.0 0.0 0.0 0.0 116-117 6.4375 0.0 0.0 0.0 0.0 118-119 7.0375 0.0 0.0 0.0 0.0 120-121 7.4125 0.0 0.0 0.0 0.0 122-123 8.025 0.0 0.0 0.0 0.0 124-125 8.575 0.0 0.0 0.0 0.0 126-127 9.5 0.0 0.0 0.0 0.0 128-129 10.35 0.0 0.0 0.0 0.0 130-131 10.8875 0.0 0.0 0.0 0.0 132-133 11.45 0.0 0.0 0.0 0.0 134-135 12.225 0.0 0.0 0.0 0.0 136-137 13.2 0.0 0.0 0.0 0.0 138-139 14.05 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTCAACC 10 0.006830828 145.0 6 CTAGTCA 10 0.006830828 145.0 3 CCTAGTC 10 0.006830828 145.0 2 TTTTTTT 105 0.0068401312 27.619047 1 >>END_MODULE SRR12919404 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12919404_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 36.305 37.0 37.0 37.0 37.0 37.0 2 36.3765 37.0 37.0 37.0 37.0 37.0 3 36.3835 37.0 37.0 37.0 37.0 37.0 4 36.3745 37.0 37.0 37.0 37.0 37.0 5 36.46 37.0 37.0 37.0 37.0 37.0 6 36.378 37.0 37.0 37.0 37.0 37.0 7 36.2995 37.0 37.0 37.0 37.0 37.0 8 36.4145 37.0 37.0 37.0 37.0 37.0 9 36.505 37.0 37.0 37.0 37.0 37.0 10-14 36.422200000000004 37.0 37.0 37.0 37.0 37.0 15-19 36.383599999999994 37.0 37.0 37.0 37.0 37.0 20-24 36.3762 37.0 37.0 37.0 37.0 37.0 25-29 36.296499999999995 37.0 37.0 37.0 37.0 37.0 30-34 36.294399999999996 37.0 37.0 37.0 37.0 37.0 35-39 36.25619999999999 37.0 37.0 37.0 37.0 37.0 40-44 36.23049999999999 37.0 37.0 37.0 37.0 37.0 45-49 36.2305 37.0 37.0 37.0 37.0 37.0 50-54 36.2032 37.0 37.0 37.0 37.0 37.0 55-59 36.18820000000001 37.0 37.0 37.0 37.0 37.0 60-64 36.1389 37.0 37.0 37.0 37.0 37.0 65-69 36.147 37.0 37.0 37.0 37.0 37.0 70-74 36.0866 37.0 37.0 37.0 37.0 37.0 75-79 36.066700000000004 37.0 37.0 37.0 37.0 37.0 80-84 36.057 37.0 37.0 37.0 37.0 37.0 85-89 36.0481 37.0 37.0 37.0 37.0 37.0 90-94 36.0247 37.0 37.0 37.0 37.0 37.0 95-99 36.077600000000004 37.0 37.0 37.0 37.0 37.0 100-104 35.962 37.0 37.0 37.0 37.0 37.0 105-109 35.997699999999995 37.0 37.0 37.0 37.0 37.0 110-114 35.9053 37.0 37.0 37.0 37.0 37.0 115-119 35.862 37.0 37.0 37.0 37.0 37.0 120-124 35.7203 37.0 37.0 37.0 37.0 37.0 125-129 35.6339 37.0 37.0 37.0 37.0 37.0 130-134 35.5026 37.0 37.0 37.0 37.0 37.0 135-139 35.3473 37.0 37.0 37.0 37.0 37.0 140-144 35.1852 37.0 37.0 37.0 32.2 37.0 145-149 34.971500000000006 37.0 37.0 37.0 27.4 37.0 150-151 34.824749999999995 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 6.0 14 1.0 15 2.0 16 2.0 17 2.0 18 1.0 19 1.0 20 3.0 21 4.0 22 6.0 23 9.0 24 7.0 25 5.0 26 5.0 27 6.0 28 8.0 29 13.0 30 15.0 31 25.0 32 32.0 33 92.0 34 202.0 35 487.0 36 2765.0 37 301.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 42.725 24.9 9.700000000000001 22.675 2 29.575000000000003 24.125 29.25 17.05 3 21.9 28.075 30.775000000000002 19.25 4 23.400000000000002 34.25 23.525 18.825 5 25.8 34.5 21.875 17.825 6 23.150000000000002 37.375 21.525 17.95 7 21.775 22.275 36.675000000000004 19.275000000000002 8 22.45 25.074999999999996 28.075 24.4 9 23.325000000000003 25.374999999999996 28.275 23.025000000000002 10-14 24.995 28.12 25.224999999999998 21.66 15-19 24.67 27.125 27.655 20.549999999999997 20-24 24.34 27.544999999999998 27.07 21.044999999999998 25-29 24.6 27.48 27.445000000000004 20.474999999999998 30-34 24.265 27.634999999999998 27.279999999999998 20.82 35-39 24.355 27.229999999999997 27.49 20.925 40-44 23.685000000000002 26.995 28.1 21.22 45-49 24.08 26.945000000000004 28.125 20.849999999999998 50-54 23.36 26.775 28.325 21.54 55-59 24.385 26.584999999999997 28.060000000000002 20.97 60-64 23.465 26.755000000000003 28.660000000000004 21.12 65-69 24.025 27.735 27.74 20.5 70-74 23.48 26.76 28.68 21.08 75-79 23.685000000000002 27.29 28.37 20.655 80-84 23.225 27.71 28.005000000000003 21.060000000000002 85-89 22.905 27.395000000000003 28.655 21.044999999999998 90-94 23.41 27.625 28.244999999999997 20.72 95-99 23.305 27.744999999999997 28.599999999999998 20.349999999999998 100-104 23.815 27.905 27.92 20.36 105-109 24.82 27.689999999999998 27.415 20.075000000000003 110-114 24.215 27.47 27.975 20.34 115-119 24.525 28.7 26.845000000000002 19.93 120-124 24.715 27.875 27.705000000000002 19.705000000000002 125-129 25.185000000000002 27.985 27.48 19.35 130-134 24.905 27.92 27.58 19.595000000000002 135-139 26.384999999999998 27.810000000000002 27.1 18.705 140-144 26.435 27.255000000000003 27.47 18.84 145-149 27.35 27.22 27.029999999999998 18.4 150-151 28.5625 27.625 25.924999999999997 17.8875 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.5 5 1.0 6 0.5 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 2.0 14 2.5 15 1.0 16 0.5 17 0.0 18 1.0 19 2.0 20 1.5 21 0.5 22 1.5 23 2.0 24 1.5 25 2.0 26 2.0 27 3.0 28 4.5 29 6.5 30 9.5 31 14.5 32 26.5 33 38.5 34 54.5 35 72.0 36 89.5 37 104.0 38 121.0 39 166.0 40 220.0 41 225.5 42 206.0 43 228.5 44 248.5 45 244.5 46 231.5 47 237.5 48 225.0 49 186.5 50 174.0 51 143.5 52 114.0 53 107.5 54 97.0 55 74.5 56 54.5 57 52.5 58 50.5 59 37.0 60 25.0 61 15.0 62 15.0 63 15.0 64 9.0 65 5.0 66 1.5 67 3.5 68 3.0 69 1.0 70 0.5 71 1.0 72 1.5 73 1.0 74 0.5 75 0.0 76 0.5 77 1.0 78 1.5 79 1.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.5 87 0.5 88 0.0 89 0.0 90 0.0 91 0.5 92 0.5 93 0.5 94 0.5 95 0.0 96 0.5 97 0.5 98 0.5 99 0.5 100 1.5 >>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 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 88.275 #Duplication Level Percentage of deduplicated Percentage of total 1 90.05947323704333 79.5 2 7.958085528178986 14.05 3 1.3593882752761257 3.5999999999999996 4 0.2832058906825262 1.0 5 0.16992353440951571 0.75 6 0.08496176720475786 0.44999999999999996 7 0.02832058906825262 0.17500000000000002 8 0.02832058906825262 0.2 9 0.0 0.0 >10 0.02832058906825262 0.27499999999999997 >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 CATTAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAAT 11 0.27499999999999997 No Hit GGTAGGAATGGGAGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGA 8 0.2 No Hit ATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAG 7 0.17500000000000002 No Hit GAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCC 6 0.15 No Hit GGGATAGATAGCCACCTATATAGTATAGCTTCCCATCTTCTTTGAGAGTT 6 0.15 No Hit AGATTACTTCCATTTCCGCCCAAGCTGCTCACAGTATACGGGCGTCGGCA 6 0.15 No Hit GGACATTAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCC 5 0.125 No Hit ATTCAAATGAGCATCCTAGTCACCGCGTTTAAAATGAACCTGCCGGCTGA 5 0.125 No Hit GGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTT 5 0.125 No Hit GGCCGATTGTCGCAGCCCGGGTCGATTATAACAACGGTGCAATCTCAGCT 5 0.125 No Hit GGAATGGGAGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGATGGT 5 0.125 No Hit GGAGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGATGGTTTTTAC 5 0.125 No Hit >>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 0.0 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 0.0125 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.07500000000000001 0.0 0.0 0.0 0.0 70-71 0.125 0.0 0.0 0.0 0.0 72-73 0.175 0.0 0.0 0.0 0.0 74-75 0.2 0.0 0.0 0.0 0.0 76-77 0.25 0.0 0.0 0.0 0.0 78-79 0.3 0.0 0.0 0.0 0.0 80-81 0.32499999999999996 0.0 0.0 0.0 0.0 82-83 0.44999999999999996 0.0 0.0 0.0 0.0 84-85 0.7 0.0 0.0 0.0 0.0 86-87 0.7875000000000001 0.0 0.0 0.0 0.0 88-89 0.9125 0.0 0.0 0.0 0.0 90-91 1.0625 0.0 0.0 0.0 0.0 92-93 1.1875 0.0 0.0 0.0 0.0 94-95 1.45 0.0 0.0 0.0 0.0 96-97 1.8375 0.0 0.0 0.0 0.0 98-99 2.2 0.0 0.0 0.0 0.0 100-101 2.4749999999999996 0.0 0.0 0.0 0.0 102-103 2.8375 0.0 0.0 0.0 0.0 104-105 3.1375 0.0 0.0 0.0 0.0 106-107 3.475 0.0 0.0 0.0 0.0 108-109 4.0875 0.0 0.0 0.0 0.0 110-111 4.725 0.0 0.0 0.0 0.0 112-113 5.3125 0.0 0.0 0.0 0.0 114-115 5.9375 0.0 0.0 0.0 0.0 116-117 6.525 0.0 0.0 0.0 0.0 118-119 7.137499999999999 0.0 0.0 0.0 0.0 120-121 7.5125 0.0 0.0 0.0 0.0 122-123 8.175 0.0 0.0 0.0 0.0 124-125 8.725 0.0 0.0 0.0 0.0 126-127 9.65 0.0 0.0 0.0 0.0 128-129 10.575 0.0 0.0 0.0 0.0 130-131 11.15 0.0 0.0 0.0 0.0 132-133 11.7625 0.0 0.0 0.0 0.0 134-135 12.575 0.0 0.0 0.0 0.0 136-137 13.5875 0.0 0.0 0.0 0.0 138-139 14.425 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TACGGTA 10 0.006830828 145.0 4 GGTAGGT 10 0.006830828 145.0 7 GTAGGTC 10 0.006830828 145.0 8 ACGGTAG 10 0.006830828 145.0 5 CGGTAGG 10 0.006830828 145.0 6 GCTTACG 10 0.006830828 145.0 1 TAGGTCC 10 0.006830828 145.0 9 >>END_MODULE Read 671702 spots for SRR12919404.sra Written 671702 spots for SRR12919404.sra Read 671702 spots for SRR12919404.sra Written 671702 spots for SRR12919404.sra Read 671702 spots for SRR12919404.sra Written 671702 spots for SRR12919404.sra Read 671702 spots for SRR12919404.sra Written 671702 spots for SRR12919404.sra Read 671702 spots for SRR12919404.sra Written 671702 spots for SRR12919404.sra Read 671702 spots for SRR12919404.sra Written 671702 spots for SRR12919404.sra Read 671720 spots for SRR12919404.sra Written 671720 spots for SRR12919404.sra Read 671702 spots for SRR12919404.sra Written 671702 spots for SRR12919404.sra Read 671702 spots for SRR12919404.sra Written 671702 spots for SRR12919404.sra Read 671702 spots for SRR12919404.sra Written 671702 spots for SRR12919404.sra Read 671702 spots for SRR12919404.sra Written 671702 spots for SRR12919404.sra Read 671702 spots for SRR12919404.sra Written 671702 spots for SRR12919404.sra Read 671702 spots for SRR12919404.sra Written 671702 spots for SRR12919404.sra Read 671702 spots for SRR12919404.sra Written 671702 spots for SRR12919404.sra Read 671702 spots for SRR12919404.sra Written 671702 spots for SRR12919404.sra Read 671702 spots for SRR12919404.sra Written 671702 spots for SRR12919404.sra Read 671702 spots for SRR12919404.sra Written 671702 spots for SRR12919404.sra Read 671702 spots for SRR12919404.sra Written 671702 spots for SRR12919404.sra Read 671702 spots for SRR12919404.sra Written 671702 spots for SRR12919404.sra Read 671702 spots for SRR12919404.sra Written 671702 spots for SRR12919404.sra SRR ids: ['SRR12919404.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_b3x7fzox SRR12919404.sra spots: 13434058 blocks: [[1, 671702], [671703, 1343404], [1343405, 2015106], [2015107, 2686808], [2686809, 3358510], [3358511, 4030212], [4030213, 4701914], [4701915, 5373616], [5373617, 6045318], [6045319, 6717020], [6717021, 7388722], [7388723, 8060424], [8060425, 8732126], [8732127, 9403828], [9403829, 10075530], [10075531, 10747232], [10747233, 11418934], [11418935, 12090636], [12090637, 12762338], [12762339, 13434058]] SRR12919404 file size 4543780 SRR12919404 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 SRR12919404 SRR12919404_1.fastq SRR12919404_2.fastq Input file: SRR12919404_1.fastq Paired file: SRR12919404_2.fastq trimmed: SRR12919404-trimmed-pair1.fastq, SRR12919404-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 Thu Feb 13 00:18:09 2025 >> started Thu Feb 13 00:29:20 2025 >> done (670.148s) 13434058 read pairs processed; of these: 12 ( 0.00%) short read pairs filtered out after trimming by size control 7490 ( 0.06%) empty read pairs filtered out after trimming by size control 13426556 (99.94%) read pairs available; of these: 2748331 (20.47%) trimmed read pairs available after processing 10678225 (79.53%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 1 0.00% 20 2 0.00% 21 1 0.00% 22 2 0.00% 23 1 0.00% 24 4 0.00% 25 3 0.00% 26 3 0.00% 27 1 0.00% 28 5 0.00% 29 4 0.00% 30 8 0.00% 31 9 0.00% 32 11 0.00% 33 7 0.00% 34 2 0.00% 35 6 0.00% 36 7 0.00% 37 8 0.00% 38 12 0.00% 39 19 0.00% 40 9 0.00% 41 23 0.00% 42 31 0.00% 43 25 0.00% 44 28 0.00% 45 31 0.00% 46 25 0.00% 47 44 0.00% 48 69 0.00% 49 73 0.00% 50 92 0.00% 51 79 0.00% 52 105 0.00% 53 120 0.00% 54 138 0.00% 55 146 0.00% 56 154 0.00% 57 218 0.00% 58 241 0.00% 59 262 0.00% 60 363 0.00% 61 411 0.00% 62 439 0.00% 63 584 0.00% 64 659 0.00% 65 664 0.00% 66 792 0.01% 67 948 0.01% 68 977 0.01% 69 1205 0.01% 70 1450 0.01% 71 1779 0.01% 72 2038 0.02% 73 2209 0.02% 74 2496 0.02% 75 2889 0.02% 76 3117 0.02% 77 3297 0.02% 78 3790 0.03% 79 4414 0.03% 80 4952 0.04% 81 5653 0.04% 82 6537 0.05% 83 7224 0.05% 84 8216 0.06% 85 8811 0.07% 86 9162 0.07% 87 9716 0.07% 88 10515 0.08% 89 11123 0.08% 90 12382 0.09% 91 13472 0.10% 92 15334 0.11% 93 17074 0.13% 94 18034 0.13% 95 18703 0.14% 96 20055 0.15% 97 20706 0.15% 98 21070 0.16% 99 22566 0.17% 100 23767 0.18% 101 24905 0.19% 102 26977 0.20% 103 27951 0.21% 104 29738 0.22% 105 31104 0.23% 106 32388 0.24% 107 32332 0.24% 108 33623 0.25% 109 33875 0.25% 110 33870 0.25% 111 36063 0.27% 112 37961 0.28% 113 40212 0.30% 114 42334 0.32% 115 42200 0.31% 116 43862 0.33% 117 43705 0.33% 118 43847 0.33% 119 43896 0.33% 120 44668 0.33% 121 45898 0.34% 122 47342 0.35% 123 49186 0.37% 124 50302 0.37% 125 51023 0.38% 126 53163 0.40% 127 52905 0.39% 128 51329 0.38% 129 52263 0.39% 130 52222 0.39% 131 53016 0.39% 132 53931 0.40% 133 55918 0.42% 134 57147 0.43% 135 58623 0.44% 136 57765 0.43% 137 58501 0.44% 138 59203 0.44% 139 58181 0.43% 140 58232 0.43% 141 58367 0.43% 142 61636 0.46% 143 61514 0.46% 144 62331 0.46% 145 64041 0.48% 146 64190 0.48% 147 63371 0.47% 148 64154 0.48% 149 62503 0.47% 150 62940 0.47% 151 10678225 79.53% 13426556 reads passed initial QC criterion=sequence-density sequence-density=0.72 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=29 prefix-density=0.72 prefix-fanout=2.0 sequence=GGAATTGAATTAATGAACTTGGTGGCAGCAAGGAAGGCGTTGTAGGAGGCTAAATAGCTAACTCCAGAGTCTGAACTTGTTTCACCAGCTACATTTGAAACACCTTGGAACACCACGAAGAGCTTTTCATTTGACA criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=149.37 fanout-score-rank=1 prefix-density=0.15 prefix-fanout=6.4 sequence=TTATCAAGCACCAAACAAACTTATTGAACTAGAAAAGATAGCTGTACATATTACAGGGGGGAAATGGACCGAAGCTCCTATGACAAAGCTACCTACAAAGGAGTTGGAGCTATTCTTTCACAACCATGCTAGTGCATTCTACAAAGAGTCAAACTCATTCAACTATTCACCTGGCCCCTCATGCTGAACTCACAACCACATAAAAGCCCTTTTTCCCTTCATTGGAATATTTAGATTTTGGCGGAGAAAAGACAATCGCCTATTCTGTGGCTGCGAGGACTGCTGGCCCCTCCACCTTAAATGTAGCACCCCAGATCTCTTCCTCCTTGGCTGGAACTGCAGTGATTTTGTTTTTAGGATTCTCAAAGCTTCTCAGTTCTCCAATTGTAGTGGAGAAGAAGCATCCTTGAGGAAAAGAAGCAAGTGACTTGCCACAAGCGCCCTTAAGCAAATCAATATTGTCTGCGAAAGCAACGTATCCATCAGCAGTGATTCCCCAATACAGAGGAAC criterion=sequence-density sequence-density=0.50 sequence-density-rank=1 fanout-score=2.15 fanout-score-rank=30 prefix-density=0.52 prefix-fanout=2.1 sequence=TGTCAAATGAAAAGCTCTTCGTGGTGTTCCAAGGTGTTTCAAATGTAGCTGGTGAAACAAGTTCAGACTCTGGAGTTAGCTATTTAGCCTCCTACAACGCCTTCCTTGCTGCCACCAAGTTCATTAATTCAATTCC criterion=fanout-score sequence-density=0.01 sequence-density-rank=39 fanout-score=14.82 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=2.9 sequence=CATTTTACCAATGCAATTGAAAGATGCTGCATGGATGCCATCGATCAACTACCTGCCGAGTACTTGAAAGTTCTTTACAGAGCTCTTCTGAATCTTTTCAGTGAAACTGAGAGTGATATGGGAAAGCAAGGACGATCCTATGCCTCATATTACTTGAAGGAGGCATTCAAAGAATTGGCGAGAGCCTACCAAGTGGAGGCGCAGTGGGCAGATGAAGGCCATGTCCCAACATTTGATGAGTATGTGCGCAATGGATTAGCCACAAGTAGTTATGGGGTAACTACAGCAGCATCCTTCGTTGAAATGGATGAAGTTGCAGGGCGGGAGGAGTATGAATGGCTAAACAGTAATCCAAAAATTATTAAAGCTGGAAAGATGATCGGTCGTTTAATGAATGACATAGCGGGCCATGAGGATGAACAAAAGAGGGGAGACTGTGCATCCGGTGTTGAATGCTACATGAAACAATATGATGCATCGGAGAAGAAAGCAATTGAAGAGATACAAAATA SRR12919404 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 13 00:37:56 Started mapping on | Feb 13 00:38:24 Finished on | Feb 13 00:52:06 Mapping speed, Million of reads per hour | 58.80 Number of input reads | 13426556 Average input read length | 291 UNIQUE READS: Uniquely mapped reads number | 9655372 Uniquely mapped reads % | 71.91% Average mapped length | 289.31 Number of splices: Total | 6479542 Number of splices: Annotated (sjdb) | 6278813 Number of splices: GT/AG | 6344052 Number of splices: GC/AG | 97857 Number of splices: AT/AC | 8232 Number of splices: Non-canonical | 29401 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.04% Deletion average length | 2.89 Insertion rate per base | 0.03% Insertion average length | 2.28 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 241712 % of reads mapped to multiple loci | 1.80% Number of reads mapped to too many loci | 197784 % of reads mapped to too many loci | 1.47% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 24.39% % of reads unmapped: other | 0.42% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 3529472 3529472 3529472 N_multimapping 241712 241712 241712 N_noFeature 351415 9498283 408122 N_ambiguous 154366 1194 53369 UnstrandedReadsAssigned:9149591 PositiveStrandReadsAssigned:155895 NegativeStrandReadsAssigned:9193881 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=149 echo kmer=145 SRR12919404 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: SRR12919404-trimmed-pair1.fastq SRR12919404-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,426,556 reads, 9,432,770 reads pseudoaligned [quant] estimated average fragment length: 209.532 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,119 rounds 52401 SRR12919404.ke.tsv 34699 SRR12919404.se.tsv 87100 total ==> SRR12919404.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1809.47 285 14.2847 Potri.005G024800.1.v4.1 1035 826.468 196 21.5083 Potri.004G059700.1.v4.1 961 752.48 3 0.361578 Potri.007G009000.2.v4.1 1416 1207.47 0 0 Potri.003G141000.2.v4.1 2943 2734.47 461 15.2899 Potri.016G087400.1.v4.1 270 97.4474 729 678.474 Potri.015G069301.1.v4.1 564 358.51 0 0 Potri.010G195200.1.v4.1 1773 1564.47 92 5.33331 Potri.012G127500.1.v4.1 977 768.48 5032 593.86 ==> SRR12919404.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 47 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 343 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 15 SRR12919404 completed mapping pipeline successfully