Starting /dee2/code/volunteer_pipeline.sh SRR12951287 current disk space = 1543574061056 free memory = 1602918404 SRR12951287 SRAfilesize bc17ea8d23eb58f58c904eb532b65064 SRR12951287.sra SRR12951287.sra file validated SRR12951287 is paired end SRR12951287 is conventional basespace SRR12951287 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951287_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.508 37.0 37.0 37.0 37.0 37.0 2 36.25725 37.0 37.0 37.0 37.0 37.0 3 36.276 37.0 37.0 37.0 37.0 37.0 4 36.5835 37.0 37.0 37.0 37.0 37.0 5 36.551 37.0 37.0 37.0 37.0 37.0 6 36.6195 37.0 37.0 37.0 37.0 37.0 7 36.4485 37.0 37.0 37.0 37.0 37.0 8 36.484 37.0 37.0 37.0 37.0 37.0 9 36.564 37.0 37.0 37.0 37.0 37.0 10-14 36.5261 37.0 37.0 37.0 37.0 37.0 15-19 36.5269 37.0 37.0 37.0 37.0 37.0 20-24 36.47580000000001 37.0 37.0 37.0 37.0 37.0 25-29 36.4505 37.0 37.0 37.0 37.0 37.0 30-34 36.4245 37.0 37.0 37.0 37.0 37.0 35-39 36.468399999999995 37.0 37.0 37.0 37.0 37.0 40-44 36.409499999999994 37.0 37.0 37.0 37.0 37.0 45-49 36.3621 37.0 37.0 37.0 37.0 37.0 50-54 36.3005 37.0 37.0 37.0 37.0 37.0 55-59 36.3053 37.0 37.0 37.0 37.0 37.0 60-64 36.275 37.0 37.0 37.0 37.0 37.0 65-69 36.2488 37.0 37.0 37.0 37.0 37.0 70-74 36.1983 37.0 37.0 37.0 37.0 37.0 75-79 36.1901 37.0 37.0 37.0 37.0 37.0 80-84 36.2108 37.0 37.0 37.0 37.0 37.0 85-89 36.1654 37.0 37.0 37.0 37.0 37.0 90-94 36.1819 37.0 37.0 37.0 37.0 37.0 95-99 36.1056 37.0 37.0 37.0 37.0 37.0 100-104 36.1459 37.0 37.0 37.0 37.0 37.0 105-109 36.1738 37.0 37.0 37.0 37.0 37.0 110-114 36.023 37.0 37.0 37.0 37.0 37.0 115-119 36.090199999999996 37.0 37.0 37.0 37.0 37.0 120-124 36.0135 37.0 37.0 37.0 37.0 37.0 125-129 35.953199999999995 37.0 37.0 37.0 37.0 37.0 130-134 35.9956 37.0 37.0 37.0 37.0 37.0 135-139 35.9375 37.0 37.0 37.0 37.0 37.0 140-144 35.7779 37.0 37.0 37.0 37.0 37.0 145-149 35.7741 37.0 37.0 37.0 37.0 37.0 150-151 35.683 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 2.0 22 0.0 23 4.0 24 1.0 25 4.0 26 7.0 27 12.0 28 16.0 29 19.0 30 22.0 31 40.0 32 60.0 33 79.0 34 139.0 35 300.0 36 2814.0 37 481.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 52.425 11.75 4.875 30.95 2 24.316871396339934 11.05540235648032 31.461519177738783 33.166207069440965 3 20.575 17.8 27.575 34.050000000000004 4 25.15 23.025000000000002 23.599999999999998 28.225 5 26.474999999999998 29.925 22.8 20.8 6 24.675 32.7 21.275 21.349999999999998 7 19.575 23.1 37.7 19.625 8 20.125 24.474999999999998 27.875 27.525 9 20.65 20.8 33.35 25.2 10-14 24.16 25.0 24.7 26.14 15-19 24.25 24.240000000000002 24.63 26.88 20-24 25.130000000000003 25.215 24.25 25.405 25-29 23.9 25.115 24.235 26.75 30-34 24.185000000000002 24.52 24.37 26.924999999999997 35-39 24.62 24.535 24.585 26.26 40-44 24.44 25.055 24.19 26.314999999999998 45-49 24.21 23.919999999999998 25.105 26.765 50-54 24.8 24.275 24.58 26.345000000000002 55-59 24.68 24.305 24.265 26.75 60-64 24.595 23.69 24.79 26.924999999999997 65-69 23.72 24.635 24.555 27.089999999999996 70-74 24.595 24.48 24.834999999999997 26.090000000000003 75-79 24.72 24.32 24.12 26.840000000000003 80-84 25.3 24.865000000000002 23.555 26.279999999999998 85-89 25.3 24.015 24.635 26.05 90-94 25.61 23.885 23.89 26.615 95-99 25.435000000000002 23.794999999999998 23.985 26.784999999999997 100-104 26.029999999999998 24.279999999999998 23.11 26.58 105-109 25.095 24.85 23.375 26.68 110-114 25.580000000000002 24.03 23.98 26.41 115-119 25.5 24.02 24.29 26.19 120-124 24.75 24.93 23.064999999999998 27.255000000000003 125-129 25.374999999999996 24.635 24.04 25.95 130-134 25.945 24.735 23.13 26.19 135-139 25.4 24.33 23.064999999999998 27.205000000000002 140-144 25.215 24.98 22.81 26.995 145-149 25.14 25.115 23.345 26.400000000000002 150-151 25.6 24.3125 22.05 28.037499999999998 >>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 0.5 6 0.5 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.5 15 0.5 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 1.5 27 2.5 28 2.0 29 1.5 30 1.5 31 6.0 32 9.5 33 12.5 34 19.5 35 32.0 36 44.5 37 54.5 38 70.0 39 81.5 40 107.0 41 135.0 42 148.5 43 171.0 44 176.5 45 166.0 46 174.0 47 178.0 48 172.5 49 167.5 50 158.0 51 151.0 52 132.0 53 122.5 54 122.5 55 104.0 56 88.5 57 80.0 58 75.0 59 77.5 60 73.5 61 63.0 62 58.5 63 74.5 64 82.0 65 77.5 66 76.0 67 66.0 68 63.0 69 48.5 70 41.0 71 50.0 72 44.5 73 35.5 74 28.0 75 22.5 76 20.0 77 13.5 78 5.5 79 2.0 80 2.5 81 2.0 82 1.0 83 1.0 84 0.5 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 0.27499999999999997 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 83.175 #Duplication Level Percentage of deduplicated Percentage of total 1 84.12984670874661 69.975 2 12.473700030057108 20.75 3 2.8854824165915236 7.199999999999999 4 0.39074241058010223 1.3 5 0.06011421701232341 0.25 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.030057108506161705 0.22499999999999998 >10 0.030057108506161705 0.3 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACACGATGACATCTCGTAT 12 0.3 TruSeq Adapter, Index 15 (97% over 36bp) GCTTCGTTGACGGTGATGTTGCGGCCATCCAGGTCCTTGCCGTTCATGCC 9 0.22499999999999998 No Hit CTCCCTTTAGACTTCAAGATATCAGCAACAGTGCCGCTCTCGAATCCACT 5 0.125 No Hit GCTGGATTGAAGGCGTGTAAGGCCAGTATGTGCCCATCTTGTAGAACTTG 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 0.0125 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 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 0.1125 0.0 0.0 0.0 0.0 66-67 0.15 0.0 0.0 0.0 0.0 68-69 0.15 0.0 0.0 0.0 0.0 70-71 0.15 0.0 0.0 0.0 0.0 72-73 0.16249999999999998 0.0 0.0 0.0 0.0 74-75 0.25 0.0 0.0 0.0 0.0 76-77 0.2875 0.0 0.0 0.0 0.0 78-79 0.3375 0.0 0.0 0.0 0.0 80-81 0.4 0.0 0.0 0.0 0.0 82-83 0.4375 0.0 0.0 0.0 0.0 84-85 0.5 0.0 0.0 0.0 0.0 86-87 0.625 0.0 0.0 0.0 0.0 88-89 0.675 0.0 0.0 0.0 0.0 90-91 0.725 0.0 0.0 0.0 0.0 92-93 0.8125 0.0 0.0 0.0 0.0 94-95 0.9 0.0 0.0 0.0 0.0 96-97 1.0750000000000002 0.0 0.0 0.0 0.0 98-99 1.4625 0.0 0.0 0.0 0.0 100-101 1.75 0.0 0.0 0.0 0.0 102-103 2.0875 0.0 0.0 0.0 0.0 104-105 2.3375000000000004 0.0 0.0 0.0 0.0 106-107 2.675 0.0 0.0 0.0 0.0 108-109 3.1 0.0 0.0 0.0 0.0 110-111 3.375 0.0 0.0 0.0 0.0 112-113 3.6625 0.0 0.0 0.0 0.0 114-115 3.95 0.0 0.0 0.0 0.0 116-117 4.225 0.0 0.0 0.0 0.0 118-119 4.675000000000001 0.0 0.0 0.0 0.0 120-121 5.0875 0.0 0.0 0.0 0.0 122-123 5.525 0.0 0.0 0.0 0.0 124-125 6.262499999999999 0.0 0.0 0.0 0.0 126-127 6.75 0.0 0.0 0.0 0.0 128-129 7.1375 0.0 0.0 0.0 0.0 130-131 7.5875 0.0 0.0 0.0 0.0 132-133 8.3625 0.0 0.0 0.0 0.0 134-135 9.037500000000001 0.0 0.0 0.0 0.0 136-137 9.75 0.0 0.0 0.0 0.0 138-139 10.3125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTATTCA 10 0.006830828 145.0 6 >>END_MODULE SRR12951287 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951287_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 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.9545 37.0 37.0 37.0 37.0 37.0 2 36.074 37.0 37.0 37.0 37.0 37.0 3 35.8405 37.0 37.0 37.0 37.0 37.0 4 35.9565 37.0 37.0 37.0 37.0 37.0 5 35.9735 37.0 37.0 37.0 37.0 37.0 6 35.949 37.0 37.0 37.0 37.0 37.0 7 35.9825 37.0 37.0 37.0 37.0 37.0 8 35.837 37.0 37.0 37.0 37.0 37.0 9 35.8965 37.0 37.0 37.0 37.0 37.0 10-14 35.9156 37.0 37.0 37.0 37.0 37.0 15-19 35.8511 37.0 37.0 37.0 37.0 37.0 20-24 35.7678 37.0 37.0 37.0 37.0 37.0 25-29 35.7251 37.0 37.0 37.0 37.0 37.0 30-34 35.6578 37.0 37.0 37.0 37.0 37.0 35-39 35.6508 37.0 37.0 37.0 37.0 37.0 40-44 35.6437 37.0 37.0 37.0 37.0 37.0 45-49 35.6135 37.0 37.0 37.0 37.0 37.0 50-54 35.5466 37.0 37.0 37.0 37.0 37.0 55-59 35.549 37.0 37.0 37.0 37.0 37.0 60-64 35.5345 37.0 37.0 37.0 37.0 37.0 65-69 35.565200000000004 37.0 37.0 37.0 37.0 37.0 70-74 35.483200000000004 37.0 37.0 37.0 37.0 37.0 75-79 35.4529 37.0 37.0 37.0 37.0 37.0 80-84 35.4319 37.0 37.0 37.0 37.0 37.0 85-89 35.4405 37.0 37.0 37.0 37.0 37.0 90-94 35.4765 37.0 37.0 37.0 37.0 37.0 95-99 35.3458 37.0 37.0 37.0 37.0 37.0 100-104 35.364999999999995 37.0 37.0 37.0 37.0 37.0 105-109 35.371 37.0 37.0 37.0 37.0 37.0 110-114 35.22619999999999 37.0 37.0 37.0 37.0 37.0 115-119 35.41 37.0 37.0 37.0 37.0 37.0 120-124 35.2749 37.0 37.0 37.0 37.0 37.0 125-129 35.226600000000005 37.0 37.0 37.0 32.2 37.0 130-134 35.1577 37.0 37.0 37.0 34.6 37.0 135-139 35.1825 37.0 37.0 37.0 32.2 37.0 140-144 35.0315 37.0 37.0 37.0 27.4 37.0 145-149 34.8275 37.0 37.0 37.0 25.0 37.0 150-151 34.6155 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 7.0 13 13.0 14 11.0 15 9.0 16 9.0 17 4.0 18 8.0 19 6.0 20 7.0 21 13.0 22 16.0 23 16.0 24 7.0 25 17.0 26 14.0 27 21.0 28 19.0 29 14.0 30 27.0 31 35.0 32 63.0 33 95.0 34 174.0 35 450.0 36 2607.0 37 338.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 49.15 20.125 6.625 24.099999999999998 2 31.65 20.575 24.525 23.25 3 25.124999999999996 24.474999999999998 28.775000000000002 21.625 4 27.650000000000002 30.85 18.25 23.25 5 30.45 31.374999999999996 18.175 20.0 6 27.025 31.924999999999997 18.35 22.7 7 25.6 19.525000000000002 31.825 23.05 8 24.25 21.725 23.25 30.775000000000002 9 26.1 20.325 25.1 28.475 10-14 28.655 24.08 21.82 25.445 15-19 27.389999999999997 23.48 22.97 26.16 20-24 27.18 25.064999999999998 22.165000000000003 25.590000000000003 25-29 27.62 24.169999999999998 22.905 25.305 30-34 27.185 24.39 23.265 25.16 35-39 26.275 24.92 23.335 25.47 40-44 27.105 24.63 22.009999999999998 26.255 45-49 27.52 24.94 22.994999999999997 24.545 50-54 27.315 24.775 23.005 24.905 55-59 27.375 24.975 23.015 24.635 60-64 27.255000000000003 24.169999999999998 23.830000000000002 24.745 65-69 27.92 24.115000000000002 23.244999999999997 24.72 70-74 27.83 24.740000000000002 22.770000000000003 24.66 75-79 27.1 24.775 23.14 24.985 80-84 27.615000000000002 24.57 23.275000000000002 24.54 85-89 27.060000000000002 24.959999999999997 22.919999999999998 25.06 90-94 26.884999999999998 24.4 23.965 24.75 95-99 27.810000000000002 24.45 23.24 24.5 100-104 27.725 24.75 22.46 25.064999999999998 105-109 27.705000000000002 24.985 22.925 24.385 110-114 27.525 25.290000000000003 22.31 24.875 115-119 27.794999999999998 25.6 23.155 23.45 120-124 27.785 25.615 22.525000000000002 24.075 125-129 28.910000000000004 25.564999999999998 22.775000000000002 22.75 130-134 28.83 24.955 23.080000000000002 23.135 135-139 28.665000000000003 25.21 22.82 23.305 140-144 28.689999999999998 24.94 23.02 23.35 145-149 29.43 25.619999999999997 22.06 22.89 150-151 31.025000000000002 24.6 22.2625 22.112499999999997 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 5 1.0 6 1.0 7 0.0 8 0.5 9 0.5 10 0.0 11 0.0 12 1.0 13 2.0 14 1.0 15 0.0 16 0.0 17 0.5 18 1.5 19 1.0 20 2.0 21 3.5 22 2.0 23 1.0 24 1.5 25 2.0 26 1.5 27 1.0 28 3.5 29 4.0 30 3.0 31 6.0 32 8.5 33 14.5 34 17.5 35 18.5 36 35.0 37 47.0 38 61.0 39 70.5 40 79.5 41 105.5 42 123.0 43 152.5 44 183.0 45 181.0 46 163.5 47 151.0 48 152.0 49 148.5 50 136.0 51 138.5 52 137.0 53 126.5 54 116.5 55 93.0 56 78.5 57 86.0 58 108.5 59 106.5 60 83.0 61 83.0 62 93.0 63 92.0 64 81.0 65 66.0 66 66.0 67 81.5 68 80.0 69 63.5 70 54.5 71 46.0 72 38.0 73 33.5 74 24.0 75 22.5 76 23.5 77 19.0 78 10.5 79 5.5 80 4.0 81 1.5 82 2.0 83 4.0 84 3.5 85 1.5 86 1.5 87 2.0 88 2.0 89 1.0 90 0.5 91 1.0 92 1.0 93 1.5 94 1.0 95 1.5 96 1.5 97 0.0 98 3.0 99 4.0 100 8.0 >>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 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 83.3 #Duplication Level Percentage of deduplicated Percentage of total 1 84.60384153661464 70.475 2 12.214885954381753 20.349999999999998 3 2.6710684273709484 6.675000000000001 4 0.33013205282112845 1.0999999999999999 5 0.09003601440576231 0.375 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.030012004801920768 0.22499999999999998 >10 0.060024009603841535 0.8 >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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 20 0.5 No Hit GTTGGCTTCTCCTCCCCCTCACTAGTCCTCGGTTCCGGTTCCGGTTCGTT 12 0.3 No Hit GGTGGGTTGGCTTCTCCTCCCCCTCACTAGTCCTCGGTTCCGGTTCCGGT 9 0.22499999999999998 No Hit CTGGAAAATGTACAGCCTCAAAGGGTTGTCGAACATTATCAAGGTTCAGG 5 0.125 No Hit CTTCCCCCCTCATCATCTTCTTCCTCGTCTCGCCCACAGCTCGCAGTTCC 5 0.125 No Hit GGCGCTGTCGCTGCCGACGGGGCTGGGGATCGTGTGCGCCAGCCCGAGGG 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 0.0125 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 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 0.1125 0.0 0.0 0.0 0.0 66-67 0.15 0.0 0.0 0.0 0.0 68-69 0.15 0.0 0.0 0.0 0.0 70-71 0.15 0.0 0.0 0.0 0.0 72-73 0.16249999999999998 0.0 0.0 0.0 0.0 74-75 0.25 0.0 0.0 0.0 0.0 76-77 0.2875 0.0 0.0 0.0 0.0 78-79 0.3375 0.0 0.0 0.0 0.0 80-81 0.42500000000000004 0.0 0.0 0.0 0.0 82-83 0.4625 0.0 0.0 0.0 0.0 84-85 0.5249999999999999 0.0 0.0 0.0 0.0 86-87 0.65 0.0 0.0 0.0 0.0 88-89 0.7 0.0 0.0 0.0 0.0 90-91 0.75 0.0 0.0 0.0 0.0 92-93 0.8374999999999999 0.0 0.0 0.0 0.0 94-95 0.925 0.0 0.0 0.0 0.0 96-97 1.0750000000000002 0.0 0.0 0.0 0.0 98-99 1.4375 0.0 0.0 0.0 0.0 100-101 1.7125 0.0 0.0 0.0 0.0 102-103 2.0125 0.0 0.0 0.0 0.0 104-105 2.2625 0.0 0.0 0.0 0.0 106-107 2.6125 0.0 0.0 0.0 0.0 108-109 3.075 0.0 0.0 0.0 0.0 110-111 3.3499999999999996 0.0 0.0 0.0 0.0 112-113 3.6375 0.0 0.0 0.0 0.0 114-115 3.9250000000000003 0.0 0.0 0.0 0.0 116-117 4.199999999999999 0.0 0.0 0.0 0.0 118-119 4.65 0.0 0.0 0.0 0.0 120-121 5.0625 0.0 0.0 0.0 0.0 122-123 5.5 0.0 0.0 0.0 0.0 124-125 6.199999999999999 0.0 0.0 0.0 0.0 126-127 6.675 0.0 0.0 0.0 0.0 128-129 7.0625 0.0 0.0 0.0 0.0 130-131 7.525 0.0 0.0 0.0 0.0 132-133 8.3625 0.0 0.0 0.0 0.0 134-135 9.037500000000001 0.0 0.0 0.0 0.0 136-137 9.75 0.0 0.0 0.0 0.0 138-139 10.3125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGTCGCC 10 0.006830828 145.0 7 >>END_MODULE Read 1545067 spots for SRR12951287.sra Written 1545067 spots for SRR12951287.sra Read 1545067 spots for SRR12951287.sra Written 1545067 spots for SRR12951287.sra Read 1545067 spots for SRR12951287.sra Written 1545067 spots for SRR12951287.sra Read 1545067 spots for SRR12951287.sra Written 1545067 spots for SRR12951287.sra Read 1545067 spots for SRR12951287.sra Written 1545067 spots for SRR12951287.sra Read 1545067 spots for SRR12951287.sra Written 1545067 spots for SRR12951287.sra Read 1545067 spots for SRR12951287.sra Written 1545067 spots for SRR12951287.sra Read 1545067 spots for SRR12951287.sra Written 1545067 spots for SRR12951287.sra Read 1545067 spots for SRR12951287.sra Written 1545067 spots for SRR12951287.sra Read 1545067 spots for SRR12951287.sra Written 1545067 spots for SRR12951287.sra Read 1545067 spots for SRR12951287.sra Written 1545067 spots for SRR12951287.sra Read 1545067 spots for SRR12951287.sra Written 1545067 spots for SRR12951287.sra Read 1545067 spots for SRR12951287.sra Written 1545067 spots for SRR12951287.sra Read 1545076 spots for SRR12951287.sra Written 1545076 spots for SRR12951287.sra Read 1545067 spots for SRR12951287.sra Written 1545067 spots for SRR12951287.sra Read 1545067 spots for SRR12951287.sra Written 1545067 spots for SRR12951287.sra Read 1545067 spots for SRR12951287.sra Written 1545067 spots for SRR12951287.sra Read 1545067 spots for SRR12951287.sra Written 1545067 spots for SRR12951287.sra Read 1545067 spots for SRR12951287.sra Written 1545067 spots for SRR12951287.sra Read 1545067 spots for SRR12951287.sra Written 1545067 spots for SRR12951287.sra SRR ids: ['SRR12951287.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_om4bcywq SRR12951287.sra spots: 30901349 blocks: [[1, 1545067], [1545068, 3090134], [3090135, 4635201], [4635202, 6180268], [6180269, 7725335], [7725336, 9270402], [9270403, 10815469], [10815470, 12360536], [12360537, 13905603], [13905604, 15450670], [15450671, 16995737], [16995738, 18540804], [18540805, 20085871], [20085872, 21630938], [21630939, 23176005], [23176006, 24721072], [24721073, 26266139], [26266140, 27811206], [27811207, 29356273], [29356274, 30901349]] SRR12951287 file size 10479929 SRR12951287 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 SRR12951287 SRR12951287_1.fastq SRR12951287_2.fastq Input file: SRR12951287_1.fastq Paired file: SRR12951287_2.fastq trimmed: SRR12951287-trimmed-pair1.fastq, SRR12951287-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 Dec 7 10:32:43 2024 >> started Sat Dec 7 10:33:19 2024 >> done (36.010s) 30901349 read pairs processed; of these: 193 ( 0.00%) short read pairs filtered out after trimming by size control 78760 ( 0.25%) empty read pairs filtered out after trimming by size control 30822396 (99.74%) read pairs available; of these: 4372493 (14.19%) trimmed read pairs available after processing 26449903 (85.81%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 17 0.00% 19 24 0.00% 20 34 0.00% 21 28 0.00% 22 69 0.00% 23 83 0.00% 24 73 0.00% 25 85 0.00% 26 86 0.00% 27 114 0.00% 28 104 0.00% 29 118 0.00% 30 115 0.00% 31 118 0.00% 32 120 0.00% 33 126 0.00% 34 110 0.00% 35 109 0.00% 36 104 0.00% 37 129 0.00% 38 123 0.00% 39 136 0.00% 40 140 0.00% 41 148 0.00% 42 168 0.00% 43 183 0.00% 44 175 0.00% 45 163 0.00% 46 212 0.00% 47 238 0.00% 48 249 0.00% 49 315 0.00% 50 323 0.00% 51 325 0.00% 52 360 0.00% 53 423 0.00% 54 422 0.00% 55 503 0.00% 56 502 0.00% 57 610 0.00% 58 686 0.00% 59 733 0.00% 60 772 0.00% 61 961 0.00% 62 1025 0.00% 63 1126 0.00% 64 1246 0.00% 65 1417 0.00% 66 1539 0.00% 67 1732 0.01% 68 1877 0.01% 69 2066 0.01% 70 2556 0.01% 71 2860 0.01% 72 3239 0.01% 73 3601 0.01% 74 4105 0.01% 75 4454 0.01% 76 4791 0.02% 77 5312 0.02% 78 5781 0.02% 79 6686 0.02% 80 7580 0.02% 81 8274 0.03% 82 9272 0.03% 83 10524 0.03% 84 11718 0.04% 85 12527 0.04% 86 13386 0.04% 87 14260 0.05% 88 15231 0.05% 89 16323 0.05% 90 18064 0.06% 91 19709 0.06% 92 21383 0.07% 93 23503 0.08% 94 24989 0.08% 95 26471 0.09% 96 27970 0.09% 97 28704 0.09% 98 29631 0.10% 99 31205 0.10% 100 33530 0.11% 101 34854 0.11% 102 37617 0.12% 103 40250 0.13% 104 41660 0.14% 105 43901 0.14% 106 45546 0.15% 107 45804 0.15% 108 47843 0.16% 109 49253 0.16% 110 50921 0.17% 111 53150 0.17% 112 55383 0.18% 113 58174 0.19% 114 60890 0.20% 115 62448 0.20% 116 64522 0.21% 117 65295 0.21% 118 66855 0.22% 119 68156 0.22% 120 69865 0.23% 121 71374 0.23% 122 72707 0.24% 123 76226 0.25% 124 79522 0.26% 125 80262 0.26% 126 82539 0.27% 127 82731 0.27% 128 83483 0.27% 129 85749 0.28% 130 85918 0.28% 131 87437 0.28% 132 91377 0.30% 133 92794 0.30% 134 93966 0.30% 135 96598 0.31% 136 98693 0.32% 137 98886 0.32% 138 99645 0.32% 139 100180 0.33% 140 99713 0.32% 141 102942 0.33% 142 103283 0.34% 143 105383 0.34% 144 107485 0.35% 145 108749 0.35% 146 109406 0.35% 147 110635 0.36% 148 110845 0.36% 149 110135 0.36% 150 111140 0.36% 151 26449903 85.81% 30822396 reads passed initial QC criterion=sequence-density sequence-density=0.23 sequence-density-rank=1 fanout-score=3.63 fanout-score-rank=30 prefix-density=0.30 prefix-fanout=2.8 sequence=GAACCGGAACCG criterion=fanout-score sequence-density=0.03 sequence-density-rank=32 fanout-score=417.95 fanout-score-rank=1 prefix-density=0.76 prefix-fanout=16.9 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.96 sequence-density-rank=1 fanout-score=2.04 fanout-score-rank=34 prefix-density=0.96 prefix-fanout=2.0 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.11 sequence-density-rank=16 fanout-score=219.13 fanout-score-rank=1 prefix-density=1.07 prefix-fanout=22.3 sequence=CGCCGCCGCCGG SRR12951287 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 10:34:03 Started mapping on | Dec 07 10:34:03 Finished on | Dec 07 10:37:06 Mapping speed, Million of reads per hour | 606.34 Number of input reads | 30822396 Average input read length | 294 UNIQUE READS: Uniquely mapped reads number | 28637284 Uniquely mapped reads % | 92.91% Average mapped length | 293.38 Number of splices: Total | 26186757 Number of splices: Annotated (sjdb) | 24357042 Number of splices: GT/AG | 25810045 Number of splices: GC/AG | 314517 Number of splices: AT/AC | 15804 Number of splices: Non-canonical | 46391 Mismatch rate per base, % | 0.24% Deletion rate per base | 0.01% Deletion average length | 2.24 Insertion rate per base | 0.01% Insertion average length | 2.43 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 341919 % of reads mapped to multiple loci | 1.11% Number of reads mapped to too many loci | 43340 % of reads mapped to too many loci | 0.14% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.08% % of reads unmapped: other | 0.76% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1843193 1843193 1843193 N_multimapping 341919 341919 341919 N_noFeature 1087077 27864394 1346274 N_ambiguous 604641 3936 90910 UnstrandedReadsAssigned:26945566 PositiveStrandReadsAssigned:768954 NegativeStrandReadsAssigned:27200100 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12951287 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: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in paired-end mode [quant] will process pair 1: SRR12951287-trimmed-pair1.fastq SRR12951287-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 30,822,396 reads, 27,933,573 reads pseudoaligned [quant] estimated average fragment length: 258.008 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,190 rounds 52973 SRR12951287.ke.tsv 35125 SRR12951287.se.tsv 88098 total ==> SRR12951287.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 679.616 0 0 PNS24247 1044 786.992 189.618 12.3709 PNS24249 1928 1670.99 403.045 12.3843 PNS24246 1044 786.992 189.618 12.3709 PNS24248 1044 786.992 189.618 12.3709 PNS24244 1471 1213.99 232.102 9.81645 PNS24243 293 105.017 0 0 KQK14069 1603 1345.99 48555.3 1852.19 KQK14071 474 244.014 90.6641 19.0771 ==> SRR12951287.se.tsv <== BRADI_1g14170v3 48152 BRADI_1g53295v3 305 BRADI_1g59795v3 522 BRADI_1g07683v3 0 BRADI_1g00485v3 31 BRADI_1g20270v3 1128 BRADI_1g74790v3 1930 BRADI_1g09890v3 0 BRADI_1g77505v3 288 BRADI_1g48960v3 0 SRR12951287 completed mapping pipeline successfully