Starting /dee2/code/volunteer_pipeline.sh SRR12670097 current disk space = 3057340321792 free memory = 1475092176 SRR12670097 SRAfilesize d04e67abd8c5da3d5e8dab9a54f9681b SRR12670097.sra SRR12670097.sra file validated SRR12670097 is paired end SRR12670097 is conventional basespace SRR12670097 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670097_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 36.635 37.0 37.0 37.0 37.0 37.0 2 36.3335 37.0 37.0 37.0 37.0 37.0 3 36.5295 37.0 37.0 37.0 37.0 37.0 4 36.674 37.0 37.0 37.0 37.0 37.0 5 36.644 37.0 37.0 37.0 37.0 37.0 6 36.667 37.0 37.0 37.0 37.0 37.0 7 36.6095 37.0 37.0 37.0 37.0 37.0 8 36.653 37.0 37.0 37.0 37.0 37.0 9 36.587 37.0 37.0 37.0 37.0 37.0 10-14 36.6068 37.0 37.0 37.0 37.0 37.0 15-19 36.60979999999999 37.0 37.0 37.0 37.0 37.0 20-24 36.533 37.0 37.0 37.0 37.0 37.0 25-29 36.492399999999996 37.0 37.0 37.0 37.0 37.0 30-34 36.5141 37.0 37.0 37.0 37.0 37.0 35-39 36.4662 37.0 37.0 37.0 37.0 37.0 40-44 36.4692 37.0 37.0 37.0 37.0 37.0 45-49 36.4576 37.0 37.0 37.0 37.0 37.0 50-54 36.4538 37.0 37.0 37.0 37.0 37.0 55-59 36.39639999999999 37.0 37.0 37.0 37.0 37.0 60-64 36.3755 37.0 37.0 37.0 37.0 37.0 65-69 36.287299999999995 37.0 37.0 37.0 37.0 37.0 70-74 36.2932 37.0 37.0 37.0 37.0 37.0 75-79 36.2911 37.0 37.0 37.0 37.0 37.0 80-84 36.304199999999994 37.0 37.0 37.0 37.0 37.0 85-89 36.2719 37.0 37.0 37.0 37.0 37.0 90-94 36.264399999999995 37.0 37.0 37.0 37.0 37.0 95-99 36.2039 37.0 37.0 37.0 37.0 37.0 100-104 36.2239 37.0 37.0 37.0 37.0 37.0 105-109 36.2275 37.0 37.0 37.0 37.0 37.0 110-114 36.1707 37.0 37.0 37.0 37.0 37.0 115-119 36.1173 37.0 37.0 37.0 37.0 37.0 120-124 36.0321 37.0 37.0 37.0 37.0 37.0 125-129 36.0026 37.0 37.0 37.0 37.0 37.0 130-134 35.957499999999996 37.0 37.0 37.0 37.0 37.0 135-139 35.8356 37.0 37.0 37.0 37.0 37.0 140-144 35.659800000000004 37.0 37.0 37.0 37.0 37.0 145-149 35.6103 37.0 37.0 37.0 37.0 37.0 150-151 35.34825 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 0.0 22 1.0 23 1.0 24 1.0 25 2.0 26 2.0 27 5.0 28 10.0 29 13.0 30 32.0 31 37.0 32 43.0 33 72.0 34 129.0 35 336.0 36 2949.0 37 366.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 41.175 12.1 5.625 41.099999999999994 2 19.001004016064257 12.976907630522089 36.92269076305221 31.099397590361445 3 17.0 17.0 27.6 38.4 4 21.925 23.25 24.625 30.2 5 23.599999999999998 29.9 24.725 21.775 6 20.349999999999998 34.0 23.849999999999998 21.8 7 16.25 25.95 39.95 17.849999999999998 8 17.5 25.900000000000002 31.15 25.45 9 18.75 22.75 33.6 24.9 10-14 19.975 29.895 27.744999999999997 22.384999999999998 15-19 20.095 27.96 27.905 24.04 20-24 20.405 27.905 28.189999999999998 23.5 25-29 19.925 27.655 28.76 23.66 30-34 19.794999999999998 28.215 27.35 24.64 35-39 21.095 28.384999999999998 27.089999999999996 23.43 40-44 19.634999999999998 29.415000000000003 27.365000000000002 23.585 45-49 20.26 28.715000000000003 28.02 23.005 50-54 20.745 27.665 27.355 24.235 55-59 20.71 27.465 27.975 23.849999999999998 60-64 20.43 28.22 27.474999999999998 23.875 65-69 21.48 27.900000000000002 27.565 23.055 70-74 21.709999999999997 28.08 26.86 23.35 75-79 20.48 28.000000000000004 27.91 23.61 80-84 21.224999999999998 28.24 27.41 23.125 85-89 21.125 28.310000000000002 26.55 24.015 90-94 21.04 28.075 27.439999999999998 23.445 95-99 20.919999999999998 28.199999999999996 26.834999999999997 24.044999999999998 100-104 21.815 27.675 27.36 23.150000000000002 105-109 21.205 28.110000000000003 26.815 23.87 110-114 21.265 28.15 27.11 23.474999999999998 115-119 21.26 28.945 26.16 23.635 120-124 21.435000000000002 28.415000000000003 26.46 23.69 125-129 21.115000000000002 27.99 26.125 24.77 130-134 21.634999999999998 27.42 26.44 24.505 135-139 21.560000000000002 28.139999999999997 26.724999999999998 23.575 140-144 21.81 26.865 26.995 24.33 145-149 22.62 27.33 26.009999999999998 24.04 150-151 21.4125 27.6625 25.662499999999998 25.2625 >>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 0.5 10 0.5 11 0.0 12 0.0 13 0.5 14 1.5 15 1.0 16 0.0 17 0.5 18 1.0 19 0.5 20 0.0 21 0.0 22 1.0 23 1.5 24 2.0 25 4.5 26 5.5 27 5.0 28 6.0 29 11.5 30 14.0 31 19.5 32 31.5 33 35.5 34 43.5 35 63.5 36 79.0 37 104.5 38 129.0 39 145.5 40 172.0 41 213.5 42 230.0 43 242.0 44 257.5 45 253.5 46 255.0 47 252.0 48 243.0 49 218.0 50 185.0 51 166.0 52 133.5 53 91.0 54 70.0 55 63.0 56 57.0 57 46.0 58 36.0 59 29.5 60 26.5 61 15.5 62 7.5 63 5.5 64 5.5 65 4.0 66 0.5 67 2.5 68 3.5 69 2.5 70 2.0 71 0.5 72 1.0 73 1.0 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 0.0 2 0.4 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 82.075 #Duplication Level Percentage of deduplicated Percentage of total 1 83.4907097167225 68.525 2 12.640877246420956 20.75 3 2.893694791349376 7.124999999999999 4 0.7005787389582698 2.3 5 0.18275967103259214 0.75 6 0.03045994517209869 0.15 7 0.03045994517209869 0.17500000000000002 8 0.0 0.0 9 0.03045994517209869 0.22499999999999998 >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 CACCTGTGGGCATGCGAGAAGAGACATTTCCATCTAAAGCTGCACAGGCT 9 0.22499999999999998 No Hit TTTACAAACAAAGTACATATCTGAGGACTCTTAAGGATTGGGAAGTATAA 7 0.17500000000000002 No Hit CAGCCTTGCGACCATACTCCCCCCAGAACCCAAAAACTTTGATTTCTCAT 6 0.15 No Hit CCATTTTCCCTTGTATGCTGGATTTCTCTTCATTGGCCTCTTCCATTCAC 5 0.125 No Hit CATCAACTTCCTGTGCTACGACGTCCCTGAGCCACATGGGATAATTCCAT 5 0.125 No Hit CCAGTGTTCTCTAGCCCAATTGAGGCTAGACGTTTCCCACAGGTAGCATT 5 0.125 No Hit GTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGG 5 0.125 No Hit ACACAGAAAAGAAGGCTGGAATCTTTGTAATAATAGCTGGAAAGATTGCG 5 0.125 No Hit CCTCAAAGTACTTGAAAATGGGGTAACACTGGTACTCAGGGTTTTCCCTG 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 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 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 0.1125 0.0 0.0 0.0 0.0 68-69 0.1375 0.0 0.0 0.0 0.0 70-71 0.16249999999999998 0.0 0.0 0.0 0.0 72-73 0.3 0.0 0.0 0.0 0.0 74-75 0.42500000000000004 0.0 0.0 0.0 0.0 76-77 0.6125 0.0 0.0 0.0 0.0 78-79 0.8125 0.0 0.0 0.0 0.0 80-81 1.1625 0.0 0.0 0.0 0.0 82-83 1.4 0.0 0.0 0.0 0.0 84-85 1.8375 0.0 0.0 0.0 0.0 86-87 2.1375 0.0 0.0 0.0 0.0 88-89 2.4375 0.0 0.0 0.0 0.0 90-91 2.825 0.0 0.0 0.0 0.0 92-93 3.1624999999999996 0.0 0.0 0.0 0.0 94-95 3.5625 0.0 0.0 0.0 0.0 96-97 4.025 0.0 0.0 0.0 0.0 98-99 4.574999999999999 0.0 0.0 0.0 0.0 100-101 5.012499999999999 0.0 0.0 0.0 0.0 102-103 5.5625 0.0 0.0 0.0 0.0 104-105 6.0375 0.0 0.0 0.0 0.0 106-107 6.925000000000001 0.0 0.0 0.0 0.0 108-109 7.4375 0.0 0.0 0.0 0.0 110-111 8.0625 0.0 0.0 0.0 0.0 112-113 8.7 0.0 0.0 0.0 0.0 114-115 9.175 0.0 0.0 0.0 0.0 116-117 10.1125 0.0 0.0 0.0 0.0 118-119 10.9 0.0 0.0 0.0 0.0 120-121 11.675 0.0 0.0 0.0 0.0 122-123 12.55 0.0 0.0 0.0 0.0 124-125 13.55 0.0 0.0 0.0 0.0 126-127 14.5875 0.0 0.0 0.0 0.0 128-129 15.6 0.0 0.0 0.0 0.0 130-131 16.35 0.0 0.0 0.0 0.0 132-133 16.9625 0.0 0.0 0.0 0.0 134-135 17.737499999999997 0.0 0.0 0.0 0.0 136-137 18.95 0.0 0.0 0.0 0.0 138-139 20.075000000000003 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12670097 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670097_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 36.4505 37.0 37.0 37.0 37.0 37.0 2 36.4365 37.0 37.0 37.0 37.0 37.0 3 36.3715 37.0 37.0 37.0 37.0 37.0 4 36.365 37.0 37.0 37.0 37.0 37.0 5 36.4855 37.0 37.0 37.0 37.0 37.0 6 36.36 37.0 37.0 37.0 37.0 37.0 7 36.369 37.0 37.0 37.0 37.0 37.0 8 36.437 37.0 37.0 37.0 37.0 37.0 9 36.3345 37.0 37.0 37.0 37.0 37.0 10-14 36.4524 37.0 37.0 37.0 37.0 37.0 15-19 36.4324 37.0 37.0 37.0 37.0 37.0 20-24 36.42139999999999 37.0 37.0 37.0 37.0 37.0 25-29 36.3326 37.0 37.0 37.0 37.0 37.0 30-34 36.306599999999996 37.0 37.0 37.0 37.0 37.0 35-39 36.279399999999995 37.0 37.0 37.0 37.0 37.0 40-44 36.27910000000001 37.0 37.0 37.0 37.0 37.0 45-49 36.29780000000001 37.0 37.0 37.0 37.0 37.0 50-54 36.2342 37.0 37.0 37.0 37.0 37.0 55-59 36.2119 37.0 37.0 37.0 37.0 37.0 60-64 36.1922 37.0 37.0 37.0 37.0 37.0 65-69 36.123400000000004 37.0 37.0 37.0 37.0 37.0 70-74 36.137299999999996 37.0 37.0 37.0 37.0 37.0 75-79 36.137299999999996 37.0 37.0 37.0 37.0 37.0 80-84 36.09929999999999 37.0 37.0 37.0 37.0 37.0 85-89 36.04109999999999 37.0 37.0 37.0 37.0 37.0 90-94 36.0824 37.0 37.0 37.0 37.0 37.0 95-99 35.9707 37.0 37.0 37.0 37.0 37.0 100-104 35.9123 37.0 37.0 37.0 37.0 37.0 105-109 35.926 37.0 37.0 37.0 37.0 37.0 110-114 35.8361 37.0 37.0 37.0 37.0 37.0 115-119 35.8814 37.0 37.0 37.0 37.0 37.0 120-124 35.6649 37.0 37.0 37.0 37.0 37.0 125-129 35.528600000000004 37.0 37.0 37.0 37.0 37.0 130-134 35.249900000000004 37.0 37.0 37.0 32.2 37.0 135-139 35.1884 37.0 37.0 37.0 29.8 37.0 140-144 34.9681 37.0 37.0 37.0 25.0 37.0 145-149 34.663 37.0 37.0 37.0 25.0 37.0 150-151 34.3475 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 2.0 14 2.0 15 4.0 16 3.0 17 1.0 18 1.0 19 2.0 20 2.0 21 1.0 22 0.0 23 0.0 24 7.0 25 3.0 26 7.0 27 15.0 28 5.0 29 15.0 30 25.0 31 50.0 32 62.0 33 99.0 34 197.0 35 491.0 36 2671.0 37 335.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.475 23.799999999999997 8.825 27.900000000000002 2 26.775 26.450000000000003 31.275 15.5 3 19.575 27.525 34.050000000000004 18.85 4 24.375 34.475 23.275000000000002 17.875 5 24.65 37.7 20.599999999999998 17.05 6 21.5 38.15 23.325000000000003 17.025000000000002 7 19.075 23.5 38.45 18.975 8 20.325 24.05 29.65 25.974999999999998 9 22.075 24.375 30.85 22.7 10-14 23.01 29.220000000000002 26.355 21.415 15-19 23.05 28.055000000000003 27.24 21.654999999999998 20-24 23.400000000000002 28.74 26.450000000000003 21.41 25-29 23.195 28.249999999999996 27.224999999999998 21.33 30-34 22.74 27.67 28.02 21.57 35-39 22.66 28.060000000000002 28.105000000000004 21.175 40-44 22.855 28.110000000000003 27.644999999999996 21.39 45-49 23.39 28.26 27.265 21.085 50-54 23.669999999999998 28.73 27.150000000000002 20.45 55-59 22.835 28.175 27.85 21.14 60-64 22.84 27.775 27.839999999999996 21.545 65-69 23.445 27.805000000000003 27.41 21.34 70-74 23.36 27.815 27.16 21.665 75-79 23.085 27.384999999999998 27.839999999999996 21.69 80-84 24.0 28.175 26.99 20.835 85-89 23.169999999999998 28.095 27.0 21.735 90-94 24.095 28.21 26.805 20.89 95-99 24.51 27.985 26.88 20.625 100-104 25.019999999999996 27.915 26.700000000000003 20.365 105-109 24.169999999999998 28.48 26.625 20.724999999999998 110-114 24.94 28.32 26.834999999999997 19.905 115-119 26.145000000000003 28.000000000000004 26.205000000000002 19.650000000000002 120-124 26.035000000000004 27.18 26.895000000000003 19.89 125-129 26.240000000000002 28.57 25.895000000000003 19.295 130-134 27.47 26.88 26.735 18.915000000000003 135-139 27.875 26.33 26.5 19.295 140-144 28.42 26.779999999999998 25.635 19.165 145-149 29.86 26.645000000000003 25.130000000000003 18.365000000000002 150-151 29.4 28.075 24.6 17.925 >>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 0.5 11 0.5 12 0.0 13 0.5 14 0.5 15 0.0 16 0.5 17 1.0 18 1.0 19 1.5 20 3.0 21 2.0 22 1.0 23 2.0 24 1.0 25 1.5 26 3.0 27 2.0 28 1.5 29 9.5 30 14.5 31 19.5 32 31.0 33 36.5 34 44.5 35 63.5 36 85.5 37 95.5 38 120.5 39 157.0 40 191.0 41 221.5 42 260.0 43 284.5 44 273.5 45 272.0 46 269.5 47 249.5 48 211.5 49 186.0 50 160.5 51 131.0 52 113.5 53 96.5 54 82.0 55 65.0 56 51.5 57 39.5 58 28.0 59 24.5 60 26.5 61 18.5 62 13.0 63 9.5 64 4.0 65 2.5 66 1.0 67 1.0 68 0.5 69 0.5 70 1.0 71 1.5 72 1.0 73 0.5 74 0.5 75 0.0 76 0.5 77 0.5 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.5 85 0.5 86 0.5 87 0.5 88 0.0 89 0.0 90 0.5 91 0.5 92 0.0 93 0.0 94 0.0 95 0.5 96 0.5 97 0.5 98 0.5 99 0.0 100 0.5 >>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 81.77499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 83.58300214001835 68.35 2 12.350963008254357 20.200000000000003 3 2.8737389177621524 7.049999999999999 4 0.8254356465912565 2.7 5 0.2751452155304189 1.125 6 0.03057169061449098 0.15 7 0.03057169061449098 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.03057169061449098 0.25 >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 GTAACTATATAAGGAACTCGGAGAACCGCTTTTAACTTGCAGATCTCTCT 10 0.25 No Hit GAAAAGGGTTCATCATTTCAAAATCCATGCAAATTTAGGAGAAGGGGATG 7 0.17500000000000002 No Hit CGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACG 6 0.15 No Hit CATAGCTTATAAGCTTGTAAGAGATGGCTTCCTCCTCTATGATCTCATCG 5 0.125 No Hit GGTGTTTCCATTTTGCAAGCCCTCTTCGTTAAAGAGCATAACGCAGTTTG 5 0.125 No Hit AGCGTCTGTAGGTGGCTTTTTAAGTCCGCCGTCAAATCCCAGGGCTCAAC 5 0.125 No Hit AGGAAGTACACATTTTTCAAGCCAAAGTTCATTTTCTATGCTACATATTT 5 0.125 No Hit TCCATTTAAGCTTAATCAATCAATCATCATGTCTAGCACCTGCGACACCT 5 0.125 No Hit AATCTAAAGGACTTCGTATTTACTGAAATTCCTTAGGAAAGGACAAGCAC 5 0.125 No Hit CCTTGGACTCCTCTGTATATCAAACCCTAAGGTTAATGTTATGGACACAT 5 0.125 No Hit GGAAAACAGAAAAAAAGAAAAATGGCCTCAGCATCACTTCTCAAGTCATC 5 0.125 No Hit GATGAGAGAGCAAAGATTCCTGATCCCGAGGCAGCGAAGCCAGATGACTG 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 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 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 0.1125 0.0 0.0 0.0 0.0 68-69 0.1375 0.0 0.0 0.0 0.0 70-71 0.16249999999999998 0.0 0.0 0.0 0.0 72-73 0.3 0.0 0.0 0.0 0.0 74-75 0.42500000000000004 0.0 0.0 0.0 0.0 76-77 0.6375 0.0 0.0 0.0 0.0 78-79 0.8625 0.0 0.0 0.0 0.0 80-81 1.2125 0.0 0.0 0.0 0.0 82-83 1.4500000000000002 0.0 0.0 0.0 0.0 84-85 1.8875000000000002 0.0 0.0 0.0 0.0 86-87 2.2 0.0 0.0 0.0 0.0 88-89 2.5125 0.0 0.0 0.0 0.0 90-91 2.9000000000000004 0.0 0.0 0.0 0.0 92-93 3.2625 0.0 0.0 0.0 0.0 94-95 3.7125000000000004 0.0 0.0 0.0 0.0 96-97 4.175000000000001 0.0 0.0 0.0 0.0 98-99 4.725 0.0 0.0 0.0 0.0 100-101 5.1625 0.0 0.0 0.0 0.0 102-103 5.7125 0.0 0.0 0.0 0.0 104-105 6.1875 0.0 0.0 0.0 0.0 106-107 7.0875 0.0 0.0 0.0 0.0 108-109 7.6125 0.0 0.0 0.0 0.0 110-111 8.2375 0.0 0.0 0.0 0.0 112-113 8.875 0.0 0.0 0.0 0.0 114-115 9.350000000000001 0.0 0.0 0.0 0.0 116-117 10.3125 0.0 0.0 0.0 0.0 118-119 11.15 0.0 0.0 0.0 0.0 120-121 11.925 0.0 0.0 0.0 0.0 122-123 12.875 0.0 0.0 0.0 0.0 124-125 13.8625 0.0 0.0 0.0 0.0 126-127 14.875 0.0 0.0 0.0 0.0 128-129 15.8875 0.0 0.0 0.0 0.0 130-131 16.637500000000003 0.0 0.0 0.0 0.0 132-133 17.2875 0.0 0.0 0.0 0.0 134-135 18.112499999999997 0.0 0.0 0.0 0.0 136-137 19.225 0.0 0.0 0.0 0.0 138-139 20.3625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTCTCTC 60 0.004491891 14.500001 10-14 >>END_MODULE Read 485894 spots for SRR12670097.sra Written 485894 spots for SRR12670097.sra Read 485894 spots for SRR12670097.sra Written 485894 spots for SRR12670097.sra Read 485894 spots for SRR12670097.sra Written 485894 spots for SRR12670097.sra Read 485894 spots for SRR12670097.sra Written 485894 spots for SRR12670097.sra Read 485894 spots for SRR12670097.sra Written 485894 spots for SRR12670097.sra Read 485894 spots for SRR12670097.sra Written 485894 spots for SRR12670097.sra Read 485894 spots for SRR12670097.sra Written 485894 spots for SRR12670097.sra Read 485894 spots for SRR12670097.sra Written 485894 spots for SRR12670097.sra Read 485894 spots for SRR12670097.sra Written 485894 spots for SRR12670097.sra Read 485894 spots for SRR12670097.sra Written 485894 spots for SRR12670097.sra Read 485894 spots for SRR12670097.sra Written 485894 spots for SRR12670097.sra Read 485894 spots for SRR12670097.sra Written 485894 spots for SRR12670097.sra Read 485894 spots for SRR12670097.sra Written 485894 spots for SRR12670097.sra Read 485894 spots for SRR12670097.sra Written 485894 spots for SRR12670097.sra Read 485894 spots for SRR12670097.sra Written 485894 spots for SRR12670097.sra Read 485899 spots for SRR12670097.sra Written 485899 spots for SRR12670097.sra Read 485894 spots for SRR12670097.sra Written 485894 spots for SRR12670097.sra Read 485894 spots for SRR12670097.sra Written 485894 spots for SRR12670097.sra Read 485894 spots for SRR12670097.sra Written 485894 spots for SRR12670097.sra Read 485894 spots for SRR12670097.sra Written 485894 spots for SRR12670097.sra SRR ids: ['SRR12670097.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_j3hprav3 SRR12670097.sra spots: 9717885 blocks: [[1, 485894], [485895, 971788], [971789, 1457682], [1457683, 1943576], [1943577, 2429470], [2429471, 2915364], [2915365, 3401258], [3401259, 3887152], [3887153, 4373046], [4373047, 4858940], [4858941, 5344834], [5344835, 5830728], [5830729, 6316622], [6316623, 6802516], [6802517, 7288410], [7288411, 7774304], [7774305, 8260198], [8260199, 8746092], [8746093, 9231986], [9231987, 9717885]] SRR12670097 file size 3281413 SRR12670097 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 SRR12670097 SRR12670097_1.fastq SRR12670097_2.fastq Input file: SRR12670097_1.fastq Paired file: SRR12670097_2.fastq trimmed: SRR12670097-trimmed-pair1.fastq, SRR12670097-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 Mon Feb 10 22:26:02 2025 >> started Mon Feb 10 22:26:13 2025 >> done (10.810s) 9717885 read pairs processed; of these: 62 ( 0.00%) short read pairs filtered out after trimming by size control 3474 ( 0.04%) empty read pairs filtered out after trimming by size control 9714349 (99.96%) read pairs available; of these: 2332483 (24.01%) trimmed read pairs available after processing 7381866 (75.99%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 4 0.00% 19 8 0.00% 20 16 0.00% 21 15 0.00% 22 13 0.00% 23 22 0.00% 24 33 0.00% 25 37 0.00% 26 57 0.00% 27 53 0.00% 28 57 0.00% 29 50 0.00% 30 71 0.00% 31 78 0.00% 32 94 0.00% 33 84 0.00% 34 59 0.00% 35 82 0.00% 36 103 0.00% 37 107 0.00% 38 135 0.00% 39 127 0.00% 40 118 0.00% 41 162 0.00% 42 140 0.00% 43 136 0.00% 44 167 0.00% 45 191 0.00% 46 201 0.00% 47 208 0.00% 48 277 0.00% 49 290 0.00% 50 322 0.00% 51 417 0.00% 52 448 0.00% 53 384 0.00% 54 416 0.00% 55 590 0.01% 56 570 0.01% 57 701 0.01% 58 794 0.01% 59 906 0.01% 60 1001 0.01% 61 1289 0.01% 62 1316 0.01% 63 1508 0.02% 64 1678 0.02% 65 1677 0.02% 66 1910 0.02% 67 2173 0.02% 68 2293 0.02% 69 2650 0.03% 70 3129 0.03% 71 3440 0.04% 72 3995 0.04% 73 4453 0.05% 74 4823 0.05% 75 5292 0.05% 76 5757 0.06% 77 6160 0.06% 78 6542 0.07% 79 7504 0.08% 80 7881 0.08% 81 8862 0.09% 82 10046 0.10% 83 10807 0.11% 84 11832 0.12% 85 12495 0.13% 86 13004 0.13% 87 13952 0.14% 88 14096 0.15% 89 14949 0.15% 90 15653 0.16% 91 17079 0.18% 92 17957 0.18% 93 19136 0.20% 94 20002 0.21% 95 21336 0.22% 96 22185 0.23% 97 22846 0.24% 98 23222 0.24% 99 23786 0.24% 100 24546 0.25% 101 24779 0.26% 102 26164 0.27% 103 27304 0.28% 104 28112 0.29% 105 29086 0.30% 106 29509 0.30% 107 30074 0.31% 108 29999 0.31% 109 30989 0.32% 110 30592 0.31% 111 31594 0.33% 112 32202 0.33% 113 32539 0.33% 114 34110 0.35% 115 35371 0.36% 116 35556 0.37% 117 35814 0.37% 118 36880 0.38% 119 36675 0.38% 120 36983 0.38% 121 37466 0.39% 122 37715 0.39% 123 38448 0.40% 124 39163 0.40% 125 39692 0.41% 126 40814 0.42% 127 40820 0.42% 128 41059 0.42% 129 40919 0.42% 130 41566 0.43% 131 41261 0.42% 132 41435 0.43% 133 42020 0.43% 134 41787 0.43% 135 43030 0.44% 136 43001 0.44% 137 43203 0.44% 138 43499 0.45% 139 44856 0.46% 140 43623 0.45% 141 44258 0.46% 142 44751 0.46% 143 44217 0.46% 144 44586 0.46% 145 44777 0.46% 146 44587 0.46% 147 45001 0.46% 148 46204 0.48% 149 45276 0.47% 150 46112 0.47% 151 7381866 75.99% 9714349 reads passed initial QC criterion=sequence-density sequence-density=0.42 sequence-density-rank=1 fanout-score=1.98 fanout-score-rank=24 prefix-density=0.43 prefix-fanout=2.0 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTTCGAGCGAAGAAGGT criterion=fanout-score sequence-density=0.02 sequence-density-rank=26 fanout-score=192.15 fanout-score-rank=1 prefix-density=0.28 prefix-fanout=15.1 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGG criterion=sequence-density sequence-density=0.71 sequence-density-rank=1 fanout-score=2.10 fanout-score-rank=23 prefix-density=0.71 prefix-fanout=2.1 sequence=CCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAATCATCATGTCTAGCACCTGCGACACCTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCA criterion=fanout-score sequence-density=0.12 sequence-density-rank=29 fanout-score=36.77 fanout-score-rank=1 prefix-density=0.34 prefix-fanout=13.2 sequence=AAAGAAAAGAAAA SRR12670097 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 10 22:26:55 Started mapping on | Feb 10 22:26:56 Finished on | Feb 10 22:28:02 Mapping speed, Million of reads per hour | 529.87 Number of input reads | 9714349 Average input read length | 287 UNIQUE READS: Uniquely mapped reads number | 9083245 Uniquely mapped reads % | 93.50% Average mapped length | 286.08 Number of splices: Total | 8675493 Number of splices: Annotated (sjdb) | 8486177 Number of splices: GT/AG | 8502783 Number of splices: GC/AG | 137923 Number of splices: AT/AC | 5674 Number of splices: Non-canonical | 29113 Mismatch rate per base, % | 0.34% Deletion rate per base | 0.03% Deletion average length | 2.94 Insertion rate per base | 0.02% Insertion average length | 2.40 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 211926 % of reads mapped to multiple loci | 2.18% Number of reads mapped to too many loci | 126038 % of reads mapped to too many loci | 1.30% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.78% % of reads unmapped: other | 0.24% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 419178 419178 419178 N_multimapping 211926 211926 211926 N_noFeature 362805 8942026 422774 N_ambiguous 131983 559 50406 UnstrandedReadsAssigned:8588457 PositiveStrandReadsAssigned:140660 NegativeStrandReadsAssigned:8610065 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=141 echo kmer=137 SRR12670097 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: SRR12670097-trimmed-pair1.fastq SRR12670097-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 9,714,349 reads, 8,681,539 reads pseudoaligned [quant] estimated average fragment length: 211.459 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,014 rounds 52401 SRR12670097.ke.tsv 34699 SRR12670097.se.tsv 87100 total ==> SRR12670097.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1807.54 334 20.6293 Potri.005G024800.1.v4.1 1035 824.541 105 14.2168 Potri.004G059700.1.v4.1 961 750.602 3 0.446208 Potri.007G009000.2.v4.1 1416 1205.54 0 0 Potri.003G141000.2.v4.1 2943 2732.54 465.35 19.0125 Potri.016G087400.1.v4.1 270 103.52 370 399.027 Potri.015G069301.1.v4.1 564 359.997 0 0 Potri.010G195200.1.v4.1 1773 1562.54 37 2.6436 Potri.012G127500.1.v4.1 977 766.587 20 2.91269 ==> SRR12670097.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 108 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 134 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 6 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 3 SRR12670097 completed mapping pipeline successfully