Starting /dee2/code/volunteer_pipeline.sh SRR12670116 current disk space = 3057466314752 free memory = 1467416636 SRR12670116 SRAfilesize 94d9c2c749c78f28080578130e1902cc SRR12670116.sra SRR12670116.sra file validated SRR12670116 is paired end SRR12670116 is conventional basespace SRR12670116 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670116_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.5785 37.0 37.0 37.0 37.0 37.0 2 36.4155 37.0 37.0 37.0 37.0 37.0 3 36.641 37.0 37.0 37.0 37.0 37.0 4 36.649 37.0 37.0 37.0 37.0 37.0 5 36.6775 37.0 37.0 37.0 37.0 37.0 6 36.648 37.0 37.0 37.0 37.0 37.0 7 36.573 37.0 37.0 37.0 37.0 37.0 8 36.6195 37.0 37.0 37.0 37.0 37.0 9 36.615 37.0 37.0 37.0 37.0 37.0 10-14 36.611599999999996 37.0 37.0 37.0 37.0 37.0 15-19 36.563 37.0 37.0 37.0 37.0 37.0 20-24 36.5245 37.0 37.0 37.0 37.0 37.0 25-29 36.5318 37.0 37.0 37.0 37.0 37.0 30-34 36.505399999999995 37.0 37.0 37.0 37.0 37.0 35-39 36.4874 37.0 37.0 37.0 37.0 37.0 40-44 36.505199999999995 37.0 37.0 37.0 37.0 37.0 45-49 36.4753 37.0 37.0 37.0 37.0 37.0 50-54 36.4551 37.0 37.0 37.0 37.0 37.0 55-59 36.442099999999996 37.0 37.0 37.0 37.0 37.0 60-64 36.380700000000004 37.0 37.0 37.0 37.0 37.0 65-69 36.328700000000005 37.0 37.0 37.0 37.0 37.0 70-74 36.3543 37.0 37.0 37.0 37.0 37.0 75-79 36.335300000000004 37.0 37.0 37.0 37.0 37.0 80-84 36.2827 37.0 37.0 37.0 37.0 37.0 85-89 36.2457 37.0 37.0 37.0 37.0 37.0 90-94 36.2529 37.0 37.0 37.0 37.0 37.0 95-99 36.211 37.0 37.0 37.0 37.0 37.0 100-104 36.2832 37.0 37.0 37.0 37.0 37.0 105-109 36.2161 37.0 37.0 37.0 37.0 37.0 110-114 36.165800000000004 37.0 37.0 37.0 37.0 37.0 115-119 36.1687 37.0 37.0 37.0 37.0 37.0 120-124 36.0379 37.0 37.0 37.0 37.0 37.0 125-129 35.9837 37.0 37.0 37.0 37.0 37.0 130-134 35.9109 37.0 37.0 37.0 37.0 37.0 135-139 35.7136 37.0 37.0 37.0 37.0 37.0 140-144 35.5088 37.0 37.0 37.0 37.0 37.0 145-149 35.3635 37.0 37.0 37.0 37.0 37.0 150-151 35.1215 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 24 1.0 25 0.0 26 4.0 27 7.0 28 10.0 29 14.0 30 20.0 31 35.0 32 54.0 33 79.0 34 172.0 35 319.0 36 2898.0 37 387.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 41.325 11.75 7.175 39.75 2 19.488977955911825 12.149298597194388 37.19939879759519 31.162324649298593 3 17.075000000000003 18.099999999999998 27.525 37.3 4 23.0 24.875 23.875 28.249999999999996 5 21.45 31.775 24.975 21.8 6 19.425 34.825 24.675 21.075 7 15.85 26.1 40.75 17.299999999999997 8 17.025000000000002 25.424999999999997 32.375 25.174999999999997 9 17.2 23.674999999999997 34.55 24.575 10-14 20.215 29.825000000000003 26.97 22.99 15-19 20.365 28.175 27.425 24.035 20-24 19.759999999999998 28.925 27.884999999999998 23.43 25-29 19.994999999999997 27.935 28.21 23.86 30-34 19.62 28.48 27.49 24.41 35-39 20.555 27.715 27.855 23.875 40-44 20.474999999999998 28.665000000000003 27.77 23.09 45-49 20.125 27.625 27.689999999999998 24.560000000000002 50-54 20.669999999999998 28.16 27.18 23.990000000000002 55-59 20.755000000000003 27.839999999999996 27.62 23.785 60-64 20.4 28.410000000000004 27.625 23.565 65-69 20.97 27.76 27.13 24.14 70-74 20.745 28.634999999999998 27.305 23.315 75-79 20.330000000000002 28.42 28.299999999999997 22.95 80-84 20.27 28.475 27.18 24.075 85-89 20.995 28.79 27.32 22.895 90-94 20.474999999999998 29.14 26.919999999999998 23.465 95-99 21.525 28.23 26.950000000000003 23.294999999999998 100-104 21.545 27.965 26.765 23.724999999999998 105-109 21.755 28.63 26.424999999999997 23.189999999999998 110-114 20.645 28.155 26.875 24.325 115-119 21.75 28.48 26.005 23.765 120-124 21.19 28.265 26.369999999999997 24.175 125-129 21.654999999999998 28.555000000000003 25.509999999999998 24.279999999999998 130-134 21.73 28.08 25.419999999999998 24.77 135-139 22.66 27.925 24.79 24.625 140-144 21.445 27.884999999999998 25.44 25.230000000000004 145-149 22.275 27.38 25.47 24.875 150-151 22.275 27.6625 25.5 24.5625 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 1.0 23 5.0 24 6.0 25 2.5 26 3.0 27 5.0 28 5.5 29 9.0 30 10.0 31 15.5 32 22.0 33 29.5 34 52.0 35 66.0 36 79.0 37 109.0 38 129.5 39 147.0 40 171.0 41 201.5 42 223.5 43 251.0 44 290.5 45 287.5 46 262.0 47 244.5 48 255.5 49 239.5 50 194.5 51 154.5 52 112.0 53 101.0 54 86.5 55 58.0 56 49.0 57 41.5 58 24.0 59 21.5 60 18.5 61 7.5 62 2.0 63 1.0 64 0.5 65 0.5 66 1.0 67 1.0 68 0.5 69 0.5 70 1.0 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 0.0 2 0.2 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 81.175 #Duplication Level Percentage of deduplicated Percentage of total 1 82.66091777024947 67.10000000000001 2 13.335386510625192 21.65 3 2.5562057283646444 6.225 4 1.0471204188481675 3.4000000000000004 5 0.4003695719125347 1.625 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source TCTTAATTTGTCCTAGTCACTGTATTCTTCACCAGTGTCATCATCGTAGT 5 0.125 No Hit CCGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACT 5 0.125 No Hit ATGTCCCAAGACCTCTTTGCCTACTTTGTCCAAGGCAAGCCCCACCTCTT 5 0.125 No Hit CGCGCTCCATTGATGTCTGTAATACGGAACTCCCCAAAGTATACCTTGCT 5 0.125 No Hit CCACACCTTCCATTTTTCCCAAAACCCTTTTCACAGCCCCAACACAGCCT 5 0.125 No Hit CTCCCCATCTGTCCTTGTCGGTCTGCTTCTTCTCATCGTACTCTGCAACA 5 0.125 No Hit CTGGTCAAGATATTGTTGTGGACAGGATCGGCCAGGTGATCCAGGAGGTT 5 0.125 No Hit GGAAGATAGGATCAGTGTTAACACACCCTGGCTTGAGAATATCTGCCCAT 5 0.125 No Hit GGAACCAACAAAGCAGCAGGAAATACAAGACACTTACAGATTACTAGCCA 5 0.125 No Hit ACTCCTCTTCCCTCCACACAAGAACGAAGATCCCAATCCATTTAGGACAG 5 0.125 No Hit CCCAGGAGTTATAAAACTTGATGATGTTTTCATGTTTCAAAGACTTCAGC 5 0.125 No Hit TTTTTTTTTTTGAGATTAAAAGAAAGAACTTTATTTGGCTTATTCTCTTA 5 0.125 No Hit GACAAGACAACAAACGACAATTTCCATTCAAGTTCAAGCAGTTTCAGCAG 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 0.0125 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 0.0875 0.0 0.0 0.0 0.0 46-47 0.1125 0.0 0.0 0.0 0.0 48-49 0.15 0.0 0.0 0.0 0.0 50-51 0.175 0.0 0.0 0.0 0.0 52-53 0.175 0.0 0.0 0.0 0.0 54-55 0.175 0.0 0.0 0.0 0.0 56-57 0.175 0.0 0.0 0.0 0.0 58-59 0.175 0.0 0.0 0.0 0.0 60-61 0.1875 0.0 0.0 0.0 0.0 62-63 0.225 0.0 0.0 0.0 0.0 64-65 0.2875 0.0 0.0 0.0 0.0 66-67 0.45 0.0 0.0 0.0 0.0 68-69 0.5 0.0 0.0 0.0 0.0 70-71 0.5125 0.0 0.0 0.0 0.0 72-73 0.5625 0.0 0.0 0.0 0.0 74-75 0.675 0.0 0.0 0.0 0.0 76-77 0.8875 0.0 0.0 0.0 0.0 78-79 1.0875 0.0 0.0 0.0 0.0 80-81 1.4 0.0 0.0 0.0 0.0 82-83 1.7625000000000002 0.0 0.0 0.0 0.0 84-85 2.0375 0.0 0.0 0.0 0.0 86-87 2.4875 0.0 0.0 0.0 0.0 88-89 2.9625 0.0 0.0 0.0 0.0 90-91 3.4125 0.0 0.0 0.0 0.0 92-93 3.9000000000000004 0.0 0.0 0.0 0.0 94-95 4.387499999999999 0.0 0.0 0.0 0.0 96-97 4.9 0.0 0.0 0.0 0.0 98-99 5.4625 0.0 0.0 0.0 0.0 100-101 6.025 0.0 0.0 0.0 0.0 102-103 6.7125 0.0 0.0 0.0 0.0 104-105 7.362500000000001 0.0 0.0 0.0 0.0 106-107 8.05 0.0 0.0 0.0 0.0 108-109 8.95 0.0 0.0 0.0 0.0 110-111 9.7 0.0 0.0 0.0 0.0 112-113 10.55 0.0 0.0 0.0 0.0 114-115 11.675 0.0 0.0 0.0 0.0 116-117 12.75 0.0 0.0 0.0 0.0 118-119 14.075 0.0 0.0 0.0 0.0 120-121 14.8625 0.0 0.0 0.0 0.0 122-123 15.6375 0.0 0.0 0.0 0.0 124-125 16.6875 0.0 0.0 0.0 0.0 126-127 17.5875 0.0 0.0 0.0 0.0 128-129 18.675 0.0 0.0 0.0 0.0 130-131 19.9625 0.0 0.0 0.0 0.0 132-133 21.2875 0.0 0.0 0.0 0.0 134-135 22.2125 0.0 0.0 0.0 0.0 136-137 23.200000000000003 0.0 0.0 0.0 0.0 138-139 24.0625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TACAGGT 10 0.006830828 145.0 9 TATACAG 10 0.006830828 145.0 7 GTATTTA 10 0.006830828 145.0 2 TATTTAT 10 0.006830828 145.0 3 TCGTACA 10 0.006830828 145.0 145 GGGGGGG 235 3.0306E-7 9.25532 140-144 >>END_MODULE SRR12670116 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670116_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 36.328 37.0 37.0 37.0 37.0 37.0 2 36.136 37.0 37.0 37.0 37.0 37.0 3 36.1225 37.0 37.0 37.0 37.0 37.0 4 36.163 37.0 37.0 37.0 37.0 37.0 5 36.243 37.0 37.0 37.0 37.0 37.0 6 36.159 37.0 37.0 37.0 37.0 37.0 7 36.207 37.0 37.0 37.0 37.0 37.0 8 36.2805 37.0 37.0 37.0 37.0 37.0 9 36.1235 37.0 37.0 37.0 37.0 37.0 10-14 36.2207 37.0 37.0 37.0 37.0 37.0 15-19 36.2328 37.0 37.0 37.0 37.0 37.0 20-24 36.135400000000004 37.0 37.0 37.0 37.0 37.0 25-29 36.082499999999996 37.0 37.0 37.0 37.0 37.0 30-34 36.0948 37.0 37.0 37.0 37.0 37.0 35-39 36.0745 37.0 37.0 37.0 37.0 37.0 40-44 35.994 37.0 37.0 37.0 37.0 37.0 45-49 36.0313 37.0 37.0 37.0 37.0 37.0 50-54 36.0028 37.0 37.0 37.0 37.0 37.0 55-59 35.988600000000005 37.0 37.0 37.0 37.0 37.0 60-64 35.916399999999996 37.0 37.0 37.0 37.0 37.0 65-69 35.9571 37.0 37.0 37.0 37.0 37.0 70-74 35.8889 37.0 37.0 37.0 37.0 37.0 75-79 35.881099999999996 37.0 37.0 37.0 37.0 37.0 80-84 35.7791 37.0 37.0 37.0 37.0 37.0 85-89 35.8497 37.0 37.0 37.0 37.0 37.0 90-94 35.822500000000005 37.0 37.0 37.0 37.0 37.0 95-99 35.748900000000006 37.0 37.0 37.0 37.0 37.0 100-104 35.733 37.0 37.0 37.0 37.0 37.0 105-109 35.669 37.0 37.0 37.0 37.0 37.0 110-114 35.5954 37.0 37.0 37.0 37.0 37.0 115-119 35.616699999999994 37.0 37.0 37.0 37.0 37.0 120-124 35.4006 37.0 37.0 37.0 37.0 37.0 125-129 35.263200000000005 37.0 37.0 37.0 32.2 37.0 130-134 35.047399999999996 37.0 37.0 37.0 29.8 37.0 135-139 34.9033 37.0 37.0 37.0 25.0 37.0 140-144 34.7312 37.0 37.0 37.0 25.0 37.0 145-149 34.3321 37.0 37.0 37.0 25.0 37.0 150-151 33.956 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 2.0 13 7.0 14 3.0 15 5.0 16 1.0 17 1.0 18 3.0 19 1.0 20 2.0 21 3.0 22 6.0 23 6.0 24 7.0 25 2.0 26 6.0 27 14.0 28 14.0 29 21.0 30 25.0 31 48.0 32 66.0 33 136.0 34 243.0 35 650.0 36 2502.0 37 226.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.875 22.8 9.275 27.05 2 26.825 26.625 30.875000000000004 15.675 3 21.425 27.750000000000004 30.65 20.175 4 24.4 35.55 22.3 17.75 5 23.549999999999997 37.3 21.525 17.625 6 20.95 37.85 24.175 17.025000000000002 7 20.05 21.975 37.824999999999996 20.150000000000002 8 21.075 25.874999999999996 28.15 24.9 9 21.6 25.324999999999996 29.075 24.0 10-14 23.635 28.57 26.69 21.105 15-19 23.03 28.549999999999997 27.529999999999998 20.89 20-24 23.47 27.515 27.92 21.095 25-29 23.18 28.549999999999997 27.265 21.005 30-34 23.615 27.810000000000002 27.515 21.060000000000002 35-39 23.169999999999998 28.24 27.91 20.68 40-44 23.46 27.834999999999997 27.865000000000002 20.84 45-49 22.78 28.49 27.555000000000003 21.175 50-54 23.05 28.449999999999996 27.689999999999998 20.810000000000002 55-59 23.39 28.22 26.855 21.535 60-64 22.975 27.229999999999997 28.52 21.275 65-69 23.82 27.67 27.439999999999998 21.07 70-74 23.525 28.275 27.045 21.154999999999998 75-79 23.84 27.595 27.994999999999997 20.57 80-84 23.915 27.884999999999998 27.36 20.84 85-89 23.745 28.32 26.985 20.95 90-94 24.495 28.255000000000003 26.490000000000002 20.76 95-99 24.805 27.74 26.790000000000003 20.665 100-104 25.575 27.57 26.63 20.225 105-109 24.59 28.65 26.655 20.105 110-114 25.505 28.125 26.590000000000003 19.78 115-119 25.885 28.860000000000003 25.575 19.68 120-124 26.555 27.884999999999998 25.72 19.84 125-129 27.26 27.865000000000002 25.7 19.175 130-134 29.28 26.105 25.480000000000004 19.134999999999998 135-139 28.439999999999998 26.974999999999998 26.36 18.224999999999998 140-144 29.98 26.889999999999997 25.064999999999998 18.065 145-149 31.25 25.055 26.21 17.485 150-151 30.837500000000002 26.437500000000004 25.0 17.724999999999998 >>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 0.5 7 1.0 8 0.5 9 0.5 10 2.0 11 2.0 12 1.0 13 0.5 14 0.5 15 0.5 16 0.5 17 1.5 18 1.5 19 1.0 20 1.0 21 1.0 22 1.5 23 1.0 24 1.0 25 1.5 26 2.0 27 2.5 28 6.5 29 8.5 30 10.5 31 18.0 32 29.0 33 36.5 34 44.5 35 65.0 36 75.0 37 94.5 38 132.0 39 164.5 40 193.0 41 210.5 42 224.5 43 252.5 44 255.5 45 262.0 46 276.5 47 264.0 48 239.5 49 214.0 50 183.0 51 149.5 52 125.5 53 100.5 54 86.0 55 66.0 56 45.5 57 33.5 58 24.5 59 23.0 60 19.0 61 11.0 62 7.0 63 4.0 64 1.5 65 1.0 66 2.0 67 1.0 68 1.5 69 1.5 70 0.5 71 0.5 72 0.5 73 0.5 74 0.0 75 0.5 76 0.5 77 1.0 78 1.5 79 0.5 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 1.0 90 1.0 91 0.0 92 0.0 93 0.5 94 0.5 95 0.0 96 0.5 97 0.5 98 0.5 99 0.5 100 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 81.8 #Duplication Level Percentage of deduplicated Percentage of total 1 83.34352078239608 68.175 2 12.836185819070906 21.0 3 2.444987775061125 6.0 4 1.0085574572127138 3.3000000000000003 5 0.3361858190709046 1.375 6 0.030562347188264057 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source CTGCATAGCTTATAAGCTTGTAAGAGATGGCTTCCTCCTCTATGATCTCA 6 0.15 No Hit AAGTTCTTGTACAGAAACCAGCTTCTTGGACCAGAGAAAGAAAAGAGAGA 5 0.125 No Hit ATGAGCTCTAGGCCTTGAAATATGTTCAAGAGGGCTTGAGGCTTAGACAA 5 0.125 No Hit GATACAAGTAGTTGCTAAAACTGCCCGTGTGCATCGGAATGAGTGGGTGG 5 0.125 No Hit AAGAAGTCTGGTCACTCCATGTTTGTCTAATATAGTATTTGCTGTAAATT 5 0.125 No Hit CAACCATGTTACGCCAAGCATCACGCCTACTGACTCGATCCATCGCCACC 5 0.125 No Hit CATATACCCGCTTCAAAATGTGTTCATTAGGAAAGTGAAGATCTTAAAGG 5 0.125 No Hit CTTGCTCACATCGAGGCACATATGAAGTCATTCAAGGCAAAGGGTGGAGA 5 0.125 No Hit AACACATTCATACCCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAA 5 0.125 No Hit CGGATTTGAGAATTGTTGAAAAACTGAGTTATTTGCATGTGGTATTCTAT 5 0.125 No Hit GGTGCTTTGAAGATTGCTGCCCTCAAAGCTCCTGGTTTTGGGGAACGGAA 5 0.125 No Hit CAGACTGTTGTCCTCAAGGTTGGTATGTCATGCGAAGGCTGTGTTGGGGC 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 0.0125 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 0.0875 0.0 0.0 0.0 0.0 46-47 0.1125 0.0 0.0 0.0 0.0 48-49 0.15 0.0 0.0 0.0 0.0 50-51 0.175 0.0 0.0 0.0 0.0 52-53 0.175 0.0 0.0 0.0 0.0 54-55 0.175 0.0 0.0 0.0 0.0 56-57 0.175 0.0 0.0 0.0 0.0 58-59 0.175 0.0 0.0 0.0 0.0 60-61 0.1875 0.0 0.0 0.0 0.0 62-63 0.225 0.0 0.0 0.0 0.0 64-65 0.2875 0.0 0.0 0.0 0.0 66-67 0.45 0.0 0.0 0.0 0.0 68-69 0.5 0.0 0.0 0.0 0.0 70-71 0.5125 0.0 0.0 0.0 0.0 72-73 0.5625 0.0 0.0 0.0 0.0 74-75 0.675 0.0 0.0 0.0 0.0 76-77 0.8875 0.0 0.0 0.0 0.0 78-79 1.0875 0.0 0.0 0.0 0.0 80-81 1.4 0.0 0.0 0.0 0.0 82-83 1.7625000000000002 0.0 0.0 0.0 0.0 84-85 2.0125 0.0 0.0 0.0 0.0 86-87 2.475 0.0 0.0 0.0 0.0 88-89 2.9625 0.0 0.0 0.0 0.0 90-91 3.4000000000000004 0.0 0.0 0.0 0.0 92-93 3.9000000000000004 0.0 0.0 0.0 0.0 94-95 4.387499999999999 0.0 0.0 0.0 0.0 96-97 4.9 0.0 0.0 0.0 0.0 98-99 5.4625 0.0 0.0 0.0 0.0 100-101 6.025 0.0 0.0 0.0 0.0 102-103 6.7125 0.0 0.0 0.0 0.0 104-105 7.3375 0.0 0.0 0.0 0.0 106-107 7.9625 0.0 0.0 0.0 0.0 108-109 8.825 0.0 0.0 0.0 0.0 110-111 9.5875 0.0 0.0 0.0 0.0 112-113 10.4375 0.0 0.0 0.0 0.0 114-115 11.575 0.0 0.0 0.0 0.0 116-117 12.675 0.0 0.0 0.0 0.0 118-119 14.0 0.0 0.0 0.0 0.0 120-121 14.8 0.0 0.0 0.0 0.0 122-123 15.5875 0.0 0.0 0.0 0.0 124-125 16.6 0.0 0.0 0.0 0.0 126-127 17.525 0.0 0.0 0.0 0.0 128-129 18.625 0.0 0.0 0.0 0.0 130-131 19.9125 0.0 0.0 0.0 0.0 132-133 21.2375 0.0 0.0 0.0 0.0 134-135 22.15 0.0 0.0 0.0 0.0 136-137 23.125 0.0 0.0 0.0 0.0 138-139 24.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTGCAGT 10 0.006830828 145.0 9 TAGTTGC 10 0.006830828 145.0 6 ATAGTTG 10 0.006830828 145.0 5 GATAGTT 10 0.006830828 145.0 4 GAGATAG 10 0.006830828 145.0 2 AGATAGT 10 0.006830828 145.0 3 TGAGATA 10 0.006830828 145.0 1 GGGGGGG 560 0.0 8.803572 140-144 >>END_MODULE Read 603169 spots for SRR12670116.sra Written 603169 spots for SRR12670116.sra Read 603169 spots for SRR12670116.sra Written 603169 spots for SRR12670116.sra Read 603169 spots for SRR12670116.sra Written 603169 spots for SRR12670116.sra Read 603169 spots for SRR12670116.sra Written 603169 spots for SRR12670116.sra Read 603177 spots for SRR12670116.sra Written 603177 spots for SRR12670116.sra Read 603169 spots for SRR12670116.sra Written 603169 spots for SRR12670116.sra Read 603169 spots for SRR12670116.sra Written 603169 spots for SRR12670116.sra Read 603169 spots for SRR12670116.sra Written 603169 spots for SRR12670116.sra Read 603169 spots for SRR12670116.sra Written 603169 spots for SRR12670116.sra Read 603169 spots for SRR12670116.sra Written 603169 spots for SRR12670116.sra Read 603169 spots for SRR12670116.sra Written 603169 spots for SRR12670116.sra Read 603169 spots for SRR12670116.sra Written 603169 spots for SRR12670116.sra Read 603169 spots for SRR12670116.sra Written 603169 spots for SRR12670116.sra Read 603169 spots for SRR12670116.sra Written 603169 spots for SRR12670116.sra Read 603169 spots for SRR12670116.sra Written 603169 spots for SRR12670116.sra Read 603169 spots for SRR12670116.sra Written 603169 spots for SRR12670116.sra Read 603169 spots for SRR12670116.sra Written 603169 spots for SRR12670116.sra Read 603169 spots for SRR12670116.sra Written 603169 spots for SRR12670116.sra Read 603169 spots for SRR12670116.sra Written 603169 spots for SRR12670116.sra Read 603169 spots for SRR12670116.sra Written 603169 spots for SRR12670116.sra SRR ids: ['SRR12670116.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_cv1om7ra SRR12670116.sra spots: 12063388 blocks: [[1, 603169], [603170, 1206338], [1206339, 1809507], [1809508, 2412676], [2412677, 3015845], [3015846, 3619014], [3619015, 4222183], [4222184, 4825352], [4825353, 5428521], [5428522, 6031690], [6031691, 6634859], [6634860, 7238028], [7238029, 7841197], [7841198, 8444366], [8444367, 9047535], [9047536, 9650704], [9650705, 10253873], [10253874, 10857042], [10857043, 11460211], [11460212, 12063388]] SRR12670116 file size 4077966 SRR12670116 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 SRR12670116 SRR12670116_1.fastq SRR12670116_2.fastq Input file: SRR12670116_1.fastq Paired file: SRR12670116_2.fastq trimmed: SRR12670116-trimmed-pair1.fastq, SRR12670116-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 23:49:07 2025 >> started Mon Feb 10 23:49:27 2025 >> done (20.701s) 12063388 read pairs processed; of these: 59 ( 0.00%) short read pairs filtered out after trimming by size control 4859 ( 0.04%) empty read pairs filtered out after trimming by size control 12058470 (99.96%) read pairs available; of these: 3397003 (28.17%) trimmed read pairs available after processing 8661467 (71.83%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 7 0.00% 20 14 0.00% 21 10 0.00% 22 12 0.00% 23 20 0.00% 24 24 0.00% 25 44 0.00% 26 45 0.00% 27 45 0.00% 28 53 0.00% 29 64 0.00% 30 85 0.00% 31 58 0.00% 32 80 0.00% 33 78 0.00% 34 88 0.00% 35 102 0.00% 36 95 0.00% 37 124 0.00% 38 148 0.00% 39 184 0.00% 40 169 0.00% 41 203 0.00% 42 213 0.00% 43 212 0.00% 44 243 0.00% 45 253 0.00% 46 297 0.00% 47 355 0.00% 48 429 0.00% 49 479 0.00% 50 549 0.00% 51 668 0.01% 52 748 0.01% 53 777 0.01% 54 789 0.01% 55 895 0.01% 56 1016 0.01% 57 1128 0.01% 58 1378 0.01% 59 1581 0.01% 60 1867 0.02% 61 2082 0.02% 62 2430 0.02% 63 2708 0.02% 64 2803 0.02% 65 3075 0.03% 66 3234 0.03% 67 3732 0.03% 68 4091 0.03% 69 4600 0.04% 70 5410 0.04% 71 6475 0.05% 72 7378 0.06% 73 8126 0.07% 74 8971 0.07% 75 9551 0.08% 76 10207 0.08% 77 10461 0.09% 78 11634 0.10% 79 13186 0.11% 80 14083 0.12% 81 16342 0.14% 82 18171 0.15% 83 19618 0.16% 84 21248 0.18% 85 22210 0.18% 86 22943 0.19% 87 23757 0.20% 88 24938 0.21% 89 25820 0.21% 90 27971 0.23% 91 29958 0.25% 92 32554 0.27% 93 34848 0.29% 94 36740 0.30% 95 38197 0.32% 96 38595 0.32% 97 38665 0.32% 98 39147 0.32% 99 39915 0.33% 100 41337 0.34% 101 42392 0.35% 102 44777 0.37% 103 46748 0.39% 104 48556 0.40% 105 49384 0.41% 106 49482 0.41% 107 48689 0.40% 108 48890 0.41% 109 48362 0.40% 110 48586 0.40% 111 49596 0.41% 112 51261 0.43% 113 51574 0.43% 114 53771 0.45% 115 54318 0.45% 116 54200 0.45% 117 54575 0.45% 118 53810 0.45% 119 52391 0.43% 120 53240 0.44% 121 53225 0.44% 122 53891 0.45% 123 55129 0.46% 124 56407 0.47% 125 56629 0.47% 126 57882 0.48% 127 57139 0.47% 128 55511 0.46% 129 54625 0.45% 130 54015 0.45% 131 53797 0.45% 132 54253 0.45% 133 55739 0.46% 134 55581 0.46% 135 56944 0.47% 136 56060 0.46% 137 56065 0.46% 138 55447 0.46% 139 54860 0.45% 140 54099 0.45% 141 52973 0.44% 142 53543 0.44% 143 53861 0.45% 144 55141 0.46% 145 55278 0.46% 146 55619 0.46% 147 55382 0.46% 148 54520 0.45% 149 53003 0.44% 150 52940 0.44% 151 8661467 71.83% 12058470 reads passed initial QC criterion=sequence-density sequence-density=0.71 sequence-density-rank=1 fanout-score=1.98 fanout-score-rank=23 prefix-density=0.72 prefix-fanout=2.0 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTT criterion=fanout-score sequence-density=0.02 sequence-density-rank=24 fanout-score=133.29 fanout-score-rank=1 prefix-density=0.28 prefix-fanout=11.8 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAG criterion=sequence-density sequence-density=0.63 sequence-density-rank=1 fanout-score=2.04 fanout-score-rank=20 prefix-density=0.63 prefix-fanout=2.0 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCA criterion=fanout-score sequence-density=0.01 sequence-density-rank=28 fanout-score=43.32 fanout-score-rank=1 prefix-density=0.17 prefix-fanout=1.8 sequence=GGAACTCAAACGCATAGCTTCCTACAAATACCCCAGCTAGCCAATACTCTCAACCACTAAACCCAAAGCTCAAAAAAAATCTTAACTGCACCCGCTCATCCAGCAATGGCAGCAGCAACAATGGCCCTCTC SRR12670116 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 10 23:50:12 Started mapping on | Feb 10 23:50:12 Finished on | Feb 10 23:52:19 Mapping speed, Million of reads per hour | 341.81 Number of input reads | 12058470 Average input read length | 283 UNIQUE READS: Uniquely mapped reads number | 11370122 Uniquely mapped reads % | 94.29% Average mapped length | 281.69 Number of splices: Total | 10646272 Number of splices: Annotated (sjdb) | 10429756 Number of splices: GT/AG | 10425550 Number of splices: GC/AG | 183237 Number of splices: AT/AC | 6427 Number of splices: Non-canonical | 31058 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.03% Deletion average length | 2.76 Insertion rate per base | 0.02% Insertion average length | 2.44 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 265791 % of reads mapped to multiple loci | 2.20% Number of reads mapped to too many loci | 15881 % of reads mapped to too many loci | 0.13% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.25% % of reads unmapped: other | 0.12% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 422557 422557 422557 N_multimapping 265791 265791 265791 N_noFeature 371776 11213941 430605 N_ambiguous 163177 524 65590 UnstrandedReadsAssigned:10835169 PositiveStrandReadsAssigned:155657 NegativeStrandReadsAssigned:10873927 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=133 echo kmer=129 SRR12670116 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: SRR12670116-trimmed-pair1.fastq SRR12670116-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 12,058,470 reads, 10,917,799 reads pseudoaligned [quant] estimated average fragment length: 205.244 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,127 rounds 52401 SRR12670116.ke.tsv 34699 SRR12670116.se.tsv 87100 total ==> SRR12670116.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1813.76 361 18.337 Potri.005G024800.1.v4.1 1035 830.756 130 14.4168 Potri.004G059700.1.v4.1 961 756.807 17 2.06949 Potri.007G009000.2.v4.1 1416 1211.76 0 0 Potri.003G141000.2.v4.1 2943 2738.76 519.471 17.4746 Potri.016G087400.1.v4.1 270 112.087 561 461.112 Potri.015G069301.1.v4.1 564 366.912 0 0 Potri.010G195200.1.v4.1 1773 1568.76 19 1.11583 Potri.012G127500.1.v4.1 977 772.785 50 5.96089 ==> SRR12670116.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 315 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 168 Potri.001G212900.v4.1 2 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 6 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 7 SRR12670116 completed mapping pipeline successfully