Starting /dee2/code/volunteer_pipeline.sh SRR12670179 current disk space = 3055513755648 free memory = 1482512520 SRR12670179 SRAfilesize c5594b3e8bfe1627b9dc9e2f886352aa SRR12670179.sra SRR12670179.sra file validated SRR12670179 is paired end SRR12670179 is conventional basespace SRR12670179 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670179_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 36.679 37.0 37.0 37.0 37.0 37.0 2 36.44325 37.0 37.0 37.0 37.0 37.0 3 36.6705 37.0 37.0 37.0 37.0 37.0 4 36.644 37.0 37.0 37.0 37.0 37.0 5 36.7125 37.0 37.0 37.0 37.0 37.0 6 36.6445 37.0 37.0 37.0 37.0 37.0 7 36.5975 37.0 37.0 37.0 37.0 37.0 8 36.631 37.0 37.0 37.0 37.0 37.0 9 36.6105 37.0 37.0 37.0 37.0 37.0 10-14 36.6289 37.0 37.0 37.0 37.0 37.0 15-19 36.634699999999995 37.0 37.0 37.0 37.0 37.0 20-24 36.577 37.0 37.0 37.0 37.0 37.0 25-29 36.5723 37.0 37.0 37.0 37.0 37.0 30-34 36.543099999999995 37.0 37.0 37.0 37.0 37.0 35-39 36.5572 37.0 37.0 37.0 37.0 37.0 40-44 36.51049999999999 37.0 37.0 37.0 37.0 37.0 45-49 36.4463 37.0 37.0 37.0 37.0 37.0 50-54 36.44689999999999 37.0 37.0 37.0 37.0 37.0 55-59 36.4018 37.0 37.0 37.0 37.0 37.0 60-64 36.398999999999994 37.0 37.0 37.0 37.0 37.0 65-69 36.3681 37.0 37.0 37.0 37.0 37.0 70-74 36.3628 37.0 37.0 37.0 37.0 37.0 75-79 36.3698 37.0 37.0 37.0 37.0 37.0 80-84 36.3667 37.0 37.0 37.0 37.0 37.0 85-89 36.3348 37.0 37.0 37.0 37.0 37.0 90-94 36.338800000000006 37.0 37.0 37.0 37.0 37.0 95-99 36.276199999999996 37.0 37.0 37.0 37.0 37.0 100-104 36.3038 37.0 37.0 37.0 37.0 37.0 105-109 36.2895 37.0 37.0 37.0 37.0 37.0 110-114 36.205600000000004 37.0 37.0 37.0 37.0 37.0 115-119 36.2159 37.0 37.0 37.0 37.0 37.0 120-124 36.119299999999996 37.0 37.0 37.0 37.0 37.0 125-129 36.0326 37.0 37.0 37.0 37.0 37.0 130-134 36.009499999999996 37.0 37.0 37.0 37.0 37.0 135-139 35.806 37.0 37.0 37.0 37.0 37.0 140-144 35.620799999999996 37.0 37.0 37.0 37.0 37.0 145-149 35.4912 37.0 37.0 37.0 37.0 37.0 150-151 35.39425 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 2.0 22 1.0 23 0.0 24 0.0 25 3.0 26 4.0 27 6.0 28 4.0 29 20.0 30 17.0 31 34.0 32 44.0 33 81.0 34 105.0 35 301.0 36 2930.0 37 448.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 36.425000000000004 11.425 6.9 45.25 2 18.29787234042553 13.667083854818523 36.17021276595745 31.864831038798496 3 17.375 17.724999999999998 26.650000000000002 38.25 4 22.400000000000002 24.224999999999998 24.85 28.525 5 22.95 30.825000000000003 24.25 21.975 6 19.35 34.525 25.45 20.674999999999997 7 14.249999999999998 26.85 43.325 15.575 8 18.525 25.55 31.65 24.275 9 18.025 24.175 35.25 22.55 10-14 19.425 29.675 28.285 22.615 15-19 20.075000000000003 27.560000000000002 28.560000000000002 23.805 20-24 19.975 27.675 28.57 23.78 25-29 19.71 27.589999999999996 28.610000000000003 24.09 30-34 20.294999999999998 28.999999999999996 27.655 23.05 35-39 20.455000000000002 28.13 27.779999999999998 23.635 40-44 19.814999999999998 29.25 27.315 23.62 45-49 20.73 27.96 27.750000000000004 23.56 50-54 20.215 28.21 27.805000000000003 23.77 55-59 20.47 28.105000000000004 27.87 23.555 60-64 20.49 27.99 27.800000000000004 23.72 65-69 21.265 27.82 27.939999999999998 22.975 70-74 19.81 28.88 27.529999999999998 23.78 75-79 20.485 28.165000000000003 27.955000000000002 23.395 80-84 20.474999999999998 28.975 27.589999999999996 22.96 85-89 20.849999999999998 28.705000000000002 27.24 23.205000000000002 90-94 21.185000000000002 28.59 26.939999999999998 23.285 95-99 21.029999999999998 28.79 27.16 23.02 100-104 21.43 28.735 27.07 22.765 105-109 22.11 28.544999999999998 26.174999999999997 23.169999999999998 110-114 21.375 29.134999999999998 25.840000000000003 23.65 115-119 22.61 29.435 25.474999999999998 22.48 120-124 21.925 28.52 26.185000000000002 23.369999999999997 125-129 22.465 28.449999999999996 25.624999999999996 23.46 130-134 21.955 29.335 25.025 23.685000000000002 135-139 23.1 28.585 24.884999999999998 23.43 140-144 22.68 28.225 25.674999999999997 23.419999999999998 145-149 22.96 27.944999999999997 25.71 23.385 150-151 23.9 27.437499999999996 24.587500000000002 24.075 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 5 0.0 6 0.0 7 0.5 8 0.5 9 0.0 10 0.0 11 0.5 12 0.5 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.5 19 0.5 20 0.0 21 0.5 22 0.5 23 0.0 24 0.0 25 0.5 26 3.0 27 8.0 28 9.5 29 11.0 30 17.0 31 27.5 32 38.0 33 50.5 34 66.0 35 76.5 36 92.0 37 124.5 38 146.0 39 152.0 40 171.5 41 187.0 42 201.0 43 247.0 44 266.0 45 255.0 46 251.0 47 233.0 48 235.5 49 232.5 50 204.5 51 163.0 52 119.0 53 88.5 54 74.0 55 63.0 56 46.5 57 39.5 58 28.5 59 19.5 60 18.0 61 10.5 62 3.0 63 3.5 64 4.5 65 3.0 66 1.5 67 1.5 68 1.5 69 0.5 70 0.0 71 0.0 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 0.125 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 81.69999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 82.95593635250918 67.77499999999999 2 13.219094247246021 21.6 3 2.7539779681762546 6.75 4 0.7343941248470013 2.4 5 0.24479804161566704 1.0 6 0.06119951040391676 0.3 7 0.03059975520195838 0.17500000000000002 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 CCCTGAAGAGTGAGTGGGAGGCTTCTTCTGAAAACTCGGAAACTCCGAGG 7 0.17500000000000002 No Hit AGCTGAACCAATTTCATGAGCCACACATCTTCAAAGTCGCAATGAAGGGT 6 0.15 No Hit TCAAATTCCTCCTCCCACTGCTACTCTCTTCTTTGTTCTTCATCTCCACG 6 0.15 No Hit ACCTTGGAGAGGAATTCCTCAGGGGAACCGTAGTCGGTGATGGATTTCTT 5 0.125 No Hit CACTGCAGCATGCTCTATGTGGTGTAACAATGTGCAAAGGCCTCCTTGTC 5 0.125 No Hit CTTTCTAATTTCAGGGTTGATAGATTGAGCTTCTGCTCTCACCACCACCA 5 0.125 No Hit AATCTGCCAAGGTGTTTCCATTGAATCCAAGATCCAAAGAAATGCTCTCC 5 0.125 No Hit ATTGAATAAGCAATCAGAAGCTTTATGTTAGAGGCTGGAGAATCAATTCA 5 0.125 No Hit CGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAGGGAT 5 0.125 No Hit GTTTGAAAAGGAAACTTTGTTTGCCCTGTTTGCTTTCTTCCCGGTGAAGG 5 0.125 No Hit AAAAATAATTCAAATTTCACAAAACATACGGCTCTCAGAAAAAAAGAAAG 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 0.025 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 0.025 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 0.05 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 0.0875 0.0 0.0 0.0 0.0 62-63 0.1125 0.0 0.0 0.0 0.0 64-65 0.125 0.0 0.0 0.0 0.0 66-67 0.2 0.0 0.0 0.0 0.0 68-69 0.225 0.0 0.0 0.0 0.0 70-71 0.2625 0.0 0.0 0.0 0.0 72-73 0.425 0.0 0.0 0.0 0.0 74-75 0.55 0.0 0.0 0.0 0.0 76-77 0.725 0.0 0.0 0.0 0.0 78-79 0.9 0.0 0.0 0.0 0.0 80-81 1.0499999999999998 0.0 0.0 0.0 0.0 82-83 1.25 0.0 0.0 0.0 0.0 84-85 1.5375 0.0 0.0 0.0 0.0 86-87 1.75 0.0 0.0 0.0 0.0 88-89 2.0999999999999996 0.0 0.0 0.0 0.0 90-91 2.5625 0.0 0.0 0.0 0.0 92-93 3.0999999999999996 0.0 0.0 0.0 0.0 94-95 3.5 0.0 0.0 0.0 0.0 96-97 4.25 0.0 0.0 0.0 0.0 98-99 5.075 0.0 0.0 0.0 0.0 100-101 5.8 0.0 0.0 0.0 0.0 102-103 6.5625 0.0 0.0 0.0 0.0 104-105 7.1625 0.0 0.0 0.0 0.0 106-107 7.574999999999999 0.0 0.0 0.0 0.0 108-109 8.5375 0.0 0.0 0.0 0.0 110-111 9.2375 0.0 0.0 0.0 0.0 112-113 9.825 0.0 0.0 0.0 0.0 114-115 10.675 0.0 0.0 0.0 0.0 116-117 11.4625 0.0 0.0 0.0 0.0 118-119 12.662500000000001 0.0 0.0 0.0 0.0 120-121 13.6125 0.0 0.0 0.0 0.0 122-123 14.6875 0.0 0.0 0.0 0.0 124-125 15.5125 0.0 0.0 0.0 0.0 126-127 16.225 0.0 0.0 0.0 0.0 128-129 17.2 0.0 0.0 0.0 0.0 130-131 18.4625 0.0 0.0 0.0 0.0 132-133 19.375 0.0 0.0 0.0 0.0 134-135 20.225 0.0 0.0 0.0 0.0 136-137 21.225 0.0 0.0 0.0 0.0 138-139 21.9625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CGCCTTT 10 0.006830828 145.0 3 TAAAATC 10 0.006830828 145.0 3 GGGGGGG 220 9.906216E-9 13.181819 145 >>END_MODULE SRR12670179 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670179_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 36.3315 37.0 37.0 37.0 37.0 37.0 2 36.215 37.0 37.0 37.0 37.0 37.0 3 36.262 37.0 37.0 37.0 37.0 37.0 4 36.269 37.0 37.0 37.0 37.0 37.0 5 36.392 37.0 37.0 37.0 37.0 37.0 6 36.2325 37.0 37.0 37.0 37.0 37.0 7 36.34 37.0 37.0 37.0 37.0 37.0 8 36.4435 37.0 37.0 37.0 37.0 37.0 9 36.282 37.0 37.0 37.0 37.0 37.0 10-14 36.3885 37.0 37.0 37.0 37.0 37.0 15-19 36.3625 37.0 37.0 37.0 37.0 37.0 20-24 36.2654 37.0 37.0 37.0 37.0 37.0 25-29 36.3107 37.0 37.0 37.0 37.0 37.0 30-34 36.20739999999999 37.0 37.0 37.0 37.0 37.0 35-39 36.153000000000006 37.0 37.0 37.0 37.0 37.0 40-44 36.1865 37.0 37.0 37.0 37.0 37.0 45-49 36.184900000000006 37.0 37.0 37.0 37.0 37.0 50-54 36.138799999999996 37.0 37.0 37.0 37.0 37.0 55-59 36.0714 37.0 37.0 37.0 37.0 37.0 60-64 36.108999999999995 37.0 37.0 37.0 37.0 37.0 65-69 36.1149 37.0 37.0 37.0 37.0 37.0 70-74 36.0458 37.0 37.0 37.0 37.0 37.0 75-79 35.977 37.0 37.0 37.0 37.0 37.0 80-84 35.949400000000004 37.0 37.0 37.0 37.0 37.0 85-89 35.994600000000005 37.0 37.0 37.0 37.0 37.0 90-94 35.897 37.0 37.0 37.0 37.0 37.0 95-99 35.9385 37.0 37.0 37.0 37.0 37.0 100-104 35.811899999999994 37.0 37.0 37.0 37.0 37.0 105-109 35.8185 37.0 37.0 37.0 37.0 37.0 110-114 35.7156 37.0 37.0 37.0 37.0 37.0 115-119 35.710300000000004 37.0 37.0 37.0 37.0 37.0 120-124 35.642700000000005 37.0 37.0 37.0 37.0 37.0 125-129 35.4326 37.0 37.0 37.0 37.0 37.0 130-134 35.3911 37.0 37.0 37.0 34.6 37.0 135-139 35.1591 37.0 37.0 37.0 29.8 37.0 140-144 34.9808 37.0 37.0 37.0 25.0 37.0 145-149 34.7065 37.0 37.0 37.0 25.0 37.0 150-151 34.626000000000005 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 2.0 14 3.0 15 3.0 16 1.0 17 2.0 18 0.0 19 1.0 20 1.0 21 1.0 22 4.0 23 3.0 24 7.0 25 9.0 26 4.0 27 13.0 28 17.0 29 14.0 30 21.0 31 43.0 32 59.0 33 88.0 34 180.0 35 674.0 36 2610.0 37 240.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.475 21.725 11.5 29.299999999999997 2 26.0 26.400000000000002 32.324999999999996 15.275 3 19.275000000000002 27.725 32.65 20.349999999999998 4 22.475 33.925 24.5 19.1 5 24.175 35.949999999999996 22.8 17.075000000000003 6 20.575 38.324999999999996 23.125 17.974999999999998 7 20.25 21.525 38.1 20.125 8 22.125 24.45 27.950000000000003 25.474999999999998 9 21.75 24.45 30.875000000000004 22.925 10-14 23.705000000000002 28.83 26.540000000000003 20.925 15-19 23.5 29.015 27.060000000000002 20.424999999999997 20-24 23.435 27.800000000000004 27.57 21.195 25-29 23.45 27.985 27.48 21.085 30-34 22.64 28.435 27.894999999999996 21.029999999999998 35-39 22.99 27.325 28.425 21.26 40-44 23.115 28.115000000000002 28.000000000000004 20.77 45-49 23.085 28.08 28.110000000000003 20.724999999999998 50-54 23.26 28.055000000000003 27.235 21.45 55-59 23.26 27.37 27.744999999999997 21.625 60-64 23.169999999999998 28.18 28.29 20.36 65-69 23.145 27.88 28.12 20.855 70-74 23.515 28.105000000000004 27.675 20.705000000000002 75-79 22.905 28.720000000000002 27.500000000000004 20.875 80-84 24.02 28.605000000000004 26.665 20.71 85-89 23.32 27.61 27.98 21.09 90-94 23.66 28.01 27.060000000000002 21.27 95-99 24.085 28.27 27.450000000000003 20.195 100-104 25.09 27.82 26.810000000000002 20.28 105-109 25.47 28.165000000000003 26.584999999999997 19.78 110-114 25.55 27.73 26.619999999999997 20.1 115-119 26.165 28.32 25.97 19.545 120-124 27.155 28.12 26.005 18.72 125-129 27.605 28.439999999999998 25.45 18.505 130-134 28.23 27.195000000000004 25.88 18.695 135-139 29.625 27.200000000000003 25.740000000000002 17.435000000000002 140-144 30.79 26.655 25.14 17.415 145-149 32.275 26.86 24.235 16.63 150-151 32.5375 25.937500000000004 24.6125 16.9125 >>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 0.5 8 0.5 9 0.0 10 0.5 11 0.5 12 0.0 13 0.0 14 0.0 15 0.5 16 0.5 17 0.0 18 0.0 19 0.0 20 0.5 21 0.5 22 0.5 23 1.5 24 2.0 25 3.0 26 4.0 27 5.0 28 10.0 29 11.0 30 12.5 31 19.0 32 24.0 33 33.5 34 54.0 35 71.5 36 91.5 37 120.0 38 138.0 39 150.5 40 182.0 41 215.0 42 250.0 43 279.0 44 282.0 45 292.0 46 275.0 47 238.5 48 214.0 49 195.0 50 163.5 51 133.5 52 114.0 53 94.0 54 75.5 55 57.5 56 46.5 57 33.5 58 26.5 59 21.5 60 14.0 61 9.0 62 6.5 63 3.0 64 1.5 65 2.0 66 1.0 67 0.5 68 1.0 69 2.5 70 2.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.5 77 1.5 78 1.0 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 0.5 88 0.5 89 0.0 90 0.0 91 0.5 92 0.5 93 0.0 94 0.0 95 0.5 96 1.0 97 1.0 98 1.0 99 0.5 100 2.0 >>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 82.1 #Duplication Level Percentage of deduplicated Percentage of total 1 83.43483556638246 68.5 2 12.850182704019488 21.099999999999998 3 2.7405602923264314 6.75 4 0.5785627283800243 1.9 5 0.2740560292326431 1.125 6 0.09135200974421437 0.44999999999999996 7 0.03045066991473812 0.17500000000000002 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 GCTTGGCCAATGGCCCCGACTCTTTGAGAAAACCAGATCAAGCTGACAAA 7 0.17500000000000002 No Hit CTTGCAGAGCAGAGATGGCATCCATGACCATGACAGCCTCATTCCTAGCT 6 0.15 No Hit AGAAGGAAACACAGAAGAAGAAGAGAATGGCAACAACAGCGATAGGGGTA 6 0.15 No Hit GACTGATGTTGCTGACGCATTGATCCTTAACCGTCTTTTTAGACAACTAT 6 0.15 No Hit TGTCAGAGTTGGACTGTATTAATCACAGATCACTTGCTAACTGAACCAGT 5 0.125 No Hit CCAGGACCCATTAAGCCGCCTGTCAAGATGCTTTCTTCGACCATTTTCGA 5 0.125 No Hit ATCACCACCACTTTCCAAACTCCACGCATAAATCTCACCGCCAGCCCACT 5 0.125 No Hit CCGGATCAAGAAATTACAAATCCTTCATGGAGGTTGTCATTTCCACATGT 5 0.125 No Hit GTACAGTTAGGATACAGAAAAAGAAACGAAACAATGACGGGAAAGCCAAT 5 0.125 No Hit CAGACACAGATTTCTTGCCCTACAATGGAGATGGATTCAAGTTGTCAGTT 5 0.125 No Hit AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 5 0.125 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 5 0.125 No Hit GCCAGAGTATGCTCAAACAGCAGTCAGTCATGATTTGCACTACATTGCTT 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 0.025 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 0.025 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 0.05 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 0.0875 0.0 0.0 0.0 0.0 62-63 0.1125 0.0 0.0 0.0 0.0 64-65 0.125 0.0 0.0 0.0 0.0 66-67 0.2 0.0 0.0 0.0 0.0 68-69 0.225 0.0 0.0 0.0 0.0 70-71 0.2625 0.0 0.0 0.0 0.0 72-73 0.425 0.0 0.0 0.0 0.0 74-75 0.55 0.0 0.0 0.0 0.0 76-77 0.725 0.0 0.0 0.0 0.0 78-79 0.9 0.0 0.0 0.0 0.0 80-81 1.025 0.0 0.0 0.0 0.0 82-83 1.225 0.0 0.0 0.0 0.0 84-85 1.5125000000000002 0.0 0.0 0.0 0.0 86-87 1.725 0.0 0.0 0.0 0.0 88-89 2.125 0.0 0.0 0.0 0.0 90-91 2.5875000000000004 0.0 0.0 0.0 0.0 92-93 3.125 0.0 0.0 0.0 0.0 94-95 3.525 0.0 0.0 0.0 0.0 96-97 4.3 0.0 0.0 0.0 0.0 98-99 5.125 0.0 0.0 0.0 0.0 100-101 5.85 0.0 0.0 0.0 0.0 102-103 6.6125 0.0 0.0 0.0 0.0 104-105 7.25 0.0 0.0 0.0 0.0 106-107 7.6625 0.0 0.0 0.0 0.0 108-109 8.625 0.0 0.0 0.0 0.0 110-111 9.4 0.0 0.0 0.0 0.0 112-113 10.0125 0.0 0.0 0.0 0.0 114-115 10.85 0.0 0.0 0.0 0.0 116-117 11.6625 0.0 0.0 0.0 0.0 118-119 12.912500000000001 0.0 0.0 0.0 0.0 120-121 13.8375 0.0 0.0 0.0 0.0 122-123 14.9875 0.0 0.0 0.0 0.0 124-125 15.8 0.0 0.0 0.0 0.0 126-127 16.5125 0.0 0.0 0.0 0.0 128-129 17.525 0.0 0.0 0.0 0.0 130-131 18.7875 0.0 0.0 0.0 0.0 132-133 19.725 0.0 0.0 0.0 0.0 134-135 20.6 0.0 0.0 0.0 0.0 136-137 21.6 0.0 0.0 0.0 0.0 138-139 22.3375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AACTGTG 10 0.006830828 145.0 6 GGGGGGG 585 7.419312E-7 6.196581 145 >>END_MODULE Read 685398 spots for SRR12670179.sra Written 685398 spots for SRR12670179.sra Read 685398 spots for SRR12670179.sra Written 685398 spots for SRR12670179.sra Read 685398 spots for SRR12670179.sra Written 685398 spots for SRR12670179.sra Read 685398 spots for SRR12670179.sra Written 685398 spots for SRR12670179.sra Read 685398 spots for SRR12670179.sra Written 685398 spots for SRR12670179.sra Read 685398 spots for SRR12670179.sra Written 685398 spots for SRR12670179.sra Read 685398 spots for SRR12670179.sra Written 685398 spots for SRR12670179.sra Read 685398 spots for SRR12670179.sra Written 685398 spots for SRR12670179.sra Read 685398 spots for SRR12670179.sra Written 685398 spots for SRR12670179.sra Read 685398 spots for SRR12670179.sra Written 685398 spots for SRR12670179.sra Read 685398 spots for SRR12670179.sra Read 685398 spots for SRR12670179.sra Written 685398 spots for SRR12670179.sra Written 685398 spots for SRR12670179.sra Read 685398 spots for SRR12670179.sra Written 685398 spots for SRR12670179.sra Read 685398 spots for SRR12670179.sra Written 685398 spots for SRR12670179.sra Read 685410 spots for SRR12670179.sra Written 685410 spots for SRR12670179.sra Read 685398 spots for SRR12670179.sra Written 685398 spots for SRR12670179.sra Read 685398 spots for SRR12670179.sra Written 685398 spots for SRR12670179.sra Read 685398 spots for SRR12670179.sra Written 685398 spots for SRR12670179.sra Read 685398 spots for SRR12670179.sra Written 685398 spots for SRR12670179.sra Read 685398 spots for SRR12670179.sra Written 685398 spots for SRR12670179.sra SRR ids: ['SRR12670179.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_lv1bt3cq SRR12670179.sra spots: 13707972 blocks: [[1, 685398], [685399, 1370796], [1370797, 2056194], [2056195, 2741592], [2741593, 3426990], [3426991, 4112388], [4112389, 4797786], [4797787, 5483184], [5483185, 6168582], [6168583, 6853980], [6853981, 7539378], [7539379, 8224776], [8224777, 8910174], [8910175, 9595572], [9595573, 10280970], [10280971, 10966368], [10966369, 11651766], [11651767, 12337164], [12337165, 13022562], [13022563, 13707972]] SRR12670179 file size 4636868 SRR12670179 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 SRR12670179 SRR12670179_1.fastq SRR12670179_2.fastq Input file: SRR12670179_1.fastq Paired file: SRR12670179_2.fastq trimmed: SRR12670179-trimmed-pair1.fastq, SRR12670179-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 Tue Feb 11 09:04:39 2025 >> started Tue Feb 11 09:04:54 2025 >> done (15.314s) 13707972 read pairs processed; of these: 102 ( 0.00%) short read pairs filtered out after trimming by size control 5148 ( 0.04%) empty read pairs filtered out after trimming by size control 13702722 (99.96%) read pairs available; of these: 3634406 (26.52%) trimmed read pairs available after processing 10068316 (73.48%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 7 0.00% 20 24 0.00% 21 23 0.00% 22 17 0.00% 23 22 0.00% 24 25 0.00% 25 37 0.00% 26 42 0.00% 27 39 0.00% 28 54 0.00% 29 49 0.00% 30 71 0.00% 31 71 0.00% 32 85 0.00% 33 102 0.00% 34 74 0.00% 35 97 0.00% 36 92 0.00% 37 120 0.00% 38 149 0.00% 39 166 0.00% 40 177 0.00% 41 231 0.00% 42 201 0.00% 43 243 0.00% 44 264 0.00% 45 266 0.00% 46 291 0.00% 47 319 0.00% 48 386 0.00% 49 497 0.00% 50 595 0.00% 51 692 0.01% 52 667 0.00% 53 783 0.01% 54 822 0.01% 55 880 0.01% 56 922 0.01% 57 1114 0.01% 58 1281 0.01% 59 1530 0.01% 60 1883 0.01% 61 2055 0.01% 62 2355 0.02% 63 2624 0.02% 64 2847 0.02% 65 2919 0.02% 66 3328 0.02% 67 3542 0.03% 68 3959 0.03% 69 4515 0.03% 70 5356 0.04% 71 6011 0.04% 72 6728 0.05% 73 7722 0.06% 74 8435 0.06% 75 9090 0.07% 76 9473 0.07% 77 10346 0.08% 78 11142 0.08% 79 12547 0.09% 80 13485 0.10% 81 15201 0.11% 82 17135 0.13% 83 18628 0.14% 84 20202 0.15% 85 21787 0.16% 86 22340 0.16% 87 23328 0.17% 88 24674 0.18% 89 26331 0.19% 90 27606 0.20% 91 30051 0.22% 92 31676 0.23% 93 34282 0.25% 94 36737 0.27% 95 38123 0.28% 96 38936 0.28% 97 40514 0.30% 98 39808 0.29% 99 41307 0.30% 100 43147 0.31% 101 43763 0.32% 102 46388 0.34% 103 48061 0.35% 104 49916 0.36% 105 50810 0.37% 106 51918 0.38% 107 52145 0.38% 108 51947 0.38% 109 52256 0.38% 110 51986 0.38% 111 53576 0.39% 112 55120 0.40% 113 55281 0.40% 114 57291 0.42% 115 58383 0.43% 116 58728 0.43% 117 59041 0.43% 118 58839 0.43% 119 58165 0.42% 120 57992 0.42% 121 59083 0.43% 122 59081 0.43% 123 60393 0.44% 124 61293 0.45% 125 61248 0.45% 126 62615 0.46% 127 61823 0.45% 128 61180 0.45% 129 60898 0.44% 130 60470 0.44% 131 59424 0.43% 132 60400 0.44% 133 61011 0.45% 134 60839 0.44% 135 61681 0.45% 136 62755 0.46% 137 61414 0.45% 138 61055 0.45% 139 61611 0.45% 140 60446 0.44% 141 60223 0.44% 142 60493 0.44% 143 60690 0.44% 144 61645 0.45% 145 61570 0.45% 146 61188 0.45% 147 60727 0.44% 148 61195 0.45% 149 60392 0.44% 150 60250 0.44% 151 10068316 73.48% 13702722 reads passed initial QC criterion=sequence-density sequence-density=0.35 sequence-density-rank=1 fanout-score=1.97 fanout-score-rank=31 prefix-density=0.35 prefix-fanout=2.0 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTTCGAGCGAAGAAGGT criterion=fanout-score sequence-density=0.03 sequence-density-rank=32 fanout-score=19.31 fanout-score-rank=1 prefix-density=0.09 prefix-fanout=6.2 sequence=AATGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTG criterion=sequence-density sequence-density=0.43 sequence-density-rank=1 fanout-score=2.06 fanout-score-rank=27 prefix-density=0.42 prefix-fanout=2.1 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=16.13 fanout-score-rank=1 prefix-density=0.02 prefix-fanout=3.9 sequence=AAAACACAATATTTTTCAGTATGAAAGCTTTAGTGATAGCTATTCTTATAGCTACCATTGCCTTCTCTCCCTTATCCATGGCAGCTCGAGAATT SRR12670179 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 09:05:39 Started mapping on | Feb 11 09:05:39 Finished on | Feb 11 09:07:14 Mapping speed, Million of reads per hour | 519.26 Number of input reads | 13702722 Average input read length | 284 UNIQUE READS: Uniquely mapped reads number | 12777715 Uniquely mapped reads % | 93.25% Average mapped length | 283.49 Number of splices: Total | 12178806 Number of splices: Annotated (sjdb) | 11873337 Number of splices: GT/AG | 11930576 Number of splices: GC/AG | 195653 Number of splices: AT/AC | 7694 Number of splices: Non-canonical | 44883 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.03% Deletion average length | 3.00 Insertion rate per base | 0.02% Insertion average length | 2.45 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 355688 % of reads mapped to multiple loci | 2.60% Number of reads mapped to too many loci | 94885 % of reads mapped to too many loci | 0.69% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.30% % of reads unmapped: other | 0.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 569319 569319 569319 N_multimapping 355688 355688 355688 N_noFeature 527150 12600259 600342 N_ambiguous 193094 866 88302 UnstrandedReadsAssigned:12057471 PositiveStrandReadsAssigned:176590 NegativeStrandReadsAssigned:12089071 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=136 echo kmer=131 SRR12670179 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: SRR12670179-trimmed-pair1.fastq SRR12670179-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,702,722 reads, 12,137,800 reads pseudoaligned [quant] estimated average fragment length: 208.817 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,104 rounds 52401 SRR12670179.ke.tsv 34699 SRR12670179.se.tsv 87100 total ==> SRR12670179.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1810.18 598 27.9509 Potri.005G024800.1.v4.1 1035 827.183 246 25.1623 Potri.004G059700.1.v4.1 961 753.23 3 0.336985 Potri.007G009000.2.v4.1 1416 1208.18 0 0 Potri.003G141000.2.v4.1 2943 2735.18 739.416 22.8728 Potri.016G087400.1.v4.1 270 109.19 710 550.165 Potri.015G069301.1.v4.1 564 363.65 0 0 Potri.010G195200.1.v4.1 1773 1565.18 148.375 8.02068 Potri.012G127500.1.v4.1 977 769.225 213 23.4284 ==> SRR12670179.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 303 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 239 Potri.001G212900.v4.1 10 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 21 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 4 SRR12670179 completed mapping pipeline successfully