Starting /dee2/code/volunteer_pipeline.sh SRR12670126 current disk space = 3057327697920 free memory = 1468297948 SRR12670126 SRAfilesize d314b3526235e1d6b3a3c37b85876eba SRR12670126.sra SRR12670126.sra file validated SRR12670126 is paired end SRR12670126 is conventional basespace SRR12670126 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670126_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 36.6115 37.0 37.0 37.0 37.0 37.0 2 36.5575 37.0 37.0 37.0 37.0 37.0 3 36.5865 37.0 37.0 37.0 37.0 37.0 4 36.716 37.0 37.0 37.0 37.0 37.0 5 36.669 37.0 37.0 37.0 37.0 37.0 6 36.656 37.0 37.0 37.0 37.0 37.0 7 36.6275 37.0 37.0 37.0 37.0 37.0 8 36.6365 37.0 37.0 37.0 37.0 37.0 9 36.591 37.0 37.0 37.0 37.0 37.0 10-14 36.6211 37.0 37.0 37.0 37.0 37.0 15-19 36.6161 37.0 37.0 37.0 37.0 37.0 20-24 36.570499999999996 37.0 37.0 37.0 37.0 37.0 25-29 36.5413 37.0 37.0 37.0 37.0 37.0 30-34 36.5169 37.0 37.0 37.0 37.0 37.0 35-39 36.504000000000005 37.0 37.0 37.0 37.0 37.0 40-44 36.474000000000004 37.0 37.0 37.0 37.0 37.0 45-49 36.5126 37.0 37.0 37.0 37.0 37.0 50-54 36.462 37.0 37.0 37.0 37.0 37.0 55-59 36.4323 37.0 37.0 37.0 37.0 37.0 60-64 36.41459999999999 37.0 37.0 37.0 37.0 37.0 65-69 36.3769 37.0 37.0 37.0 37.0 37.0 70-74 36.3164 37.0 37.0 37.0 37.0 37.0 75-79 36.3322 37.0 37.0 37.0 37.0 37.0 80-84 36.337300000000006 37.0 37.0 37.0 37.0 37.0 85-89 36.282000000000004 37.0 37.0 37.0 37.0 37.0 90-94 36.3091 37.0 37.0 37.0 37.0 37.0 95-99 36.25 37.0 37.0 37.0 37.0 37.0 100-104 36.2596 37.0 37.0 37.0 37.0 37.0 105-109 36.265100000000004 37.0 37.0 37.0 37.0 37.0 110-114 36.170899999999996 37.0 37.0 37.0 37.0 37.0 115-119 36.2087 37.0 37.0 37.0 37.0 37.0 120-124 36.132400000000004 37.0 37.0 37.0 37.0 37.0 125-129 36.0382 37.0 37.0 37.0 37.0 37.0 130-134 35.9851 37.0 37.0 37.0 37.0 37.0 135-139 35.8737 37.0 37.0 37.0 37.0 37.0 140-144 35.750600000000006 37.0 37.0 37.0 37.0 37.0 145-149 35.6909 37.0 37.0 37.0 37.0 37.0 150-151 35.459999999999994 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 1.0 21 0.0 22 0.0 23 0.0 24 0.0 25 2.0 26 4.0 27 7.0 28 15.0 29 22.0 30 16.0 31 28.0 32 37.0 33 65.0 34 106.0 35 301.0 36 3024.0 37 371.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 38.275 11.65 5.775 44.3 2 16.566566566566568 12.612612612612612 39.88988988988989 30.930930930930934 3 16.275000000000002 16.275000000000002 28.375 39.074999999999996 4 21.7 24.925 22.55 30.825000000000003 5 23.575 31.674999999999997 24.6 20.150000000000002 6 19.950000000000003 33.15 24.95 21.95 7 16.150000000000002 26.174999999999997 40.849999999999994 16.825000000000003 8 17.224999999999998 25.650000000000002 32.225 24.9 9 18.224999999999998 23.0 35.925000000000004 22.85 10-14 19.84 29.535 27.139999999999997 23.485 15-19 19.685 28.384999999999998 27.97 23.96 20-24 20.294999999999998 28.52 27.99 23.195 25-29 19.965 27.72 28.57 23.745 30-34 20.349999999999998 28.49 27.375 23.785 35-39 20.46 27.515 28.18 23.845 40-44 20.275000000000002 29.585 27.045 23.095 45-49 20.380000000000003 28.199999999999996 28.095 23.325000000000003 50-54 20.24 29.15 27.555000000000003 23.055 55-59 20.145 28.785 27.145000000000003 23.925 60-64 20.11 28.89 27.47 23.53 65-69 20.125 28.005000000000003 28.345 23.525 70-74 20.44 28.860000000000003 27.650000000000002 23.05 75-79 20.79 28.249999999999996 27.185 23.775 80-84 20.380000000000003 28.475 27.77 23.375 85-89 20.595 28.48 27.500000000000004 23.425 90-94 20.674999999999997 29.03 26.525 23.77 95-99 20.48 29.68 26.55 23.29 100-104 21.7 28.634999999999998 26.474999999999998 23.189999999999998 105-109 20.595 28.395 27.52 23.49 110-114 21.455 27.82 27.05 23.674999999999997 115-119 21.11 28.38 26.534999999999997 23.974999999999998 120-124 20.91 27.860000000000003 26.775 24.455 125-129 20.635 28.415000000000003 26.495 24.455 130-134 21.275 27.939999999999998 26.405 24.38 135-139 20.915 27.779999999999998 26.945000000000004 24.36 140-144 21.65 26.935 26.755000000000003 24.66 145-149 21.19 26.495 27.334999999999997 24.98 150-151 21.425 26.0 26.8625 25.7125 >>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 0.5 18 0.5 19 0.0 20 0.0 21 1.5 22 2.0 23 2.0 24 3.0 25 6.0 26 9.0 27 8.0 28 8.0 29 9.0 30 13.0 31 19.0 32 33.0 33 41.5 34 50.5 35 69.0 36 95.5 37 120.5 38 132.5 39 148.5 40 173.0 41 201.5 42 232.5 43 261.5 44 283.0 45 270.5 46 236.5 47 232.5 48 236.5 49 219.5 50 186.0 51 160.5 52 128.0 53 96.0 54 78.0 55 62.5 56 48.5 57 31.0 58 23.5 59 20.0 60 14.0 61 13.0 62 8.0 63 2.0 64 4.5 65 3.0 66 0.0 67 0.0 68 0.0 69 0.0 70 0.5 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 0.5 97 0.5 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.1 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 81.3 #Duplication Level Percentage of deduplicated Percentage of total 1 82.56457564575645 67.125 2 13.499384993849938 21.95 3 2.6445264452644524 6.45 4 1.014760147601476 3.3000000000000003 5 0.24600246002460024 1.0 6 0.0 0.0 7 0.03075030750307503 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 CTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAAC 7 0.17500000000000002 No Hit CCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCC 5 0.125 No Hit CCACCTTGTTTCTTCTTACTGATTCCAAACTCTCCCATGTTAGAAAACTC 5 0.125 No Hit CTCCAACTTTCATCCACCAGCGGCATCATCTGGTCCAACATTACCAGCCG 5 0.125 No Hit CCTTGTCCTTAGTTGCCCAGGAGATTCCTTCTTTGTTGGCAATAACACCT 5 0.125 No Hit CAAATCACTAGTAGGTAGAATCGGAGCTTCATTCGCATCCTTAGGCAACC 5 0.125 No Hit CCCAATAAAAAGGAAGAGGTAAAGCATTTTGCCAAGGTCTAAGTACAATT 5 0.125 No Hit CACGCTCACCACCAGGTAGCTGAACAGTCACAGCAGCATAGTCAATGCCA 5 0.125 No Hit GTTCGAATTGTGAGGTATAGCAGGACTCAATTGTGTGATGACCACTATTA 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0125 0.0 0.0 0.0 0.0 60-61 0.07500000000000001 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.15 0.0 0.0 0.0 0.0 68-69 0.1875 0.0 0.0 0.0 0.0 70-71 0.275 0.0 0.0 0.0 0.0 72-73 0.3375 0.0 0.0 0.0 0.0 74-75 0.375 0.0 0.0 0.0 0.0 76-77 0.4375 0.0 0.0 0.0 0.0 78-79 0.525 0.0 0.0 0.0 0.0 80-81 0.7625 0.0 0.0 0.0 0.0 82-83 1.0125 0.0 0.0 0.0 0.0 84-85 1.25 0.0 0.0 0.0 0.0 86-87 1.5750000000000002 0.0 0.0 0.0 0.0 88-89 1.9125 0.0 0.0 0.0 0.0 90-91 2.5374999999999996 0.0 0.0 0.0 0.0 92-93 3.0125 0.0 0.0 0.0 0.0 94-95 3.7375 0.0 0.0 0.0 0.0 96-97 4.3375 0.0 0.0 0.0 0.0 98-99 4.975 0.0 0.0 0.0 0.0 100-101 5.5625 0.0 0.0 0.0 0.0 102-103 6.2875 0.0 0.0 0.0 0.0 104-105 7.275 0.0 0.0 0.0 0.0 106-107 8.2125 0.0 0.0 0.0 0.0 108-109 9.125 0.0 0.0 0.0 0.0 110-111 9.85 0.0 0.0 0.0 0.0 112-113 10.9375 0.0 0.0 0.0 0.0 114-115 12.0875 0.0 0.0 0.0 0.0 116-117 12.95 0.0 0.0 0.0 0.0 118-119 14.162500000000001 0.0 0.0 0.0 0.0 120-121 15.225 0.0 0.0 0.0 0.0 122-123 16.175 0.0 0.0 0.0 0.0 124-125 17.2625 0.0 0.0 0.0 0.0 126-127 18.125 0.0 0.0 0.0 0.0 128-129 19.025 0.0 0.0 0.0 0.0 130-131 20.275 0.0 0.0 0.0 0.0 132-133 21.1875 0.0 0.0 0.0 0.0 134-135 22.0 0.0 0.0 0.0 0.0 136-137 23.125 0.0 0.0 0.0 0.0 138-139 24.4 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCCTTTT 10 0.006830828 145.0 7 GCGACTC 10 0.006830828 145.0 1 ACTCATC 10 0.006830828 145.0 4 TCATGTC 10 0.006830828 145.0 2 CTCATCT 10 0.006830828 145.0 5 GACTCAT 10 0.006830828 145.0 3 CGACTCA 10 0.006830828 145.0 2 >>END_MODULE SRR12670126 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670126_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.436 37.0 37.0 37.0 37.0 37.0 2 36.4005 37.0 37.0 37.0 37.0 37.0 3 36.349 37.0 37.0 37.0 37.0 37.0 4 36.3705 37.0 37.0 37.0 37.0 37.0 5 36.4575 37.0 37.0 37.0 37.0 37.0 6 36.4505 37.0 37.0 37.0 37.0 37.0 7 36.405 37.0 37.0 37.0 37.0 37.0 8 36.5045 37.0 37.0 37.0 37.0 37.0 9 36.385 37.0 37.0 37.0 37.0 37.0 10-14 36.486799999999995 37.0 37.0 37.0 37.0 37.0 15-19 36.484899999999996 37.0 37.0 37.0 37.0 37.0 20-24 36.4555 37.0 37.0 37.0 37.0 37.0 25-29 36.4246 37.0 37.0 37.0 37.0 37.0 30-34 36.414 37.0 37.0 37.0 37.0 37.0 35-39 36.3973 37.0 37.0 37.0 37.0 37.0 40-44 36.3909 37.0 37.0 37.0 37.0 37.0 45-49 36.35850000000001 37.0 37.0 37.0 37.0 37.0 50-54 36.3223 37.0 37.0 37.0 37.0 37.0 55-59 36.300799999999995 37.0 37.0 37.0 37.0 37.0 60-64 36.2826 37.0 37.0 37.0 37.0 37.0 65-69 36.2667 37.0 37.0 37.0 37.0 37.0 70-74 36.2505 37.0 37.0 37.0 37.0 37.0 75-79 36.222899999999996 37.0 37.0 37.0 37.0 37.0 80-84 36.2238 37.0 37.0 37.0 37.0 37.0 85-89 36.19709999999999 37.0 37.0 37.0 37.0 37.0 90-94 36.2333 37.0 37.0 37.0 37.0 37.0 95-99 36.1416 37.0 37.0 37.0 37.0 37.0 100-104 36.03099999999999 37.0 37.0 37.0 37.0 37.0 105-109 36.0869 37.0 37.0 37.0 37.0 37.0 110-114 35.9342 37.0 37.0 37.0 37.0 37.0 115-119 35.925799999999995 37.0 37.0 37.0 37.0 37.0 120-124 35.7447 37.0 37.0 37.0 37.0 37.0 125-129 35.5006 37.0 37.0 37.0 37.0 37.0 130-134 35.1714 37.0 37.0 37.0 34.6 37.0 135-139 34.928799999999995 37.0 37.0 37.0 25.0 37.0 140-144 34.63 37.0 37.0 37.0 25.0 37.0 145-149 34.2304 37.0 37.0 37.0 25.0 37.0 150-151 33.90375 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 3.0 15 0.0 16 0.0 17 1.0 18 0.0 19 0.0 20 0.0 21 2.0 22 1.0 23 3.0 24 3.0 25 9.0 26 8.0 27 8.0 28 9.0 29 12.0 30 22.0 31 47.0 32 62.0 33 130.0 34 230.0 35 487.0 36 2582.0 37 381.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.35 21.2 10.25 29.2 2 26.275 27.175 32.45 14.099999999999998 3 19.325 27.85 33.175 19.650000000000002 4 24.05 33.550000000000004 24.099999999999998 18.3 5 24.3 36.475 22.2 17.025000000000002 6 20.325 38.625 22.75 18.3 7 19.2 22.025 38.9 19.875 8 19.625 26.025 28.849999999999998 25.5 9 21.099999999999998 23.95 31.974999999999998 22.975 10-14 22.759999999999998 29.270000000000003 26.52 21.45 15-19 22.82 28.535 27.894999999999996 20.75 20-24 22.79 28.425 27.705000000000002 21.08 25-29 22.845 28.48 27.83 20.845 30-34 22.655 27.815 27.939999999999998 21.59 35-39 22.439999999999998 27.935 28.439999999999998 21.185000000000002 40-44 22.939999999999998 28.7 27.855 20.505000000000003 45-49 23.29 28.410000000000004 28.139999999999997 20.16 50-54 23.080000000000002 28.165000000000003 27.810000000000002 20.945 55-59 22.935 27.47 27.994999999999997 21.6 60-64 23.655 27.650000000000002 28.34 20.355 65-69 23.064999999999998 27.615000000000002 28.43 20.89 70-74 23.835 28.115000000000002 27.400000000000002 20.65 75-79 23.425 28.09 27.425 21.060000000000002 80-84 23.294999999999998 28.42 27.445000000000004 20.84 85-89 23.275000000000002 28.17 27.785 20.77 90-94 24.485 27.634999999999998 27.334999999999997 20.544999999999998 95-99 24.055 29.01 26.669999999999998 20.265 100-104 24.735 28.199999999999996 26.66 20.405 105-109 24.625 27.865000000000002 27.47 20.04 110-114 25.83 27.474999999999998 27.045 19.650000000000002 115-119 25.245 28.88 26.405 19.470000000000002 120-124 26.38 27.965 26.44 19.215 125-129 26.965 27.57 26.590000000000003 18.875 130-134 27.915 26.634999999999998 26.805 18.645 135-139 28.34 26.605 26.919999999999998 18.135 140-144 29.375 26.75 26.38 17.495 145-149 30.335 25.590000000000003 25.785000000000004 18.29 150-151 31.7375 25.887500000000003 25.8 16.575 >>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 0.5 9 1.0 10 0.5 11 0.0 12 0.5 13 1.0 14 0.5 15 0.0 16 0.0 17 0.5 18 0.5 19 0.0 20 0.0 21 0.5 22 2.0 23 2.0 24 4.0 25 4.5 26 2.5 27 4.5 28 12.0 29 17.0 30 18.5 31 21.5 32 27.0 33 32.5 34 41.0 35 76.5 36 102.0 37 104.0 38 126.5 39 159.5 40 193.5 41 235.0 42 264.0 43 282.0 44 282.0 45 266.0 46 260.0 47 243.5 48 214.0 49 199.5 50 164.5 51 134.5 52 115.5 53 80.5 54 73.5 55 64.5 56 41.5 57 31.5 58 25.5 59 14.0 60 12.5 61 14.5 62 7.0 63 2.0 64 1.0 65 0.5 66 1.0 67 0.5 68 0.5 69 2.0 70 1.5 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 1.5 80 1.5 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 0.5 91 0.5 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.5 99 1.0 100 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 80.95 #Duplication Level Percentage of deduplicated Percentage of total 1 82.3656578134651 66.675 2 13.52686843730698 21.9 3 2.655960469425571 6.45 4 1.1426806670784435 3.6999999999999997 5 0.2779493514515133 1.125 6 0.030883261272390366 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 CAAAAAAAATCTTAACTGCACCCGCTCATCCAGCAATGGCAGCAGCAACA 6 0.15 No Hit ATTTGATCGAGGTTTATATGTTGAGAAATGGACATCCTTTGTGAAGGAGC 5 0.125 No Hit CTTCAGCGGCTAGGGCTTTCTCTTCTGCTCCGGCTCCCATCCCAGCAACT 5 0.125 No Hit GGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAA 5 0.125 No Hit GATTCATTTGCCTTCAAGCCCGGCAAATACAATGCTAAGAAGATCTGCTT 5 0.125 No Hit CTCAATCTCTCTCTCCTTGTCATCTTCTCTCTCCTCTTTATCTCCGCAGT 5 0.125 No Hit GGTGTCTAAGTCGTCCCAGAACTTGATGTGTCCCTAGCTATATCTGTTAG 5 0.125 No Hit TGGGCTGCTCTTCGAGCTTTTGGTAATTGTGCCTATGCGGGTGCCTGTAG 5 0.125 No Hit ATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAAT 5 0.125 No Hit CATTGCTGTTGGAGGTGGTTTTGGATCTTATCTACTGGGTTTGAATAGGA 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0125 0.0 0.0 0.0 0.0 60-61 0.07500000000000001 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.15 0.0 0.0 0.0 0.0 68-69 0.1875 0.0 0.0 0.0 0.0 70-71 0.275 0.0 0.0 0.0 0.0 72-73 0.3375 0.0 0.0 0.0 0.0 74-75 0.375 0.0 0.0 0.0 0.0 76-77 0.4375 0.0 0.0 0.0 0.0 78-79 0.525 0.0 0.0 0.0 0.0 80-81 0.7625 0.0 0.0 0.0 0.0 82-83 1.0125 0.0 0.0 0.0 0.0 84-85 1.25 0.0 0.0 0.0 0.0 86-87 1.5750000000000002 0.0 0.0 0.0 0.0 88-89 1.9125 0.0 0.0 0.0 0.0 90-91 2.5625 0.0 0.0 0.0 0.0 92-93 3.0375 0.0 0.0 0.0 0.0 94-95 3.7625 0.0 0.0 0.0 0.0 96-97 4.3625 0.0 0.0 0.0 0.0 98-99 5.025 0.0 0.0 0.0 0.0 100-101 5.6125 0.0 0.0 0.0 0.0 102-103 6.35 0.0 0.0 0.0 0.0 104-105 7.325 0.0 0.0 0.0 0.0 106-107 8.2625 0.0 0.0 0.0 0.0 108-109 9.15 0.0 0.0 0.0 0.0 110-111 9.875 0.0 0.0 0.0 0.0 112-113 10.9625 0.0 0.0 0.0 0.0 114-115 12.1125 0.0 0.0 0.0 0.0 116-117 12.975 0.0 0.0 0.0 0.0 118-119 14.1875 0.0 0.0 0.0 0.0 120-121 15.25 0.0 0.0 0.0 0.0 122-123 16.2 0.0 0.0 0.0 0.0 124-125 17.2875 0.0 0.0 0.0 0.0 126-127 18.15 0.0 0.0 0.0 0.0 128-129 19.075 0.0 0.0 0.0 0.0 130-131 20.3375 0.0 0.0 0.0 0.0 132-133 21.275 0.0 0.0 0.0 0.0 134-135 22.125 0.0 0.0 0.0 0.0 136-137 23.25 0.0 0.0 0.0 0.0 138-139 24.525 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTCGACT 10 0.006830828 145.0 9 AATCTCG 10 0.006830828 145.0 6 ATCTCGA 10 0.006830828 145.0 7 ATCTAGC 10 0.006830828 145.0 6 GTCAAAA 10 0.006830828 145.0 1 CAATCTC 10 0.006830828 145.0 5 TGTCAAT 10 0.006830828 145.0 2 TCTCGAC 10 0.006830828 145.0 8 TACTGGC 10 0.006830828 145.0 145 AATCAAT 20 0.00593511 29.0 40-44 GGGGGGG 110 0.0017637183 10.545455 135-139 >>END_MODULE Read 597478 spots for SRR12670126.sra Written 597478 spots for SRR12670126.sra Read 597478 spots for SRR12670126.sra Written 597478 spots for SRR12670126.sra Read 597478 spots for SRR12670126.sra Written 597478 spots for SRR12670126.sra Read 597478 spots for SRR12670126.sra Written 597478 spots for SRR12670126.sra Read 597478 spots for SRR12670126.sra Written 597478 spots for SRR12670126.sra Read 597478 spots for SRR12670126.sra Written 597478 spots for SRR12670126.sra Read 597478 spots for SRR12670126.sra Written 597478 spots for SRR12670126.sra Read 597478 spots for SRR12670126.sra Written 597478 spots for SRR12670126.sra Read 597478 spots for SRR12670126.sra Written 597478 spots for SRR12670126.sra Read 597478 spots for SRR12670126.sra Written 597478 spots for SRR12670126.sra Read 597496 spots for SRR12670126.sra Written 597496 spots for SRR12670126.sra Read 597478 spots for SRR12670126.sra Written 597478 spots for SRR12670126.sra Read 597478 spots for SRR12670126.sra Written 597478 spots for SRR12670126.sra Read 597478 spots for SRR12670126.sra Written 597478 spots for SRR12670126.sra Read 597478 spots for SRR12670126.sra Written 597478 spots for SRR12670126.sra Read 597478 spots for SRR12670126.sra Written 597478 spots for SRR12670126.sra Read 597478 spots for SRR12670126.sra Written 597478 spots for SRR12670126.sra Read 597478 spots for SRR12670126.sra Written 597478 spots for SRR12670126.sra Read 597478 spots for SRR12670126.sra Written 597478 spots for SRR12670126.sra Read 597478 spots for SRR12670126.sra Written 597478 spots for SRR12670126.sra SRR ids: ['SRR12670126.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ghgoehjc SRR12670126.sra spots: 11949578 blocks: [[1, 597478], [597479, 1194956], [1194957, 1792434], [1792435, 2389912], [2389913, 2987390], [2987391, 3584868], [3584869, 4182346], [4182347, 4779824], [4779825, 5377302], [5377303, 5974780], [5974781, 6572258], [6572259, 7169736], [7169737, 7767214], [7767215, 8364692], [8364693, 8962170], [8962171, 9559648], [9559649, 10157126], [10157127, 10754604], [10754605, 11352082], [11352083, 11949578]] SRR12670126 file size 4039289 SRR12670126 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 SRR12670126 SRR12670126_1.fastq SRR12670126_2.fastq Input file: SRR12670126_1.fastq Paired file: SRR12670126_2.fastq trimmed: SRR12670126-trimmed-pair1.fastq, SRR12670126-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 00:25:13 2025 >> started Tue Feb 11 00:25:32 2025 >> done (19.660s) 11949578 read pairs processed; of these: 70 ( 0.00%) short read pairs filtered out after trimming by size control 2632 ( 0.02%) empty read pairs filtered out after trimming by size control 11946876 (99.98%) read pairs available; of these: 3613143 (30.24%) trimmed read pairs available after processing 8333733 (69.76%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 1 0.00% 20 7 0.00% 21 6 0.00% 22 14 0.00% 23 10 0.00% 24 12 0.00% 25 18 0.00% 26 28 0.00% 27 17 0.00% 28 28 0.00% 29 31 0.00% 30 53 0.00% 31 67 0.00% 32 54 0.00% 33 71 0.00% 34 71 0.00% 35 80 0.00% 36 74 0.00% 37 87 0.00% 38 101 0.00% 39 132 0.00% 40 174 0.00% 41 163 0.00% 42 169 0.00% 43 186 0.00% 44 179 0.00% 45 229 0.00% 46 248 0.00% 47 296 0.00% 48 348 0.00% 49 408 0.00% 50 486 0.00% 51 533 0.00% 52 584 0.00% 53 633 0.01% 54 667 0.01% 55 674 0.01% 56 812 0.01% 57 867 0.01% 58 1079 0.01% 59 1259 0.01% 60 1524 0.01% 61 1618 0.01% 62 1888 0.02% 63 2125 0.02% 64 2397 0.02% 65 2498 0.02% 66 2819 0.02% 67 3120 0.03% 68 3318 0.03% 69 4057 0.03% 70 4722 0.04% 71 5228 0.04% 72 5861 0.05% 73 6841 0.06% 74 7341 0.06% 75 7960 0.07% 76 8670 0.07% 77 9076 0.08% 78 10095 0.08% 79 11187 0.09% 80 12478 0.10% 81 13988 0.12% 82 15885 0.13% 83 16956 0.14% 84 18865 0.16% 85 20123 0.17% 86 21221 0.18% 87 22109 0.19% 88 23577 0.20% 89 24676 0.21% 90 26619 0.22% 91 28486 0.24% 92 30660 0.26% 93 32885 0.28% 94 35471 0.30% 95 37317 0.31% 96 37613 0.31% 97 39496 0.33% 98 39936 0.33% 99 40581 0.34% 100 42506 0.36% 101 43565 0.36% 102 46142 0.39% 103 48291 0.40% 104 49212 0.41% 105 50598 0.42% 106 51895 0.43% 107 52187 0.44% 108 51905 0.43% 109 53418 0.45% 110 52847 0.44% 111 54213 0.45% 112 55430 0.46% 113 55913 0.47% 114 57795 0.48% 115 59273 0.50% 116 59123 0.49% 117 59373 0.50% 118 60253 0.50% 119 59174 0.50% 120 59629 0.50% 121 60013 0.50% 122 60207 0.50% 123 61158 0.51% 124 62018 0.52% 125 62172 0.52% 126 62926 0.53% 127 62723 0.53% 128 61587 0.52% 129 61606 0.52% 130 61713 0.52% 131 61144 0.51% 132 61282 0.51% 133 61385 0.51% 134 62036 0.52% 135 62420 0.52% 136 62836 0.53% 137 62463 0.52% 138 61785 0.52% 139 61981 0.52% 140 60789 0.51% 141 60527 0.51% 142 60455 0.51% 143 60372 0.51% 144 60688 0.51% 145 60766 0.51% 146 60916 0.51% 147 60253 0.50% 148 61105 0.51% 149 59570 0.50% 150 59260 0.50% 151 8333733 69.76% 11946876 reads passed initial QC criterion=sequence-density sequence-density=0.36 sequence-density-rank=1 fanout-score=2.15 fanout-score-rank=32 prefix-density=0.37 prefix-fanout=2.1 sequence=TGAGATGCCTCAGTGCATCCAAACATGGGTAGCTTCCACATAGTCCAGTAGCGTCCATCATAGTACCCTGGTGAGCTGTGGTGCTCACGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTTCGAGCGAAGAAGGTAATCAATTTCCTTGGCCAATTCCTCCTCTGTGAGATCTGGAAGGTAAGAAAGAGTCTCGAACTTCTTCAATCCAGTTGGTGGCCACACCTGCATGCATTGAACTCGTCCACCATTGCTTGCAATGGAAGTAATGTCATTAGCCTTTCTGGTACTGACTGGGAAAGCTGCGGCAGACTTGAGACCATTGAATGGTGCCACCATGTTGGCTTGT criterion=fanout-score sequence-density=0.02 sequence-density-rank=35 fanout-score=240.61 fanout-score-rank=1 prefix-density=0.27 prefix-fanout=16.8 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGTTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTG criterion=sequence-density sequence-density=0.36 sequence-density-rank=1 fanout-score=2.92 fanout-score-rank=24 prefix-density=0.42 prefix-fanout=2.5 sequence=ACAAGCCAACATGGTGGCACCATTCAATGGTCTCAAGTCTGCCGCAGCTTTCCCAGTCAGTACCAGAAAGGCTAATGACATTACTTCCATTGCAAGCAATGGTGGACGAGTTCAATGCATGCAGGTGTGGCCACCAACTGGATTGAAGAAGTTCGAGACTCTTTCTTACCTTCCAGATCTCACAGAGGAGGAATTGGCCAAGGAAATTGATTACCTTCTTCGCTCGAAGTGGGTTCCTTGCTTGGAATTCGAGTTGGAGAAAGGTTGGGTCTACCGTGAGCACCACAGCTCACCAGGGTACTATGATGGACGCTACTGGACTATGTGGAAGCTACCCATGTTTGGATGCACTGAGGCATCTCAAGTGTTGCTTGAGCTTGAGGAGGCAAAGAAAGCTTACCCTAACGCCTTTATCCGTATAATCGGATTCGACAACACGCGTCAAGTGCAGTGCATCAGCTTTATTGCCGCCAAGCCAAAAGGTGTCTAAGTCGTCCCAGAACTTGATGTG criterion=fanout-score sequence-density=0.12 sequence-density-rank=13 fanout-score=44.59 fanout-score-rank=1 prefix-density=0.36 prefix-fanout=14.5 sequence=AAAGAAAAGAAAA SRR12670126 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 00:26:21 Started mapping on | Feb 11 00:26:21 Finished on | Feb 11 00:28:08 Mapping speed, Million of reads per hour | 401.95 Number of input reads | 11946876 Average input read length | 282 UNIQUE READS: Uniquely mapped reads number | 11211799 Uniquely mapped reads % | 93.85% Average mapped length | 281.23 Number of splices: Total | 10553619 Number of splices: Annotated (sjdb) | 10308287 Number of splices: GT/AG | 10342508 Number of splices: GC/AG | 168004 Number of splices: AT/AC | 6387 Number of splices: Non-canonical | 36720 Mismatch rate per base, % | 0.33% Deletion rate per base | 0.03% Deletion average length | 2.78 Insertion rate per base | 0.02% Insertion average length | 2.42 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 274909 % of reads mapped to multiple loci | 2.30% Number of reads mapped to too many loci | 63123 % of reads mapped to too many loci | 0.53% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.17% % of reads unmapped: other | 0.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 460168 460168 460168 N_multimapping 274909 274909 274909 N_noFeature 469457 11072895 532923 N_ambiguous 138486 507 62757 UnstrandedReadsAssigned:10603856 PositiveStrandReadsAssigned:138397 NegativeStrandReadsAssigned:10616119 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=131 echo kmer=127 SRR12670126 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: SRR12670126-trimmed-pair1.fastq SRR12670126-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 11,946,876 reads, 10,675,525 reads pseudoaligned [quant] estimated average fragment length: 197.648 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,056 rounds 52401 SRR12670126.ke.tsv 34699 SRR12670126.se.tsv 87100 total ==> SRR12670126.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1821.35 434 24.1567 Potri.005G024800.1.v4.1 1035 838.352 160 19.348 Potri.004G059700.1.v4.1 961 764.397 7 0.92837 Potri.007G009000.2.v4.1 1416 1219.35 0 0 Potri.003G141000.2.v4.1 2943 2746.35 561 20.7085 Potri.016G087400.1.v4.1 270 111.681 438 397.592 Potri.015G069301.1.v4.1 564 372.769 0 0 Potri.010G195200.1.v4.1 1773 1576.35 86 5.53079 Potri.012G127500.1.v4.1 977 780.388 48 6.23553 ==> SRR12670126.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 170 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 155 Potri.001G212900.v4.1 8 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 14 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 2 SRR12670126 completed mapping pipeline successfully