Starting /dee2/code/volunteer_pipeline.sh SRR12670128 current disk space = 3057044983808 free memory = 1575140092 SRR12670128 SRAfilesize 9535e21551a6ea5b335f3e17dab726a7 SRR12670128.sra SRR12670128.sra file validated SRR12670128 is paired end SRR12670128 is conventional basespace SRR12670128 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670128_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 36.581 37.0 37.0 37.0 37.0 37.0 2 36.479 37.0 37.0 37.0 37.0 37.0 3 36.625 37.0 37.0 37.0 37.0 37.0 4 36.6355 37.0 37.0 37.0 37.0 37.0 5 36.678 37.0 37.0 37.0 37.0 37.0 6 36.677 37.0 37.0 37.0 37.0 37.0 7 36.596 37.0 37.0 37.0 37.0 37.0 8 36.6175 37.0 37.0 37.0 37.0 37.0 9 36.6175 37.0 37.0 37.0 37.0 37.0 10-14 36.613600000000005 37.0 37.0 37.0 37.0 37.0 15-19 36.6126 37.0 37.0 37.0 37.0 37.0 20-24 36.545 37.0 37.0 37.0 37.0 37.0 25-29 36.53680000000001 37.0 37.0 37.0 37.0 37.0 30-34 36.547900000000006 37.0 37.0 37.0 37.0 37.0 35-39 36.48819999999999 37.0 37.0 37.0 37.0 37.0 40-44 36.485699999999994 37.0 37.0 37.0 37.0 37.0 45-49 36.4828 37.0 37.0 37.0 37.0 37.0 50-54 36.4269 37.0 37.0 37.0 37.0 37.0 55-59 36.3818 37.0 37.0 37.0 37.0 37.0 60-64 36.3811 37.0 37.0 37.0 37.0 37.0 65-69 36.3451 37.0 37.0 37.0 37.0 37.0 70-74 36.3444 37.0 37.0 37.0 37.0 37.0 75-79 36.32899999999999 37.0 37.0 37.0 37.0 37.0 80-84 36.3351 37.0 37.0 37.0 37.0 37.0 85-89 36.268800000000006 37.0 37.0 37.0 37.0 37.0 90-94 36.2847 37.0 37.0 37.0 37.0 37.0 95-99 36.1987 37.0 37.0 37.0 37.0 37.0 100-104 36.2276 37.0 37.0 37.0 37.0 37.0 105-109 36.221999999999994 37.0 37.0 37.0 37.0 37.0 110-114 36.1421 37.0 37.0 37.0 37.0 37.0 115-119 36.17620000000001 37.0 37.0 37.0 37.0 37.0 120-124 36.087 37.0 37.0 37.0 37.0 37.0 125-129 36.049299999999995 37.0 37.0 37.0 37.0 37.0 130-134 35.965999999999994 37.0 37.0 37.0 37.0 37.0 135-139 35.882 37.0 37.0 37.0 37.0 37.0 140-144 35.8221 37.0 37.0 37.0 37.0 37.0 145-149 35.7841 37.0 37.0 37.0 37.0 37.0 150-151 35.59025 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 0.0 24 1.0 25 3.0 26 3.0 27 7.0 28 9.0 29 16.0 30 22.0 31 42.0 32 33.0 33 70.0 34 138.0 35 285.0 36 2969.0 37 401.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 38.725 12.2 7.625 41.449999999999996 2 18.336673346693384 13.301603206412826 36.89879759519038 31.462925851703403 3 16.85 18.325 27.325 37.5 4 22.925 25.275 23.025000000000002 28.775000000000002 5 23.075000000000003 30.325000000000003 23.474999999999998 23.125 6 19.525000000000002 35.975 22.85 21.65 7 16.35 25.924999999999997 41.075 16.650000000000002 8 16.55 24.349999999999998 32.45 26.650000000000002 9 18.025 22.55 33.925 25.5 10-14 19.88 29.225 27.250000000000004 23.645 15-19 20.415 27.994999999999997 27.38 24.21 20-24 20.06 27.915 28.134999999999998 23.89 25-29 20.305 27.765 27.74 24.19 30-34 19.835 28.785 27.500000000000004 23.880000000000003 35-39 20.205000000000002 28.205000000000002 27.345000000000002 24.245 40-44 20.805 28.655 26.674999999999997 23.865 45-49 20.585 27.68 27.605 24.13 50-54 20.075000000000003 28.105000000000004 27.275 24.545 55-59 20.335 28.439999999999998 27.485 23.74 60-64 20.825 27.98 27.339999999999996 23.855 65-69 20.095 28.51 27.334999999999997 24.060000000000002 70-74 20.745 28.24 27.505000000000003 23.51 75-79 20.69 27.775 28.025 23.51 80-84 20.695 28.025 27.66 23.62 85-89 20.919999999999998 27.935 27.755000000000003 23.39 90-94 20.86 27.884999999999998 27.355 23.9 95-99 20.615 28.1 26.695 24.59 100-104 21.255 27.544999999999998 27.66 23.54 105-109 21.305 27.224999999999998 27.474999999999998 23.995 110-114 20.919999999999998 28.535 26.945000000000004 23.599999999999998 115-119 20.36 27.625 27.279999999999998 24.735 120-124 21.445 27.13 26.815 24.610000000000003 125-129 20.655 27.785 26.88 24.68 130-134 21.535 26.924999999999997 26.845000000000002 24.695 135-139 21.790000000000003 27.505000000000003 26.36 24.345 140-144 21.995 27.125 26.290000000000003 24.59 145-149 22.34 27.6 26.090000000000003 23.97 150-151 21.3875 27.462500000000002 27.6625 23.4875 >>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 0.5 15 0.5 16 0.0 17 0.0 18 0.5 19 0.5 20 0.0 21 0.5 22 1.0 23 1.5 24 1.5 25 2.0 26 4.0 27 5.0 28 11.0 29 12.5 30 11.5 31 19.5 32 28.5 33 44.5 34 52.5 35 61.5 36 77.5 37 91.0 38 113.5 39 132.0 40 180.5 41 210.5 42 210.5 43 228.5 44 237.5 45 278.5 46 289.5 47 252.5 48 238.5 49 217.5 50 187.0 51 164.5 52 133.5 53 108.5 54 96.0 55 79.0 56 61.0 57 44.0 58 30.0 59 24.0 60 19.5 61 11.5 62 8.5 63 7.0 64 4.5 65 2.0 66 0.5 67 0.5 68 0.5 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 0.0 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 79.475 #Duplication Level Percentage of deduplicated Percentage of total 1 81.47216105693614 64.75 2 13.557722554262346 21.55 3 3.3658383139351997 8.025 4 1.1324315822585718 3.5999999999999996 5 0.31456432840515886 1.25 6 0.09436929852154766 0.44999999999999996 7 0.031456432840515886 0.17500000000000002 8 0.031456432840515886 0.2 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 GCCTTTGCATAAGATGATTCTCTGGGAAAATGATCGTAGTGTCAAGTTTC 8 0.2 No Hit AAGAGAAGTAGAGAGGTAGATATCTTCTGGGCCTGCCCAAGACATTGATT 7 0.17500000000000002 No Hit CTCAGGATTAGTACTTGTATCAGGTTCTATATGAGTCATTTTGCATACGC 6 0.15 No Hit ACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTA 6 0.15 No Hit CGCCCGATTCAGCATCCGAATCCAGAAGCTAAAAACAAAAACAAAGTAGA 6 0.15 No Hit GTCCACTTCAAAAACACTTTTTGAGACTGTTCCACTGGTCCCTCTTTCCA 5 0.125 No Hit GGTGGAGGAGCATTCTCATTCAAAAATGGTGCTACCCGATTCGGATCGCC 5 0.125 No Hit CTGCTTTCAGGAGTCTCATCATGGTTTGAGCTTGAATTAGATGAGCGGAA 5 0.125 No Hit GCCTCTGCCATCTTATGAGTGGTTTCCCTCTTTTTTATGGCTTCACCGGT 5 0.125 No Hit CTCAGCTTTTGCAATGCCCCTTCCTATAGATTCTGATACAAACCGAGCAA 5 0.125 No Hit ATTGAGATAAATTAGTGTTGCAGTTGCTCCCTCGGATCCCCATCTTCTTC 5 0.125 No Hit CCACACCAGAGGCCACAGACATGGCCAATACATAACAATGAAGAAGACAC 5 0.125 No Hit TCCTTCCTCTCTTCCACACTTCTCACAGGATTCCGTTTGACCCCAAACCC 5 0.125 No Hit CCGGGATTCAAGTACTCTCCATTCTCTGATTTATCAACTTCATATGACGA 5 0.125 No Hit ATGGGGGTGAAGAGAGAGGCTTGAGTAGCCATTGCCATGAAGGATTGGAG 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 0.037500000000000006 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.16249999999999998 0.0 0.0 0.0 0.0 62-63 0.175 0.0 0.0 0.0 0.0 64-65 0.1875 0.0 0.0 0.0 0.0 66-67 0.25 0.0 0.0 0.0 0.0 68-69 0.2625 0.0 0.0 0.0 0.0 70-71 0.325 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 0.475 0.0 0.0 0.0 0.0 78-79 0.5375000000000001 0.0 0.0 0.0 0.0 80-81 0.675 0.0 0.0 0.0 0.0 82-83 0.8 0.0 0.0 0.0 0.0 84-85 1.0125 0.0 0.0 0.0 0.0 86-87 1.25 0.0 0.0 0.0 0.0 88-89 1.5125 0.0 0.0 0.0 0.0 90-91 1.75 0.0 0.0 0.0 0.0 92-93 1.9625 0.0 0.0 0.0 0.0 94-95 2.2874999999999996 0.0 0.0 0.0 0.0 96-97 2.6125 0.0 0.0 0.0 0.0 98-99 2.9625000000000004 0.0 0.0 0.0 0.0 100-101 3.35 0.0 0.0 0.0 0.0 102-103 3.9250000000000003 0.0 0.0 0.0 0.0 104-105 4.2 0.0 0.0 0.0 0.0 106-107 4.6875 0.0 0.0 0.0 0.0 108-109 5.5 0.0 0.0 0.0 0.0 110-111 6.0 0.0 0.0 0.0 0.0 112-113 6.775 0.0 0.0 0.0 0.0 114-115 7.2625 0.0 0.0 0.0 0.0 116-117 7.9625 0.0 0.0 0.0 0.0 118-119 8.412500000000001 0.0 0.0 0.0 0.0 120-121 8.975 0.0 0.0 0.0 0.0 122-123 9.625 0.0 0.0 0.0 0.0 124-125 10.162500000000001 0.0 0.0 0.0 0.0 126-127 10.7375 0.0 0.0 0.0 0.0 128-129 11.399999999999999 0.0 0.0 0.0 0.0 130-131 12.2 0.0 0.0 0.0 0.0 132-133 12.8625 0.0 0.0 0.0 0.0 134-135 13.55 0.0 0.0 0.0 0.0 136-137 14.3 0.0 0.0 0.0 0.0 138-139 15.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12670128 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670128_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 36.381 37.0 37.0 37.0 37.0 37.0 2 36.3345 37.0 37.0 37.0 37.0 37.0 3 36.2615 37.0 37.0 37.0 37.0 37.0 4 36.3805 37.0 37.0 37.0 37.0 37.0 5 36.4005 37.0 37.0 37.0 37.0 37.0 6 36.3385 37.0 37.0 37.0 37.0 37.0 7 36.4525 37.0 37.0 37.0 37.0 37.0 8 36.446 37.0 37.0 37.0 37.0 37.0 9 36.3735 37.0 37.0 37.0 37.0 37.0 10-14 36.4384 37.0 37.0 37.0 37.0 37.0 15-19 36.3857 37.0 37.0 37.0 37.0 37.0 20-24 36.3186 37.0 37.0 37.0 37.0 37.0 25-29 36.293099999999995 37.0 37.0 37.0 37.0 37.0 30-34 36.2608 37.0 37.0 37.0 37.0 37.0 35-39 36.2043 37.0 37.0 37.0 37.0 37.0 40-44 36.199 37.0 37.0 37.0 37.0 37.0 45-49 36.1848 37.0 37.0 37.0 37.0 37.0 50-54 36.140100000000004 37.0 37.0 37.0 37.0 37.0 55-59 36.10979999999999 37.0 37.0 37.0 37.0 37.0 60-64 36.0875 37.0 37.0 37.0 37.0 37.0 65-69 36.10850000000001 37.0 37.0 37.0 37.0 37.0 70-74 36.039 37.0 37.0 37.0 37.0 37.0 75-79 36.0023 37.0 37.0 37.0 37.0 37.0 80-84 35.990700000000004 37.0 37.0 37.0 37.0 37.0 85-89 35.9321 37.0 37.0 37.0 37.0 37.0 90-94 35.9466 37.0 37.0 37.0 37.0 37.0 95-99 35.8791 37.0 37.0 37.0 37.0 37.0 100-104 35.8275 37.0 37.0 37.0 37.0 37.0 105-109 35.8252 37.0 37.0 37.0 37.0 37.0 110-114 35.7706 37.0 37.0 37.0 37.0 37.0 115-119 35.776700000000005 37.0 37.0 37.0 37.0 37.0 120-124 35.7268 37.0 37.0 37.0 37.0 37.0 125-129 35.6417 37.0 37.0 37.0 37.0 37.0 130-134 35.5111 37.0 37.0 37.0 37.0 37.0 135-139 35.57119999999999 37.0 37.0 37.0 37.0 37.0 140-144 35.387299999999996 37.0 37.0 37.0 37.0 37.0 145-149 35.1613 37.0 37.0 37.0 32.2 37.0 150-151 34.883250000000004 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 3.0 13 3.0 14 5.0 15 4.0 16 3.0 17 0.0 18 1.0 19 2.0 20 2.0 21 0.0 22 4.0 23 1.0 24 5.0 25 6.0 26 7.0 27 10.0 28 10.0 29 14.0 30 25.0 31 35.0 32 56.0 33 92.0 34 177.0 35 459.0 36 2743.0 37 333.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.225 21.575 12.475 28.725 2 27.0 27.150000000000002 28.825 17.025000000000002 3 21.875 29.025000000000002 29.65 19.45 4 24.15 32.824999999999996 22.400000000000002 20.625 5 25.275 36.0 21.25 17.474999999999998 6 21.675 38.925 22.05 17.349999999999998 7 20.974999999999998 21.475 37.625 19.925 8 21.9 24.875 28.1 25.124999999999996 9 21.9 24.7 29.525000000000002 23.875 10-14 24.12 28.46 25.705 21.715 15-19 23.49 28.365000000000002 26.57 21.575 20-24 23.935000000000002 28.549999999999997 26.805 20.71 25-29 23.200000000000003 28.325 27.639999999999997 20.835 30-34 23.455000000000002 28.035 27.195000000000004 21.315 35-39 23.845 27.839999999999996 27.3 21.015 40-44 22.85 28.395 27.575 21.18 45-49 22.925 28.23 26.945000000000004 21.9 50-54 23.419999999999998 27.735 26.650000000000002 22.195 55-59 23.585 28.165000000000003 26.83 21.42 60-64 24.05 27.715 27.6 20.635 65-69 23.34 27.555000000000003 27.66 21.445 70-74 23.76 27.405 27.48 21.355 75-79 23.775 28.139999999999997 26.46 21.625 80-84 23.865 28.444999999999997 26.61 21.08 85-89 24.4 27.3 26.740000000000002 21.560000000000002 90-94 24.185000000000002 27.88 26.955000000000002 20.979999999999997 95-99 24.08 28.044999999999998 27.215 20.66 100-104 24.515 28.15 26.71 20.625 105-109 25.19 27.644999999999996 27.169999999999998 19.994999999999997 110-114 25.21 27.77 26.465 20.555 115-119 25.275 27.775 26.735 20.215 120-124 25.785000000000004 27.800000000000004 26.145000000000003 20.27 125-129 26.305 27.355 26.740000000000002 19.6 130-134 26.75 28.244999999999997 26.005 19.0 135-139 27.284999999999997 26.63 26.240000000000002 19.845 140-144 27.255000000000003 26.665 27.175 18.905 145-149 27.62 27.18 25.990000000000002 19.21 150-151 27.125 26.0 27.3125 19.5625 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 1.0 1 0.5 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 1.0 16 1.0 17 1.0 18 1.5 19 0.5 20 0.0 21 0.0 22 0.0 23 1.5 24 2.0 25 1.0 26 3.0 27 4.5 28 3.0 29 8.0 30 9.5 31 7.0 32 13.0 33 24.0 34 36.0 35 50.0 36 68.5 37 87.0 38 123.5 39 162.0 40 190.5 41 216.0 42 229.0 43 264.5 44 291.0 45 282.5 46 260.5 47 243.5 48 237.5 49 219.0 50 189.5 51 150.5 52 127.5 53 103.0 54 88.0 55 82.0 56 53.0 57 38.0 58 33.5 59 27.0 60 18.0 61 9.0 62 7.5 63 5.5 64 2.5 65 1.5 66 0.5 67 1.0 68 1.0 69 0.0 70 1.0 71 1.5 72 0.5 73 0.0 74 1.0 75 1.0 76 0.5 77 0.5 78 0.0 79 0.5 80 1.0 81 0.5 82 0.0 83 0.5 84 0.5 85 0.0 86 0.5 87 0.5 88 0.0 89 0.5 90 1.0 91 1.0 92 0.5 93 0.0 94 0.0 95 0.5 96 0.5 97 0.0 98 0.0 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 79.7 #Duplication Level Percentage of deduplicated Percentage of total 1 81.30489335006274 64.8 2 13.98996235884567 22.3 3 3.1994981179422837 7.6499999999999995 4 1.1606022584692597 3.6999999999999997 5 0.21957340025094102 0.8750000000000001 6 0.06273525721455457 0.3 7 0.031367628607277286 0.17500000000000002 8 0.031367628607277286 0.2 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 CTGGTGTTCACTATATAAGGGATGTGGCAGATGCTGACTCATTAATATCA 8 0.2 No Hit GGGGGAGAGAGAGAGAGAGAGTTGTTGTTGTGTCTGTGTGTGTGGTTAAA 7 0.17500000000000002 No Hit AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 6 0.15 No Hit CCAAAATCACCAATATCACTCAACACCTTCCAATCTCCAATCCTTCATGG 6 0.15 No Hit CTGGGAAATAAGATTCTGGTGCAGAAAACAGCTCAAAGCAGATATCCTGC 5 0.125 No Hit GTCTATGCAAGGTCTCCTCCTCATTACGAGGAGGACATTTTGCATCGACG 5 0.125 No Hit GGAGAGGATCTCTTGAGTTTGGAGACCACCTCTGAGGTAGGAACACTGAA 5 0.125 No Hit AACAAATATTTCGCCTCGTTGGTTTTGTAGTGGACTCGTGAAGGAATGGC 5 0.125 No Hit CAGTCATAGCAGCAAGAACCACCGCCATCTCTCTGGTCTCTCTCTGCGTG 5 0.125 No Hit GTATGGTCCCTGCCTGTTGTGGCTTTCAAGCATCCGCAGATTCCCTTGCC 5 0.125 No Hit ATTAAGATCACACAAAAGCATCTTCGTTCTGATTCGCACTGTCCAGTCTG 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 0.037500000000000006 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.16249999999999998 0.0 0.0 0.0 0.0 62-63 0.175 0.0 0.0 0.0 0.0 64-65 0.1875 0.0 0.0 0.0 0.0 66-67 0.25 0.0 0.0 0.0 0.0 68-69 0.2625 0.0 0.0 0.0 0.0 70-71 0.325 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 0.475 0.0 0.0 0.0 0.0 78-79 0.5375000000000001 0.0 0.0 0.0 0.0 80-81 0.675 0.0 0.0 0.0 0.0 82-83 0.8 0.0 0.0 0.0 0.0 84-85 0.9874999999999999 0.0 0.0 0.0 0.0 86-87 1.225 0.0 0.0 0.0 0.0 88-89 1.4875 0.0 0.0 0.0 0.0 90-91 1.725 0.0 0.0 0.0 0.0 92-93 1.9375 0.0 0.0 0.0 0.0 94-95 2.2625 0.0 0.0 0.0 0.0 96-97 2.5875000000000004 0.0 0.0 0.0 0.0 98-99 2.925 0.0 0.0 0.0 0.0 100-101 3.3 0.0 0.0 0.0 0.0 102-103 3.85 0.0 0.0 0.0 0.0 104-105 4.125 0.0 0.0 0.0 0.0 106-107 4.612500000000001 0.0 0.0 0.0 0.0 108-109 5.425000000000001 0.0 0.0 0.0 0.0 110-111 5.9375 0.0 0.0 0.0 0.0 112-113 6.725 0.0 0.0 0.0 0.0 114-115 7.2125 0.0 0.0 0.0 0.0 116-117 7.9125 0.0 0.0 0.0 0.0 118-119 8.3625 0.0 0.0 0.0 0.0 120-121 8.925 0.0 0.0 0.0 0.0 122-123 9.600000000000001 0.0 0.0 0.0 0.0 124-125 10.1125 0.0 0.0 0.0 0.0 126-127 10.7 0.0 0.0 0.0 0.0 128-129 11.3375 0.0 0.0 0.0 0.0 130-131 12.125 0.0 0.0 0.0 0.0 132-133 12.8125 0.0 0.0 0.0 0.0 134-135 13.5 0.0 0.0 0.0 0.0 136-137 14.2375 0.0 0.0 0.0 0.0 138-139 14.95 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 761789 spots for SRR12670128.sra Written 761789 spots for SRR12670128.sra Read 761789 spots for SRR12670128.sra Written 761789 spots for SRR12670128.sra Read 761789 spots for SRR12670128.sra Written 761789 spots for SRR12670128.sra Read 761789 spots for SRR12670128.sra Written 761789 spots for SRR12670128.sra Read 761789 spots for SRR12670128.sra Written 761789 spots for SRR12670128.sra Read 761789 spots for SRR12670128.sra Written 761789 spots for SRR12670128.sra Read 761789 spots for SRR12670128.sra Written 761789 spots for SRR12670128.sra Read 761789 spots for SRR12670128.sra Written 761789 spots for SRR12670128.sra Read 761789 spots for SRR12670128.sra Written 761789 spots for SRR12670128.sra Read 761789 spots for SRR12670128.sra Written 761789 spots for SRR12670128.sra Read 761789 spots for SRR12670128.sra Written 761789 spots for SRR12670128.sra Read 761789 spots for SRR12670128.sra Written 761789 spots for SRR12670128.sra Read 761789 spots for SRR12670128.sra Written 761789 spots for SRR12670128.sra Read 761789 spots for SRR12670128.sra Written 761789 spots for SRR12670128.sra Read 761789 spots for SRR12670128.sra Written 761789 spots for SRR12670128.sra Read 761789 spots for SRR12670128.sra Written 761789 spots for SRR12670128.sra Read 761789 spots for SRR12670128.sra Written 761789 spots for SRR12670128.sra Read 761789 spots for SRR12670128.sra Written 761789 spots for SRR12670128.sra Read 761789 spots for SRR12670128.sra Written 761789 spots for SRR12670128.sra Read 761802 spots for SRR12670128.sra Written 761802 spots for SRR12670128.sra SRR ids: ['SRR12670128.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ps2v0rko SRR12670128.sra spots: 15235793 blocks: [[1, 761789], [761790, 1523578], [1523579, 2285367], [2285368, 3047156], [3047157, 3808945], [3808946, 4570734], [4570735, 5332523], [5332524, 6094312], [6094313, 6856101], [6856102, 7617890], [7617891, 8379679], [8379680, 9141468], [9141469, 9903257], [9903258, 10665046], [10665047, 11426835], [11426836, 12188624], [12188625, 12950413], [12950414, 13712202], [13712203, 14473991], [14473992, 15235793]] SRR12670128 file size 5156088 SRR12670128 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 SRR12670128 SRR12670128_1.fastq SRR12670128_2.fastq Input file: SRR12670128_1.fastq Paired file: SRR12670128_2.fastq trimmed: SRR12670128-trimmed-pair1.fastq, SRR12670128-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 01:23:06 2025 >> started Tue Feb 11 01:23:27 2025 >> done (21.026s) 15235793 read pairs processed; of these: 97 ( 0.00%) short read pairs filtered out after trimming by size control 5567 ( 0.04%) empty read pairs filtered out after trimming by size control 15230129 (99.96%) read pairs available; of these: 2752690 (18.07%) trimmed read pairs available after processing 12477439 (81.93%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 13 0.00% 20 20 0.00% 21 25 0.00% 22 20 0.00% 23 37 0.00% 24 48 0.00% 25 58 0.00% 26 63 0.00% 27 73 0.00% 28 105 0.00% 29 108 0.00% 30 70 0.00% 31 117 0.00% 32 110 0.00% 33 129 0.00% 34 119 0.00% 35 129 0.00% 36 141 0.00% 37 151 0.00% 38 137 0.00% 39 170 0.00% 40 164 0.00% 41 203 0.00% 42 230 0.00% 43 231 0.00% 44 247 0.00% 45 233 0.00% 46 290 0.00% 47 298 0.00% 48 383 0.00% 49 439 0.00% 50 495 0.00% 51 542 0.00% 52 598 0.00% 53 569 0.00% 54 629 0.00% 55 664 0.00% 56 724 0.00% 57 787 0.01% 58 939 0.01% 59 1177 0.01% 60 1309 0.01% 61 1531 0.01% 62 1659 0.01% 63 1791 0.01% 64 1914 0.01% 65 2073 0.01% 66 2205 0.01% 67 2432 0.02% 68 2504 0.02% 69 3079 0.02% 70 3456 0.02% 71 3969 0.03% 72 4510 0.03% 73 5310 0.03% 74 5563 0.04% 75 5796 0.04% 76 6253 0.04% 77 6629 0.04% 78 7151 0.05% 79 7906 0.05% 80 8595 0.06% 81 9958 0.07% 82 10916 0.07% 83 11670 0.08% 84 12898 0.08% 85 13968 0.09% 86 14319 0.09% 87 14881 0.10% 88 15568 0.10% 89 16146 0.11% 90 17279 0.11% 91 18622 0.12% 92 19964 0.13% 93 21217 0.14% 94 22617 0.15% 95 23973 0.16% 96 24463 0.16% 97 25023 0.16% 98 25010 0.16% 99 25708 0.17% 100 26697 0.18% 101 27277 0.18% 102 29243 0.19% 103 30456 0.20% 104 31986 0.21% 105 33035 0.22% 106 33557 0.22% 107 33662 0.22% 108 33627 0.22% 109 33878 0.22% 110 34334 0.23% 111 35214 0.23% 112 36963 0.24% 113 37648 0.25% 114 39469 0.26% 115 40570 0.27% 116 41525 0.27% 117 41362 0.27% 118 41729 0.27% 119 41584 0.27% 120 42269 0.28% 121 42742 0.28% 122 43576 0.29% 123 45154 0.30% 124 46050 0.30% 125 47246 0.31% 126 48076 0.32% 127 48493 0.32% 128 48227 0.32% 129 47989 0.32% 130 48678 0.32% 131 48568 0.32% 132 48977 0.32% 133 50574 0.33% 134 51731 0.34% 135 53329 0.35% 136 52977 0.35% 137 53435 0.35% 138 53566 0.35% 139 54666 0.36% 140 53362 0.35% 141 54558 0.36% 142 54876 0.36% 143 56118 0.37% 144 57131 0.38% 145 57562 0.38% 146 59098 0.39% 147 58806 0.39% 148 60069 0.39% 149 58969 0.39% 150 60477 0.40% 151 12477439 81.93% 15230129 reads passed initial QC criterion=sequence-density sequence-density=0.45 sequence-density-rank=1 fanout-score=2.36 fanout-score-rank=25 prefix-density=0.48 prefix-fanout=2.2 sequence=TGAGATGCCTCAGTGCATCCAAACATGGGTAG criterion=fanout-score sequence-density=0.02 sequence-density-rank=33 fanout-score=188.55 fanout-score-rank=1 prefix-density=0.24 prefix-fanout=16.2 sequence=CTGCTGCTGCATTTATTAGAGAAGGAGATGCTGGTAATCTCCATTTCACAAGTTCATTAATCTCGATCGAAAATATGGCTCATTTAAGCATATACAAAGTACATCTGGGAAAGAAAGTTAAGAACCAAGATAGGGTCACTGATATTTGGATGATGTTCATACGGAGAGGGAGGGAGAAAGGCTGTACTCAAGCCCCCAGAGCTCAAAACTGCCTTTGACAAAATCATAATAACCACCCTTCAGTCCTAGAGTTTTGTTCACCAAGCCATCTCTCACAAACGGGTAGGTTAGCAAGTGTCCAAGGGACACGTTCACTGCCTCCTTTTCACATTGTGTACAGAGGTCTGGGAAAGGTGCATTGGCATGTTCTGCTAAAACCTTAGTCTTGGCAGGGTAGCAAACTTTGACCCAGTCTTCTATGAAATCAGTTGATGTTGTTCCATCATAAGGGAAGGACATGAGGCCCTTAATTCCACCACAGGCGCTGTGTCCAATGACCACAATGTATTCC criterion=sequence-density sequence-density=1.04 sequence-density-rank=1 fanout-score=2.27 fanout-score-rank=25 prefix-density=1.07 prefix-fanout=2.2 sequence=CCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAATCATCATGTCTAGCACCTGCGACACCTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCA criterion=fanout-score sequence-density=0.16 sequence-density-rank=15 fanout-score=13.23 fanout-score-rank=1 prefix-density=0.39 prefix-fanout=5.4 sequence=GTGCCAAGGTCT SRR12670128 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 01:24:09 Started mapping on | Feb 11 01:24:09 Finished on | Feb 11 01:26:03 Mapping speed, Million of reads per hour | 480.95 Number of input reads | 15230129 Average input read length | 291 UNIQUE READS: Uniquely mapped reads number | 14083412 Uniquely mapped reads % | 92.47% Average mapped length | 290.07 Number of splices: Total | 13752992 Number of splices: Annotated (sjdb) | 13482187 Number of splices: GT/AG | 13455919 Number of splices: GC/AG | 240219 Number of splices: AT/AC | 9057 Number of splices: Non-canonical | 47797 Mismatch rate per base, % | 0.33% Deletion rate per base | 0.02% Deletion average length | 2.84 Insertion rate per base | 0.02% Insertion average length | 2.34 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 374387 % of reads mapped to multiple loci | 2.46% Number of reads mapped to too many loci | 45072 % of reads mapped to too many loci | 0.30% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.64% % of reads unmapped: other | 0.14% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 772330 772330 772330 N_multimapping 374387 374387 374387 N_noFeature 376765 13807657 459512 N_ambiguous 277915 834 84466 UnstrandedReadsAssigned:13428732 PositiveStrandReadsAssigned:274921 NegativeStrandReadsAssigned:13539434 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12670128 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: SRR12670128-trimmed-pair1.fastq SRR12670128-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 15,230,129 reads, 13,581,560 reads pseudoaligned [quant] estimated average fragment length: 224.835 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,145 rounds 52401 SRR12670128.ke.tsv 34699 SRR12670128.se.tsv 87100 total ==> SRR12670128.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1794.16 481 16.0296 Potri.005G024800.1.v4.1 1035 811.165 131 9.6561 Potri.004G059700.1.v4.1 961 737.254 0 0 Potri.007G009000.2.v4.1 1416 1192.16 0 0 Potri.003G141000.2.v4.1 2943 2719.16 536.457 11.7961 Potri.016G087400.1.v4.1 270 96.2518 568.568 353.194 Potri.015G069301.1.v4.1 564 347.178 0 0 Potri.010G195200.1.v4.1 1773 1549.16 38 1.46665 Potri.012G127500.1.v4.1 977 753.223 81 6.42986 ==> SRR12670128.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 54 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 277 Potri.001G212900.v4.1 197 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 4 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR12670128 completed mapping pipeline successfully