Starting /dee2/code/volunteer_pipeline.sh SRR12670143 current disk space = 3056976408576 free memory = 1473265176 SRR12670143 SRAfilesize 5221223b9873de853a171c05fb0ab9b5 SRR12670143.sra SRR12670143.sra file validated SRR12670143 is paired end SRR12670143 is conventional basespace SRR12670143 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670143_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 36.57 37.0 37.0 37.0 37.0 37.0 2 36.397 37.0 37.0 37.0 37.0 37.0 3 36.605 37.0 37.0 37.0 37.0 37.0 4 36.5975 37.0 37.0 37.0 37.0 37.0 5 36.711 37.0 37.0 37.0 37.0 37.0 6 36.6645 37.0 37.0 37.0 37.0 37.0 7 36.57 37.0 37.0 37.0 37.0 37.0 8 36.6025 37.0 37.0 37.0 37.0 37.0 9 36.638 37.0 37.0 37.0 37.0 37.0 10-14 36.6243 37.0 37.0 37.0 37.0 37.0 15-19 36.574400000000004 37.0 37.0 37.0 37.0 37.0 20-24 36.56400000000001 37.0 37.0 37.0 37.0 37.0 25-29 36.5304 37.0 37.0 37.0 37.0 37.0 30-34 36.476 37.0 37.0 37.0 37.0 37.0 35-39 36.5008 37.0 37.0 37.0 37.0 37.0 40-44 36.49059999999999 37.0 37.0 37.0 37.0 37.0 45-49 36.393299999999996 37.0 37.0 37.0 37.0 37.0 50-54 36.36 37.0 37.0 37.0 37.0 37.0 55-59 36.36900000000001 37.0 37.0 37.0 37.0 37.0 60-64 36.3683 37.0 37.0 37.0 37.0 37.0 65-69 36.2741 37.0 37.0 37.0 37.0 37.0 70-74 36.2838 37.0 37.0 37.0 37.0 37.0 75-79 36.3298 37.0 37.0 37.0 37.0 37.0 80-84 36.3116 37.0 37.0 37.0 37.0 37.0 85-89 36.3052 37.0 37.0 37.0 37.0 37.0 90-94 36.2868 37.0 37.0 37.0 37.0 37.0 95-99 36.236900000000006 37.0 37.0 37.0 37.0 37.0 100-104 36.2492 37.0 37.0 37.0 37.0 37.0 105-109 36.2483 37.0 37.0 37.0 37.0 37.0 110-114 36.137 37.0 37.0 37.0 37.0 37.0 115-119 36.132 37.0 37.0 37.0 37.0 37.0 120-124 35.969 37.0 37.0 37.0 37.0 37.0 125-129 35.856899999999996 37.0 37.0 37.0 37.0 37.0 130-134 35.7726 37.0 37.0 37.0 37.0 37.0 135-139 35.533699999999996 37.0 37.0 37.0 34.6 37.0 140-144 35.254599999999996 37.0 37.0 37.0 34.6 37.0 145-149 35.1149 37.0 37.0 37.0 27.4 37.0 150-151 34.7245 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 1.0 24 2.0 25 3.0 26 0.0 27 10.0 28 15.0 29 16.0 30 29.0 31 52.0 32 45.0 33 63.0 34 201.0 35 351.0 36 2796.0 37 416.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 43.974999999999994 9.8 5.625 40.6 2 18.843843843843842 12.137137137137136 38.56356356356356 30.455455455455454 3 17.1 16.900000000000002 28.249999999999996 37.75 4 22.075 24.85 25.025 28.050000000000004 5 22.775000000000002 29.799999999999997 24.8 22.625 6 20.375 35.3 24.375 19.950000000000003 7 15.049999999999999 24.45 41.9 18.6 8 17.599999999999998 25.874999999999996 32.75 23.775 9 17.1 22.225 35.65 25.025 10-14 20.544999999999998 29.459999999999997 27.265 22.73 15-19 19.96 28.189999999999998 27.96 23.89 20-24 20.955 28.410000000000004 27.42 23.215 25-29 20.285 28.67 28.035 23.01 30-34 20.285 28.044999999999998 28.08 23.59 35-39 20.415 28.08 28.07 23.435 40-44 20.615 28.13 27.650000000000002 23.605 45-49 20.625 28.825 27.565 22.985 50-54 20.615 27.83 28.07 23.485 55-59 20.16 27.72 27.82 24.3 60-64 20.27 28.084999999999997 28.165000000000003 23.48 65-69 20.865000000000002 28.395 27.975 22.765 70-74 21.305 27.685 27.605 23.405 75-79 20.595 28.634999999999998 27.715 23.055 80-84 21.335 28.335 27.57 22.759999999999998 85-89 21.455 28.560000000000002 26.72 23.265 90-94 21.740000000000002 28.785 26.495 22.98 95-99 21.125 28.884999999999998 26.064999999999998 23.925 100-104 21.775 28.365000000000002 26.279999999999998 23.580000000000002 105-109 21.595 28.205000000000002 26.255 23.945 110-114 21.465 28.835 26.565 23.135 115-119 21.990000000000002 28.355000000000004 26.005 23.65 120-124 21.935 28.215 25.740000000000002 24.11 125-129 21.84 27.96 26.165 24.035 130-134 22.15 27.384999999999998 26.58 23.885 135-139 22.495 26.945000000000004 26.35 24.21 140-144 22.5 26.255 27.1 24.145 145-149 23.275000000000002 25.745 26.534999999999997 24.445 150-151 24.5 26.3625 25.650000000000002 23.4875 >>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 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.5 13 0.5 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 0.5 23 1.5 24 1.5 25 3.5 26 3.5 27 4.5 28 7.0 29 6.0 30 11.0 31 16.0 32 26.5 33 37.0 34 48.0 35 69.0 36 81.5 37 122.5 38 161.5 39 146.0 40 159.5 41 211.0 42 236.0 43 244.5 44 274.5 45 283.0 46 258.0 47 242.0 48 234.5 49 211.0 50 178.5 51 149.5 52 118.0 53 108.5 54 86.0 55 57.5 56 50.0 57 39.5 58 28.0 59 24.5 60 16.5 61 8.0 62 7.5 63 5.5 64 4.0 65 4.0 66 4.5 67 4.0 68 2.5 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 0.1 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 80.10000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 81.74157303370787 65.47500000000001 2 13.545568039950062 21.7 3 3.4019975031210987 8.175 4 0.9051186017478152 2.9000000000000004 5 0.2808988764044944 1.125 6 0.09363295880149813 0.44999999999999996 7 0.031210986267166042 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 CGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCA 7 0.17500000000000002 No Hit GGCAATGAGATCTCTAGCATTTGTTATTTTCTTGTCAACAAGAAGCAACT 6 0.15 No Hit CGGCTTCTGATGGTTGGTACCGAATCCACCCAAACCTCCAACAGCTCCAT 6 0.15 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACGGATTCGTATCTCGTAT 6 0.15 TruSeq Adapter, Index 2 (97% over 37bp) GGCAGGTGAGGAATCAACCATAATAGTTTCACTGAACAAATTTGGAAGGA 5 0.125 No Hit GCCTGTTGGTGGCAGAGCATTTCCTGGGGATGTAAAGATCCATGTTCTGT 5 0.125 No Hit TTTTTTTTTACAATTCACTCCTTTCATTGCATACCATCAGTGTAATTCCA 5 0.125 No Hit CAGGAACGTAGATTCTTTTCTTGATAGATTTTCCATCCAGGAACTTGGAG 5 0.125 No Hit CTGCTATGCACTTTCCCTCGACCATATCCATATGCTGTTGTTAACTACAT 5 0.125 No Hit GTTTTTATCTGTGAATGATCGCTTGAGCTATCTATACCTAGAAGATCATA 5 0.125 No Hit CTCGGCCTGACTCAATATGCTTGACATCCTCCACGAGGATTTCGTAATGC 5 0.125 No Hit GCCATATCCAAAAAATCCTTCTTTAAGGGGCTTAACAACCCGGATACATA 5 0.125 No Hit GTCCGACCATACTTGAGTAATAAGAGAAATGGGGTCCAGTCGATCTAGTG 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 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.07500000000000001 0.0 0.0 0.0 0.0 54-55 0.15 0.0 0.0 0.0 0.0 56-57 0.175 0.0 0.0 0.0 0.0 58-59 0.2 0.0 0.0 0.0 0.0 60-61 0.2 0.0 0.0 0.0 0.0 62-63 0.25 0.0 0.0 0.0 0.0 64-65 0.3125 0.0 0.0 0.0 0.0 66-67 0.475 0.0 0.0 0.0 0.0 68-69 0.5375000000000001 0.0 0.0 0.0 0.0 70-71 0.8500000000000001 0.0 0.0 0.0 0.0 72-73 1.025 0.0 0.0 0.0 0.0 74-75 1.425 0.0 0.0 0.0 0.0 76-77 1.8125 0.0 0.0 0.0 0.0 78-79 2.0875 0.0 0.0 0.0 0.0 80-81 2.4 0.0 0.0 0.0 0.0 82-83 3.0250000000000004 0.0 0.0 0.0 0.0 84-85 3.8625 0.0 0.0 0.0 0.0 86-87 4.4 0.0 0.0 0.0 0.0 88-89 5.0375 0.0 0.0 0.0 0.0 90-91 5.775 0.0 0.0 0.0 0.0 92-93 6.625 0.0 0.0 0.0 0.0 94-95 7.75 0.0 0.0 0.0 0.0 96-97 8.787500000000001 0.0 0.0 0.0 0.0 98-99 9.7375 0.0 0.0 0.0 0.0 100-101 10.774999999999999 0.0 0.0 0.0 0.0 102-103 11.825 0.0 0.0 0.0 0.0 104-105 13.0375 0.0 0.0 0.0 0.0 106-107 14.1 0.0 0.0 0.0 0.0 108-109 14.975000000000001 0.0 0.0 0.0 0.0 110-111 16.2375 0.0 0.0 0.0 0.0 112-113 17.475 0.0 0.0 0.0 0.0 114-115 18.8 0.0 0.0 0.0 0.0 116-117 20.2625 0.0 0.0 0.0 0.0 118-119 21.15 0.0 0.0 0.0 0.0 120-121 21.95 0.0 0.0 0.0 0.0 122-123 23.362499999999997 0.0 0.0 0.0 0.0 124-125 25.012500000000003 0.0 0.0 0.0 0.0 126-127 26.2375 0.0 0.0 0.0 0.0 128-129 27.4 0.0 0.0 0.0 0.0 130-131 28.4625 0.0 0.0 0.0 0.0 132-133 29.65 0.0 0.0 0.0 0.0 134-135 30.6625 0.0 0.0 0.0 0.0 136-137 31.7125 0.0 0.0 0.0 0.0 138-139 33.05 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGGGGG 75 3.4954483E-6 29.000002 145 >>END_MODULE SRR12670143 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670143_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 36.3785 37.0 37.0 37.0 37.0 37.0 2 36.2585 37.0 37.0 37.0 37.0 37.0 3 36.2485 37.0 37.0 37.0 37.0 37.0 4 36.3145 37.0 37.0 37.0 37.0 37.0 5 36.4405 37.0 37.0 37.0 37.0 37.0 6 36.3345 37.0 37.0 37.0 37.0 37.0 7 36.3415 37.0 37.0 37.0 37.0 37.0 8 36.321 37.0 37.0 37.0 37.0 37.0 9 36.3795 37.0 37.0 37.0 37.0 37.0 10-14 36.382400000000004 37.0 37.0 37.0 37.0 37.0 15-19 36.348400000000005 37.0 37.0 37.0 37.0 37.0 20-24 36.3152 37.0 37.0 37.0 37.0 37.0 25-29 36.28490000000001 37.0 37.0 37.0 37.0 37.0 30-34 36.2109 37.0 37.0 37.0 37.0 37.0 35-39 36.2154 37.0 37.0 37.0 37.0 37.0 40-44 36.2339 37.0 37.0 37.0 37.0 37.0 45-49 36.208000000000006 37.0 37.0 37.0 37.0 37.0 50-54 36.218500000000006 37.0 37.0 37.0 37.0 37.0 55-59 36.105 37.0 37.0 37.0 37.0 37.0 60-64 36.1781 37.0 37.0 37.0 37.0 37.0 65-69 36.16459999999999 37.0 37.0 37.0 37.0 37.0 70-74 36.1394 37.0 37.0 37.0 37.0 37.0 75-79 36.099900000000005 37.0 37.0 37.0 37.0 37.0 80-84 36.0697 37.0 37.0 37.0 37.0 37.0 85-89 36.0152 37.0 37.0 37.0 37.0 37.0 90-94 36.0066 37.0 37.0 37.0 37.0 37.0 95-99 35.98 37.0 37.0 37.0 37.0 37.0 100-104 35.8339 37.0 37.0 37.0 37.0 37.0 105-109 35.694599999999994 37.0 37.0 37.0 37.0 37.0 110-114 35.6305 37.0 37.0 37.0 37.0 37.0 115-119 35.5438 37.0 37.0 37.0 37.0 37.0 120-124 35.2884 37.0 37.0 37.0 37.0 37.0 125-129 35.1849 37.0 37.0 37.0 32.2 37.0 130-134 34.8759 37.0 37.0 37.0 25.0 37.0 135-139 34.705299999999994 37.0 37.0 37.0 25.0 37.0 140-144 34.2644 37.0 37.0 37.0 25.0 37.0 145-149 33.929899999999996 37.0 37.0 37.0 25.0 37.0 150-151 33.713 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 2.0 14 1.0 15 6.0 16 2.0 17 1.0 18 2.0 19 1.0 20 1.0 21 3.0 22 4.0 23 8.0 24 8.0 25 3.0 26 7.0 27 10.0 28 7.0 29 29.0 30 24.0 31 33.0 32 73.0 33 147.0 34 243.0 35 655.0 36 2436.0 37 294.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 42.25 22.675 8.1 26.974999999999998 2 26.3 26.1 31.75 15.85 3 20.375 27.075 32.725 19.825 4 23.599999999999998 34.4 23.775 18.224999999999998 5 24.7 36.8 21.275 17.224999999999998 6 21.05 40.050000000000004 22.975 15.925 7 21.025 21.95 38.324999999999996 18.7 8 19.975 25.5 28.975 25.55 9 23.05 25.374999999999996 29.049999999999997 22.525000000000002 10-14 23.59 29.2 26.724999999999998 20.485 15-19 23.13 27.925 27.485 21.46 20-24 22.79 28.78 27.505000000000003 20.925 25-29 23.3 28.310000000000002 28.084999999999997 20.305 30-34 23.425 28.139999999999997 28.060000000000002 20.375 35-39 22.67 28.455000000000002 27.584999999999997 21.29 40-44 23.39 28.134999999999998 27.87 20.605 45-49 23.1 28.46 27.91 20.53 50-54 23.205000000000002 27.815 28.044999999999998 20.935000000000002 55-59 23.794999999999998 27.905 27.41 20.89 60-64 23.305 27.384999999999998 28.17 21.14 65-69 23.385 27.76 28.13 20.724999999999998 70-74 23.665 27.575 27.474999999999998 21.285 75-79 23.28 28.655 27.16 20.905 80-84 23.89 28.265 27.36 20.485 85-89 24.605 28.945 25.845000000000002 20.605 90-94 24.645 29.04 26.25 20.064999999999998 95-99 25.03 28.055000000000003 26.965 19.950000000000003 100-104 25.85 28.38 25.650000000000002 20.119999999999997 105-109 26.765 27.865000000000002 26.36 19.009999999999998 110-114 27.310000000000002 28.134999999999998 25.83 18.725 115-119 28.410000000000004 28.265 25.15 18.175 120-124 29.549999999999997 27.93 25.52 17.0 125-129 30.835 26.490000000000002 25.215 17.46 130-134 32.005 26.605 24.73 16.66 135-139 34.17 25.740000000000002 23.815 16.275000000000002 140-144 35.18 24.925 23.794999999999998 16.1 145-149 36.964999999999996 24.495 23.575 14.965 150-151 38.125 25.275 22.4875 14.1125 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 1.0 7 1.0 8 0.0 9 0.5 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 1.5 19 2.0 20 1.0 21 1.5 22 3.0 23 2.5 24 1.0 25 1.0 26 3.5 27 4.0 28 4.0 29 9.5 30 11.5 31 13.5 32 18.0 33 33.0 34 48.5 35 70.0 36 95.5 37 114.5 38 146.0 39 181.0 40 201.5 41 212.5 42 246.0 43 253.5 44 249.0 45 292.5 46 286.0 47 250.0 48 231.0 49 188.0 50 160.0 51 133.5 52 113.0 53 93.0 54 68.0 55 57.5 56 40.5 57 35.5 58 30.5 59 22.5 60 16.0 61 9.0 62 8.0 63 4.5 64 2.5 65 1.0 66 1.0 67 1.5 68 2.0 69 1.5 70 0.5 71 1.0 72 1.0 73 0.5 74 1.0 75 0.5 76 0.0 77 0.5 78 0.5 79 0.5 80 1.5 81 1.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.5 90 0.5 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 1.0 100 2.5 >>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 80.325 #Duplication Level Percentage of deduplicated Percentage of total 1 81.97945845004668 65.85 2 13.47650171179583 21.65 3 3.2057267351384997 7.725 4 0.8714596949891068 2.8000000000000003 5 0.3734827264239029 1.5 6 0.06224712107065049 0.3 7 0.031123560535325244 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 AGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTAT 7 0.17500000000000002 No Hit GGAGTGGTGACTCTTGAAGAGGGAAAAAGCGCTGATAATAGTCTCTATGT 6 0.15 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 6 0.15 No Hit GTTCCGCTGATGTACTTGATCTAGTAAAACAAAGCATTTTACAAGGTGGG 5 0.125 No Hit CAGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTA 5 0.125 No Hit CAATGACAACCAGAATCTTAACCCCAAAAACCTTCACTTCCTTCCCTCCG 5 0.125 No Hit CTCTATCAAATCGAACAACCAAACCTCTTTTGAATCAAAACGACCAAGCA 5 0.125 No Hit CTCTCCTCTTCCTGGTGATTAAGAGCTTTAACTGTATTTTTGGGTAGCAA 5 0.125 No Hit CTGATTACCTGAAGGAGTCTACCATAGTTCTTCCAGTTCAGATCAATGGC 5 0.125 No Hit AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 5 0.125 No Hit GACCACAGGGTGTGGAATACAAAGGTCTGGCCTTCTGGCAGAAGAGGTTG 5 0.125 No Hit CACATATAGAGGGTGTAATAGCTAAGTAGCCTGTAAGAGATGGCTTCCTC 5 0.125 No Hit CATTCACGCTTGTAATGCTCACGAAACCTGTAAGAATAGCACCCAATTAT 5 0.125 No Hit CAAAACTAGCTAGCTCTCTCTCCCTCCTTCTCTCACTAGATCGACTGGAC 5 0.125 No Hit GCTGCTCTCAGTGATGGGATTGTTAAGAAGGTGCTTCCTGTTCAATGAAG 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 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.07500000000000001 0.0 0.0 0.0 0.0 54-55 0.15 0.0 0.0 0.0 0.0 56-57 0.175 0.0 0.0 0.0 0.0 58-59 0.2 0.0 0.0 0.0 0.0 60-61 0.2 0.0 0.0 0.0 0.0 62-63 0.25 0.0 0.0 0.0 0.0 64-65 0.3125 0.0 0.0 0.0 0.0 66-67 0.5 0.0 0.0 0.0 0.0 68-69 0.5625 0.0 0.0 0.0 0.0 70-71 0.875 0.0 0.0 0.0 0.0 72-73 1.05 0.0 0.0 0.0 0.0 74-75 1.45 0.0 0.0 0.0 0.0 76-77 1.8375 0.0 0.0 0.0 0.0 78-79 2.1125 0.0 0.0 0.0 0.0 80-81 2.425 0.0 0.0 0.0 0.0 82-83 3.05 0.0 0.0 0.0 0.0 84-85 3.9 0.0 0.0 0.0 0.0 86-87 4.449999999999999 0.0 0.0 0.0 0.0 88-89 5.0875 0.0 0.0 0.0 0.0 90-91 5.8375 0.0 0.0 0.0 0.0 92-93 6.725 0.0 0.0 0.0 0.0 94-95 7.8 0.0 0.0 0.0 0.0 96-97 8.8125 0.0 0.0 0.0 0.0 98-99 9.787500000000001 0.0 0.0 0.0 0.0 100-101 10.8375 0.0 0.0 0.0 0.0 102-103 11.925 0.0 0.0 0.0 0.0 104-105 13.1625 0.0 0.0 0.0 0.0 106-107 14.25 0.0 0.0 0.0 0.0 108-109 15.149999999999999 0.0 0.0 0.0 0.0 110-111 16.4 0.0 0.0 0.0 0.0 112-113 17.65 0.0 0.0 0.0 0.0 114-115 18.9375 0.0 0.0 0.0 0.0 116-117 20.375 0.0 0.0 0.0 0.0 118-119 21.2875 0.0 0.0 0.0 0.0 120-121 22.1 0.0 0.0 0.0 0.0 122-123 23.549999999999997 0.0 0.0 0.0 0.0 124-125 25.262500000000003 0.0 0.0 0.0 0.0 126-127 26.475 0.0 0.0 0.0 0.0 128-129 27.625 0.0 0.0 0.0 0.0 130-131 28.7375 0.0 0.0 0.0 0.0 132-133 29.924999999999997 0.0 0.0 0.0 0.0 134-135 30.9375 0.0 0.0 0.0 0.0 136-137 32.075 0.0 0.0 0.0 0.0 138-139 33.425 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGGGGG 690 0.0 8.405797 145 >>END_MODULE Read 522478 spots for SRR12670143.sra Written 522478 spots for SRR12670143.sra Read 522478 spots for SRR12670143.sra Written 522478 spots for SRR12670143.sra Read 522478 spots for SRR12670143.sra Written 522478 spots for SRR12670143.sra Read 522478 spots for SRR12670143.sra Written 522478 spots for SRR12670143.sra Read 522478 spots for SRR12670143.sra Written 522478 spots for SRR12670143.sra Read 522478 spots for SRR12670143.sra Written 522478 spots for SRR12670143.sra Read 522478 spots for SRR12670143.sra Written 522478 spots for SRR12670143.sra Read 522478 spots for SRR12670143.sra Written 522478 spots for SRR12670143.sra Read 522478 spots for SRR12670143.sra Written 522478 spots for SRR12670143.sra Read 522478 spots for SRR12670143.sra Written 522478 spots for SRR12670143.sra Read 522478 spots for SRR12670143.sra Written 522478 spots for SRR12670143.sra Read 522478 spots for SRR12670143.sra Written 522478 spots for SRR12670143.sra Read 522478 spots for SRR12670143.sra Written 522478 spots for SRR12670143.sra Read 522478 spots for SRR12670143.sra Written 522478 spots for SRR12670143.sra Read 522478 spots for SRR12670143.sra Written 522478 spots for SRR12670143.sra Read 522478 spots for SRR12670143.sra Written 522478 spots for SRR12670143.sra Read 522478 spots for SRR12670143.sra Written 522478 spots for SRR12670143.sra Read 522478 spots for SRR12670143.sra Written 522478 spots for SRR12670143.sra Read 522478 spots for SRR12670143.sra Written 522478 spots for SRR12670143.sra Read 522482 spots for SRR12670143.sra Written 522482 spots for SRR12670143.sra SRR ids: ['SRR12670143.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_hlvhriy0 SRR12670143.sra spots: 10449564 blocks: [[1, 522478], [522479, 1044956], [1044957, 1567434], [1567435, 2089912], [2089913, 2612390], [2612391, 3134868], [3134869, 3657346], [3657347, 4179824], [4179825, 4702302], [4702303, 5224780], [5224781, 5747258], [5747259, 6269736], [6269737, 6792214], [6792215, 7314692], [7314693, 7837170], [7837171, 8359648], [8359649, 8882126], [8882127, 9404604], [9404605, 9927082], [9927083, 10449564]] SRR12670143 file size 3529518 SRR12670143 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 SRR12670143 SRR12670143_1.fastq SRR12670143_2.fastq Input file: SRR12670143_1.fastq Paired file: SRR12670143_2.fastq trimmed: SRR12670143-trimmed-pair1.fastq, SRR12670143-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 02:26:12 2025 >> started Tue Feb 11 02:29:20 2025 >> done (188.259s) 10449564 read pairs processed; of these: 127 ( 0.00%) short read pairs filtered out after trimming by size control 14010 ( 0.13%) empty read pairs filtered out after trimming by size control 10435427 (99.86%) read pairs available; of these: 4030530 (38.62%) trimmed read pairs available after processing 6404897 (61.38%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 8 0.00% 19 3 0.00% 20 7 0.00% 21 20 0.00% 22 27 0.00% 23 24 0.00% 24 26 0.00% 25 43 0.00% 26 48 0.00% 27 48 0.00% 28 47 0.00% 29 71 0.00% 30 64 0.00% 31 85 0.00% 32 92 0.00% 33 114 0.00% 34 120 0.00% 35 123 0.00% 36 146 0.00% 37 158 0.00% 38 194 0.00% 39 211 0.00% 40 266 0.00% 41 272 0.00% 42 311 0.00% 43 326 0.00% 44 334 0.00% 45 370 0.00% 46 407 0.00% 47 465 0.00% 48 571 0.01% 49 706 0.01% 50 867 0.01% 51 902 0.01% 52 1040 0.01% 53 1081 0.01% 54 1099 0.01% 55 1313 0.01% 56 1453 0.01% 57 1601 0.02% 58 1991 0.02% 59 2173 0.02% 60 2635 0.03% 61 3050 0.03% 62 3352 0.03% 63 3777 0.04% 64 3983 0.04% 65 4524 0.04% 66 4702 0.05% 67 5173 0.05% 68 5891 0.06% 69 6865 0.07% 70 7671 0.07% 71 8624 0.08% 72 10014 0.10% 73 10981 0.11% 74 11993 0.11% 75 12991 0.12% 76 13978 0.13% 77 14961 0.14% 78 16221 0.16% 79 18300 0.18% 80 19618 0.19% 81 21600 0.21% 82 23684 0.23% 83 25752 0.25% 84 27726 0.27% 85 29306 0.28% 86 31220 0.30% 87 31924 0.31% 88 33764 0.32% 89 35104 0.34% 90 37360 0.36% 91 39257 0.38% 92 41678 0.40% 93 44478 0.43% 94 46218 0.44% 95 48461 0.46% 96 49229 0.47% 97 50031 0.48% 98 50607 0.48% 99 51427 0.49% 100 53065 0.51% 101 53801 0.52% 102 55931 0.54% 103 57303 0.55% 104 58591 0.56% 105 59752 0.57% 106 60672 0.58% 107 60013 0.58% 108 59526 0.57% 109 59959 0.57% 110 60686 0.58% 111 60797 0.58% 112 62215 0.60% 113 62024 0.59% 114 62871 0.60% 115 63609 0.61% 116 63729 0.61% 117 64159 0.61% 118 63832 0.61% 119 62475 0.60% 120 63397 0.61% 121 63480 0.61% 122 63754 0.61% 123 64460 0.62% 124 64852 0.62% 125 63781 0.61% 126 64378 0.62% 127 63682 0.61% 128 62671 0.60% 129 63061 0.60% 130 62567 0.60% 131 61100 0.59% 132 61914 0.59% 133 62443 0.60% 134 61715 0.59% 135 61782 0.59% 136 61694 0.59% 137 60897 0.58% 138 60553 0.58% 139 61391 0.59% 140 59155 0.57% 141 59936 0.57% 142 59864 0.57% 143 58641 0.56% 144 59412 0.57% 145 58984 0.57% 146 58362 0.56% 147 58543 0.56% 148 58004 0.56% 149 56712 0.54% 150 56978 0.55% 151 6404897 61.38% 10435427 reads passed initial QC criterion=sequence-density sequence-density=0.29 sequence-density-rank=1 fanout-score=3.15 fanout-score-rank=16 prefix-density=0.36 prefix-fanout=2.5 sequence=GAGGAAGCCATCTCTTACA criterion=fanout-score sequence-density=0.04 sequence-density-rank=28 fanout-score=30.62 fanout-score-rank=1 prefix-density=0.15 prefix-fanout=8.4 sequence=AATGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTGTAGC criterion=sequence-density sequence-density=0.46 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=32 prefix-density=0.45 prefix-fanout=2.0 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.02 sequence-density-rank=33 fanout-score=59.36 fanout-score-rank=1 prefix-density=0.10 prefix-fanout=9.5 sequence=AAACCCAAAGCTCAAAAAAAATCTTAACTGCACCCGCTCATCCAGCAATGGCAGCAGCAACAATGGCCCTCTC SRR12670143 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 02:47:04 Started mapping on | Feb 11 02:47:09 Finished on | Feb 11 03:22:47 Mapping speed, Million of reads per hour | 17.57 Number of input reads | 10435427 Average input read length | 275 UNIQUE READS: Uniquely mapped reads number | 9799445 Uniquely mapped reads % | 93.91% Average mapped length | 273.40 Number of splices: Total | 8846971 Number of splices: Annotated (sjdb) | 8631835 Number of splices: GT/AG | 8666766 Number of splices: GC/AG | 138176 Number of splices: AT/AC | 5896 Number of splices: Non-canonical | 36133 Mismatch rate per base, % | 0.34% Deletion rate per base | 0.03% Deletion average length | 2.85 Insertion rate per base | 0.02% Insertion average length | 2.37 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 240698 % of reads mapped to multiple loci | 2.31% Number of reads mapped to too many loci | 37585 % of reads mapped to too many loci | 0.36% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.30% % of reads unmapped: other | 0.13% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 395284 395284 395284 N_multimapping 240698 240698 240698 N_noFeature 408263 9654313 483157 N_ambiguous 123496 586 52864 UnstrandedReadsAssigned:9267686 PositiveStrandReadsAssigned:144546 NegativeStrandReadsAssigned:9263424 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=118 echo kmer=113 SRR12670143 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: SRR12670143-trimmed-pair1.fastq SRR12670143-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 10,435,427 reads, 9,311,026 reads pseudoaligned [quant] estimated average fragment length: 179.397 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 981 rounds 52401 SRR12670143.ke.tsv 34699 SRR12670143.se.tsv 87100 total ==> SRR12670143.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1839.6 593 36.5842 Potri.005G024800.1.v4.1 1035 856.603 143 18.9461 Potri.004G059700.1.v4.1 961 782.684 0 0 Potri.007G009000.2.v4.1 1416 1237.6 0 0 Potri.003G141000.2.v4.1 2943 2764.6 506 20.7721 Potri.016G087400.1.v4.1 270 119.843 409 387.323 Potri.015G069301.1.v4.1 564 390.516 0 0 Potri.010G195200.1.v4.1 1773 1594.6 44 3.13158 Potri.012G127500.1.v4.1 977 798.644 51 7.24737 ==> SRR12670143.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 162 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 130 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 8 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 24 SRR12670143 completed mapping pipeline successfully