Starting /dee2/code/volunteer_pipeline.sh SRR12670135 current disk space = 3057265709056 free memory = 1460571536 SRR12670135 SRAfilesize bc438566722c232107156f83b266d7cd SRR12670135.sra SRR12670135.sra file validated SRR12670135 is paired end SRR12670135 is conventional basespace SRR12670135 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670135_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 36.6725 37.0 37.0 37.0 37.0 37.0 2 36.495 37.0 37.0 37.0 37.0 37.0 3 36.5745 37.0 37.0 37.0 37.0 37.0 4 36.702 37.0 37.0 37.0 37.0 37.0 5 36.703 37.0 37.0 37.0 37.0 37.0 6 36.65 37.0 37.0 37.0 37.0 37.0 7 36.688 37.0 37.0 37.0 37.0 37.0 8 36.6455 37.0 37.0 37.0 37.0 37.0 9 36.676 37.0 37.0 37.0 37.0 37.0 10-14 36.669799999999995 37.0 37.0 37.0 37.0 37.0 15-19 36.6314 37.0 37.0 37.0 37.0 37.0 20-24 36.6077 37.0 37.0 37.0 37.0 37.0 25-29 36.5935 37.0 37.0 37.0 37.0 37.0 30-34 36.5505 37.0 37.0 37.0 37.0 37.0 35-39 36.5268 37.0 37.0 37.0 37.0 37.0 40-44 36.5111 37.0 37.0 37.0 37.0 37.0 45-49 36.4811 37.0 37.0 37.0 37.0 37.0 50-54 36.4949 37.0 37.0 37.0 37.0 37.0 55-59 36.4746 37.0 37.0 37.0 37.0 37.0 60-64 36.4518 37.0 37.0 37.0 37.0 37.0 65-69 36.4203 37.0 37.0 37.0 37.0 37.0 70-74 36.3949 37.0 37.0 37.0 37.0 37.0 75-79 36.3532 37.0 37.0 37.0 37.0 37.0 80-84 36.4103 37.0 37.0 37.0 37.0 37.0 85-89 36.34 37.0 37.0 37.0 37.0 37.0 90-94 36.336 37.0 37.0 37.0 37.0 37.0 95-99 36.33540000000001 37.0 37.0 37.0 37.0 37.0 100-104 36.34349999999999 37.0 37.0 37.0 37.0 37.0 105-109 36.3586 37.0 37.0 37.0 37.0 37.0 110-114 36.3082 37.0 37.0 37.0 37.0 37.0 115-119 36.2624 37.0 37.0 37.0 37.0 37.0 120-124 36.2128 37.0 37.0 37.0 37.0 37.0 125-129 36.1745 37.0 37.0 37.0 37.0 37.0 130-134 36.0256 37.0 37.0 37.0 37.0 37.0 135-139 35.9203 37.0 37.0 37.0 37.0 37.0 140-144 35.7155 37.0 37.0 37.0 37.0 37.0 145-149 35.5188 37.0 37.0 37.0 37.0 37.0 150-151 35.247749999999996 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 1.0 24 0.0 25 0.0 26 2.0 27 5.0 28 5.0 29 10.0 30 22.0 31 29.0 32 40.0 33 63.0 34 124.0 35 319.0 36 2982.0 37 397.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 48.475 11.875 5.55 34.1 2 21.478696741854638 11.729323308270677 36.31578947368421 30.476190476190478 3 16.875 16.075 31.125000000000004 35.925000000000004 4 22.05 26.35 24.025 27.575 5 23.825 31.05 23.95 21.175 6 20.424999999999997 34.449999999999996 23.674999999999997 21.45 7 17.4 26.174999999999997 39.324999999999996 17.1 8 18.625 25.35 31.35 24.675 9 17.375 22.85 36.449999999999996 23.325000000000003 10-14 20.560000000000002 29.12 26.825 23.494999999999997 15-19 20.830000000000002 27.805000000000003 27.605 23.76 20-24 20.005 27.38 27.97 24.645 25-29 20.695 28.249999999999996 27.005000000000003 24.05 30-34 20.59 27.765 27.375 24.27 35-39 20.424999999999997 27.650000000000002 27.99 23.935000000000002 40-44 20.865000000000002 28.754999999999995 26.41 23.97 45-49 20.95 27.779999999999998 27.384999999999998 23.885 50-54 20.415 28.4 27.735 23.45 55-59 21.04 27.755000000000003 26.985 24.22 60-64 20.810000000000002 27.665 27.589999999999996 23.935000000000002 65-69 21.245 27.855 27.455000000000002 23.445 70-74 20.990000000000002 28.305000000000003 26.915 23.79 75-79 20.825 27.92 27.63 23.625 80-84 21.795 27.57 26.939999999999998 23.695 85-89 21.6 28.43 26.384999999999998 23.585 90-94 21.16 27.400000000000002 27.55 23.89 95-99 21.55 28.299999999999997 26.625 23.525 100-104 21.44 27.944999999999997 26.995 23.62 105-109 21.445 28.225 26.615 23.715 110-114 21.87 28.68 25.779999999999998 23.669999999999998 115-119 22.165000000000003 27.839999999999996 25.564999999999998 24.43 120-124 22.35 28.005000000000003 25.619999999999997 24.025 125-129 22.645 28.455000000000002 24.975 23.925 130-134 22.21 28.04 25.395 24.355 135-139 23.03 28.294999999999998 24.42 24.255 140-144 23.494999999999997 28.16 25.05 23.294999999999998 145-149 23.09 27.24 25.619999999999997 24.05 150-151 24.1125 26.674999999999997 26.3 22.912499999999998 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 1.0 22 1.0 23 1.5 24 3.5 25 2.0 26 2.5 27 4.5 28 4.5 29 6.5 30 13.0 31 20.0 32 22.0 33 28.5 34 43.0 35 54.0 36 75.5 37 91.5 38 105.0 39 131.0 40 163.5 41 194.5 42 221.5 43 233.5 44 246.0 45 274.5 46 266.0 47 248.5 48 239.0 49 238.5 50 225.0 51 186.5 52 157.5 53 121.0 54 96.0 55 72.0 56 51.0 57 45.0 58 31.5 59 29.5 60 21.5 61 8.5 62 5.0 63 3.5 64 3.5 65 2.5 66 2.0 67 1.0 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 0.25 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 81.35 #Duplication Level Percentage of deduplicated Percentage of total 1 82.5138291333743 67.125 2 13.675476336816224 22.25 3 2.8887523048555623 7.049999999999999 4 0.5531653349723417 1.7999999999999998 5 0.15365703749231713 0.625 6 0.15365703749231713 0.75 7 0.030731407498463426 0.17500000000000002 8 0.0 0.0 9 0.030731407498463426 0.22499999999999998 >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 CATATTGCTGCCTTAGGCTACCCAAGTTGTCTAGAGCTCCCTCAAACAAG 9 0.22499999999999998 No Hit ATTACTTTCCCAAGTGCAATAGGGTGGACTGCTTTGGAAGAGTAACCCCC 7 0.17500000000000002 No Hit CTCGCCTCTTACAGCATACTGAACCTTCTTGACATTTTCATTCAACGATT 6 0.15 No Hit CTCCCTTGAACCATCTCTTGTCTCCAGCTTGTGCCTTGCAAATGTAAAGC 6 0.15 No Hit CTAAGCAAACAGCTCCGCTTGAAACAGCAGTCTCGACAATAGTAATGGGA 6 0.15 No Hit AGTGACGATGATGGGGACACGTGGATTCTCCTCCTTGTTGTACATGCCGG 6 0.15 No Hit AATAATTATCAAAAAGCTCGTGATCACGTGTATCCTACTAAAGGTGCTGA 6 0.15 No Hit CCCTGGTGAGCTGTGGTGCTCACGGTAGACCCAACCTTTCTCCAACTCGA 5 0.125 No Hit CCTGGACCAAGAAGGTGACCTAACAACATCTCTCAACCCCTTAGGAGAAG 5 0.125 No Hit GACCTCGTTGTCTCGGTAGCCACAAGCGAAGCAGTTGGTCGACATAATGA 5 0.125 No Hit GGTACACTGCACATCAGGCATTATCCCAACTTGATCTATGTCATGAAGTG 5 0.125 No Hit GCCCTGTATCCCTCTCCTTTGCAACCCTCAGACTTTGCAGGGAGGGGCTG 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 0.025 0.0 0.0 0.0 0.0 24-25 0.05 0.0 0.0 0.0 0.0 26-27 0.05 0.0 0.0 0.0 0.0 28-29 0.05 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.05 0.0 0.0 0.0 0.0 36-37 0.05 0.0 0.0 0.0 0.0 38-39 0.05 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 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 0.05 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 0.0625 0.0 0.0 0.0 0.0 62-63 0.15 0.0 0.0 0.0 0.0 64-65 0.175 0.0 0.0 0.0 0.0 66-67 0.2375 0.0 0.0 0.0 0.0 68-69 0.3125 0.0 0.0 0.0 0.0 70-71 0.35 0.0 0.0 0.0 0.0 72-73 0.4125 0.0 0.0 0.0 0.0 74-75 0.6000000000000001 0.0 0.0 0.0 0.0 76-77 0.8125 0.0 0.0 0.0 0.0 78-79 0.9750000000000001 0.0 0.0 0.0 0.0 80-81 1.4375 0.0 0.0 0.0 0.0 82-83 1.7875 0.0 0.0 0.0 0.0 84-85 2.1125 0.0 0.0 0.0 0.0 86-87 2.5625 0.0 0.0 0.0 0.0 88-89 3.25 0.0 0.0 0.0 0.0 90-91 3.8875 0.0 0.0 0.0 0.0 92-93 4.4375 0.0 0.0 0.0 0.0 94-95 5.125 0.0 0.0 0.0 0.0 96-97 5.8 0.0 0.0 0.0 0.0 98-99 6.6 0.0 0.0 0.0 0.0 100-101 7.4875 0.0 0.0 0.0 0.0 102-103 8.1875 0.0 0.0 0.0 0.0 104-105 9.3 0.0 0.0 0.0 0.0 106-107 10.5625 0.0 0.0 0.0 0.0 108-109 11.375 0.0 0.0 0.0 0.0 110-111 12.162500000000001 0.0 0.0 0.0 0.0 112-113 13.25 0.0 0.0 0.0 0.0 114-115 14.600000000000001 0.0 0.0 0.0 0.0 116-117 15.675 0.0 0.0 0.0 0.0 118-119 16.5375 0.0 0.0 0.0 0.0 120-121 17.6875 0.0 0.0 0.0 0.0 122-123 18.775 0.0 0.0 0.0 0.0 124-125 19.7875 0.0 0.0 0.0 0.0 126-127 20.8 0.0 0.0 0.0 0.0 128-129 21.8125 0.0 0.0 0.0 0.0 130-131 23.049999999999997 0.0 0.0 0.0 0.0 132-133 24.299999999999997 0.0 0.0 0.0 0.0 134-135 25.525 0.0 0.0 0.0 0.0 136-137 26.4875 0.0 0.0 0.0 0.0 138-139 27.4375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12670135 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670135_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 36.323 37.0 37.0 37.0 37.0 37.0 2 36.0705 37.0 37.0 37.0 37.0 37.0 3 36.259 37.0 37.0 37.0 37.0 37.0 4 36.3165 37.0 37.0 37.0 37.0 37.0 5 36.354 37.0 37.0 37.0 37.0 37.0 6 36.35 37.0 37.0 37.0 37.0 37.0 7 36.2715 37.0 37.0 37.0 37.0 37.0 8 36.4555 37.0 37.0 37.0 37.0 37.0 9 36.4295 37.0 37.0 37.0 37.0 37.0 10-14 36.383799999999994 37.0 37.0 37.0 37.0 37.0 15-19 36.363 37.0 37.0 37.0 37.0 37.0 20-24 36.3267 37.0 37.0 37.0 37.0 37.0 25-29 36.2934 37.0 37.0 37.0 37.0 37.0 30-34 36.264300000000006 37.0 37.0 37.0 37.0 37.0 35-39 36.2431 37.0 37.0 37.0 37.0 37.0 40-44 36.1871 37.0 37.0 37.0 37.0 37.0 45-49 36.2207 37.0 37.0 37.0 37.0 37.0 50-54 36.1391 37.0 37.0 37.0 37.0 37.0 55-59 36.148199999999996 37.0 37.0 37.0 37.0 37.0 60-64 36.1372 37.0 37.0 37.0 37.0 37.0 65-69 36.07619999999999 37.0 37.0 37.0 37.0 37.0 70-74 36.064 37.0 37.0 37.0 37.0 37.0 75-79 36.062 37.0 37.0 37.0 37.0 37.0 80-84 36.0254 37.0 37.0 37.0 37.0 37.0 85-89 36.0065 37.0 37.0 37.0 37.0 37.0 90-94 35.9938 37.0 37.0 37.0 37.0 37.0 95-99 35.8936 37.0 37.0 37.0 37.0 37.0 100-104 35.8894 37.0 37.0 37.0 37.0 37.0 105-109 35.779700000000005 37.0 37.0 37.0 37.0 37.0 110-114 35.6971 37.0 37.0 37.0 37.0 37.0 115-119 35.742399999999996 37.0 37.0 37.0 37.0 37.0 120-124 35.5727 37.0 37.0 37.0 37.0 37.0 125-129 35.4541 37.0 37.0 37.0 37.0 37.0 130-134 35.2429 37.0 37.0 37.0 34.6 37.0 135-139 35.004999999999995 37.0 37.0 37.0 25.0 37.0 140-144 34.8267 37.0 37.0 37.0 25.0 37.0 145-149 34.49730000000001 37.0 37.0 37.0 25.0 37.0 150-151 34.177499999999995 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 2.0 14 1.0 15 1.0 16 2.0 17 1.0 18 1.0 19 0.0 20 0.0 21 0.0 22 2.0 23 2.0 24 5.0 25 8.0 26 7.0 27 8.0 28 8.0 29 16.0 30 23.0 31 42.0 32 64.0 33 103.0 34 243.0 35 733.0 36 2518.0 37 209.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.95 25.074999999999996 7.95 24.025 2 28.275 27.575 28.849999999999998 15.299999999999999 3 21.224999999999998 27.075 32.875 18.825 4 23.5 34.150000000000006 24.275 18.075 5 24.375 38.95 20.95 15.725 6 22.675 38.15 22.525000000000002 16.650000000000002 7 20.724999999999998 20.95 38.375 19.950000000000003 8 19.950000000000003 26.35 29.65 24.05 9 22.525000000000002 24.975 29.45 23.05 10-14 23.055 29.544999999999998 26.340000000000003 21.060000000000002 15-19 22.685 28.255000000000003 27.775 21.285 20-24 23.28 27.905 28.044999999999998 20.77 25-29 23.05 27.815 28.005000000000003 21.13 30-34 23.47 27.755000000000003 27.66 21.115000000000002 35-39 22.925 27.96 27.284999999999997 21.83 40-44 23.735 27.334999999999997 27.98 20.95 45-49 23.28 27.544999999999998 26.924999999999997 22.25 50-54 23.064999999999998 28.105000000000004 27.500000000000004 21.33 55-59 22.97 28.194999999999997 27.66 21.175 60-64 23.775 26.665 28.335 21.224999999999998 65-69 23.075000000000003 27.165 27.894999999999996 21.865000000000002 70-74 23.74 27.905 27.24 21.115000000000002 75-79 23.32 27.825 27.18 21.675 80-84 24.15 28.26 26.605 20.985 85-89 25.0 28.57 26.119999999999997 20.31 90-94 24.47 27.26 26.314999999999998 21.955 95-99 25.0 27.68 26.96 20.36 100-104 25.424999999999997 27.93 26.205000000000002 20.44 105-109 25.885 27.815 26.314999999999998 19.985 110-114 26.43 28.549999999999997 25.41 19.61 115-119 27.57 28.58 24.795 19.055 120-124 28.310000000000002 27.389999999999997 25.685000000000002 18.615000000000002 125-129 29.099999999999998 27.694999999999997 24.55 18.655 130-134 30.285 28.060000000000002 23.94 17.715 135-139 31.374999999999996 26.545 24.349999999999998 17.73 140-144 33.08 26.52 23.575 16.825000000000003 145-149 35.065000000000005 25.165 23.885 15.885 150-151 35.5375 25.85 22.325 16.287499999999998 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.5 3 1.5 4 1.0 5 0.0 6 0.5 7 0.5 8 0.5 9 0.5 10 0.0 11 0.0 12 0.0 13 0.0 14 0.5 15 1.0 16 1.5 17 1.5 18 0.5 19 0.0 20 0.0 21 0.0 22 0.0 23 0.5 24 2.5 25 2.0 26 1.0 27 3.0 28 3.0 29 6.5 30 14.0 31 19.5 32 20.5 33 27.5 34 47.0 35 61.0 36 75.5 37 101.5 38 119.5 39 144.5 40 195.0 41 217.0 42 222.0 43 264.0 44 276.0 45 259.0 46 259.5 47 237.0 48 226.0 49 221.0 50 191.5 51 168.5 52 140.0 53 104.5 54 89.5 55 75.0 56 52.5 57 42.5 58 32.0 59 23.5 60 13.5 61 6.5 62 5.0 63 2.5 64 2.5 65 1.5 66 0.5 67 0.0 68 0.0 69 0.0 70 0.5 71 0.5 72 1.0 73 1.0 74 0.0 75 0.0 76 0.0 77 0.0 78 1.0 79 1.0 80 1.0 81 1.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.5 89 0.5 90 0.0 91 0.0 92 0.0 93 0.0 94 0.5 95 0.5 96 0.0 97 0.0 98 0.0 99 0.0 100 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 81.625 #Duplication Level Percentage of deduplicated Percentage of total 1 83.03215926493108 67.77499999999999 2 13.35375191424196 21.8 3 2.572741194486983 6.3 4 0.5206738131699847 1.7000000000000002 5 0.27565084226646247 1.125 6 0.18376722817764166 0.8999999999999999 7 0.030627871362940276 0.17500000000000002 8 0.0 0.0 9 0.030627871362940276 0.22499999999999998 >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 TTTTATTTTTAAAAAATGTTAGGAGTGTTTAGCAGCGCGATTGTGTCGCC 9 0.22499999999999998 No Hit GCAAAGATGACTCCTAACATCACCGACATAACACAGCCTGCTAGGGTGTC 7 0.17500000000000002 No Hit GAAGAAGGGAAAGATGTGCTGCCTCTTCATCAACGATCTTGATGCCGGAG 6 0.15 No Hit AGATTTGATGAGCATGACCGCGATTCGTTCCATTTAAGATTGCAATTTGC 6 0.15 No Hit CAAGGACTGCTGATGGAGATGAAGGTGGCAAGCACCAACTTATCACAGCC 6 0.15 No Hit AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 6 0.15 No Hit TAATTCTTTCTTCTAAATCACTTTGTTAATTTCTGATACCAAGCAGTGTA 6 0.15 No Hit GACGAGTTCAATGCATGCAGGTGTGGCCACCAACTGGATTGAAGAAGTTC 6 0.15 No Hit GGCAAGCACAAGCTTGCGACCAAGGAGGACTTTGAGCAGCACCGTCGAAA 5 0.125 No Hit AACACATGATCCACTTGTTGTGCTTGTCAATGAGGGAAGTGCAAGCGCAA 5 0.125 No Hit GAGCTTGAGTGCATTCTTCTAAGTAAAAGAAATCCCTTAATTTCATCACA 5 0.125 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 5 0.125 No Hit GGTTATTCATCGACCGGAGAGTTTAGCTGGGTCGAGGAGGGAGTTTCCTA 5 0.125 No Hit AGAGTAGCATCCTTAGCGTTGCTGGTTTACTTTCCTAACAATCCTCAAAA 5 0.125 No Hit AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 5 0.125 No Hit GAAAAATTCTTCCCTTGTGCGTGCAGCCCAGCCCCAGCAGAAAACACACA 5 0.125 No Hit AGTAAAAACAACCGGTTTATTCCAAATTCTTTGAAATTCATTTCTTCTTG 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 0.025 0.0 0.0 0.0 0.0 24-25 0.05 0.0 0.0 0.0 0.0 26-27 0.05 0.0 0.0 0.0 0.0 28-29 0.05 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.05 0.0 0.0 0.0 0.0 36-37 0.05 0.0 0.0 0.0 0.0 38-39 0.05 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 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 0.05 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 0.0625 0.0 0.0 0.0 0.0 62-63 0.15 0.0 0.0 0.0 0.0 64-65 0.175 0.0 0.0 0.0 0.0 66-67 0.2375 0.0 0.0 0.0 0.0 68-69 0.3125 0.0 0.0 0.0 0.0 70-71 0.35 0.0 0.0 0.0 0.0 72-73 0.4125 0.0 0.0 0.0 0.0 74-75 0.6000000000000001 0.0 0.0 0.0 0.0 76-77 0.8125 0.0 0.0 0.0 0.0 78-79 0.9750000000000001 0.0 0.0 0.0 0.0 80-81 1.4625 0.0 0.0 0.0 0.0 82-83 1.8375 0.0 0.0 0.0 0.0 84-85 2.1625 0.0 0.0 0.0 0.0 86-87 2.6125 0.0 0.0 0.0 0.0 88-89 3.3 0.0 0.0 0.0 0.0 90-91 3.9375 0.0 0.0 0.0 0.0 92-93 4.4875 0.0 0.0 0.0 0.0 94-95 5.175 0.0 0.0 0.0 0.0 96-97 5.85 0.0 0.0 0.0 0.0 98-99 6.6875 0.0 0.0 0.0 0.0 100-101 7.6125 0.0 0.0 0.0 0.0 102-103 8.325 0.0 0.0 0.0 0.0 104-105 9.475 0.0 0.0 0.0 0.0 106-107 10.7375 0.0 0.0 0.0 0.0 108-109 11.55 0.0 0.0 0.0 0.0 110-111 12.337499999999999 0.0 0.0 0.0 0.0 112-113 13.425 0.0 0.0 0.0 0.0 114-115 14.75 0.0 0.0 0.0 0.0 116-117 15.825 0.0 0.0 0.0 0.0 118-119 16.6875 0.0 0.0 0.0 0.0 120-121 17.8375 0.0 0.0 0.0 0.0 122-123 18.9 0.0 0.0 0.0 0.0 124-125 19.8875 0.0 0.0 0.0 0.0 126-127 20.9125 0.0 0.0 0.0 0.0 128-129 21.9375 0.0 0.0 0.0 0.0 130-131 23.174999999999997 0.0 0.0 0.0 0.0 132-133 24.424999999999997 0.0 0.0 0.0 0.0 134-135 25.65 0.0 0.0 0.0 0.0 136-137 26.625 0.0 0.0 0.0 0.0 138-139 27.575 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTTTTTC 10 0.006830828 145.0 1 >>END_MODULE Read 671748 spots for SRR12670135.sra Written 671748 spots for SRR12670135.sra Read 671748 spots for SRR12670135.sra Written 671748 spots for SRR12670135.sra Read 671748 spots for SRR12670135.sra Written 671748 spots for SRR12670135.sra Read 671748 spots for SRR12670135.sra Written 671748 spots for SRR12670135.sra Read 671748 spots for SRR12670135.sra Written 671748 spots for SRR12670135.sra Read 671748 spots for SRR12670135.sra Written 671748 spots for SRR12670135.sra Read 671748 spots for SRR12670135.sra Written 671748 spots for SRR12670135.sra Read 671748 spots for SRR12670135.sra Written 671748 spots for SRR12670135.sra Read 671748 spots for SRR12670135.sra Written 671748 spots for SRR12670135.sra Read 671754 spots for SRR12670135.sra Written 671754 spots for SRR12670135.sra Read 671748 spots for SRR12670135.sra Written 671748 spots for SRR12670135.sra Read 671748 spots for SRR12670135.sra Written 671748 spots for SRR12670135.sra Read 671748 spots for SRR12670135.sra Written 671748 spots for SRR12670135.sra Read 671748 spots for SRR12670135.sra Written 671748 spots for SRR12670135.sra Read 671748 spots for SRR12670135.sra Written 671748 spots for SRR12670135.sra Read 671748 spots for SRR12670135.sra Written 671748 spots for SRR12670135.sra Read 671748 spots for SRR12670135.sra Written 671748 spots for SRR12670135.sra Read 671748 spots for SRR12670135.sra Written 671748 spots for SRR12670135.sra Read 671748 spots for SRR12670135.sra Written 671748 spots for SRR12670135.sra Read 671748 spots for SRR12670135.sra Written 671748 spots for SRR12670135.sra SRR ids: ['SRR12670135.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_vhgvyrgu SRR12670135.sra spots: 13434966 blocks: [[1, 671748], [671749, 1343496], [1343497, 2015244], [2015245, 2686992], [2686993, 3358740], [3358741, 4030488], [4030489, 4702236], [4702237, 5373984], [5373985, 6045732], [6045733, 6717480], [6717481, 7389228], [7389229, 8060976], [8060977, 8732724], [8732725, 9404472], [9404473, 10076220], [10076221, 10747968], [10747969, 11419716], [11419717, 12091464], [12091465, 12763212], [12763213, 13434966]] SRR12670135 file size 4544088 SRR12670135 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 SRR12670135 SRR12670135_1.fastq SRR12670135_2.fastq Input file: SRR12670135_1.fastq Paired file: SRR12670135_2.fastq trimmed: SRR12670135-trimmed-pair1.fastq, SRR12670135-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 01:03:24 2025 >> started Tue Feb 11 01:03:46 2025 >> done (22.268s) 13434966 read pairs processed; of these: 115 ( 0.00%) short read pairs filtered out after trimming by size control 13772 ( 0.10%) empty read pairs filtered out after trimming by size control 13421079 (99.90%) read pairs available; of these: 4175336 (31.11%) trimmed read pairs available after processing 9245743 (68.89%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 6 0.00% 19 11 0.00% 20 33 0.00% 21 35 0.00% 22 56 0.00% 23 67 0.00% 24 105 0.00% 25 97 0.00% 26 130 0.00% 27 134 0.00% 28 110 0.00% 29 127 0.00% 30 134 0.00% 31 160 0.00% 32 167 0.00% 33 186 0.00% 34 199 0.00% 35 234 0.00% 36 203 0.00% 37 234 0.00% 38 247 0.00% 39 300 0.00% 40 346 0.00% 41 340 0.00% 42 357 0.00% 43 364 0.00% 44 402 0.00% 45 431 0.00% 46 540 0.00% 47 588 0.00% 48 693 0.01% 49 828 0.01% 50 961 0.01% 51 1033 0.01% 52 1120 0.01% 53 1220 0.01% 54 1182 0.01% 55 1396 0.01% 56 1550 0.01% 57 1726 0.01% 58 2052 0.02% 59 2303 0.02% 60 2753 0.02% 61 3262 0.02% 62 3735 0.03% 63 3834 0.03% 64 4155 0.03% 65 4472 0.03% 66 4973 0.04% 67 5259 0.04% 68 6037 0.04% 69 6858 0.05% 70 8211 0.06% 71 9096 0.07% 72 10355 0.08% 73 11320 0.08% 74 12279 0.09% 75 13199 0.10% 76 14044 0.10% 77 14742 0.11% 78 16296 0.12% 79 17756 0.13% 80 19742 0.15% 81 21752 0.16% 82 24109 0.18% 83 25996 0.19% 84 27685 0.21% 85 29423 0.22% 86 30261 0.23% 87 31373 0.23% 88 32771 0.24% 89 34055 0.25% 90 36797 0.27% 91 38794 0.29% 92 40932 0.30% 93 43947 0.33% 94 45558 0.34% 95 47829 0.36% 96 48284 0.36% 97 49112 0.37% 98 49183 0.37% 99 50479 0.38% 100 51749 0.39% 101 52368 0.39% 102 55554 0.41% 103 56505 0.42% 104 58577 0.44% 105 59476 0.44% 106 59825 0.45% 107 59868 0.45% 108 59542 0.44% 109 59637 0.44% 110 59348 0.44% 111 61063 0.45% 112 62456 0.47% 113 63101 0.47% 114 64781 0.48% 115 65203 0.49% 116 65624 0.49% 117 65928 0.49% 118 65083 0.48% 119 64542 0.48% 120 64392 0.48% 121 65069 0.48% 122 64924 0.48% 123 66287 0.49% 124 67793 0.51% 125 67277 0.50% 126 68296 0.51% 127 67479 0.50% 128 67359 0.50% 129 66406 0.49% 130 65968 0.49% 131 65596 0.49% 132 65941 0.49% 133 66954 0.50% 134 66881 0.50% 135 67237 0.50% 136 66947 0.50% 137 66019 0.49% 138 66431 0.49% 139 66429 0.49% 140 64776 0.48% 141 65224 0.49% 142 64352 0.48% 143 65033 0.48% 144 65840 0.49% 145 65374 0.49% 146 65079 0.48% 147 64301 0.48% 148 64435 0.48% 149 63881 0.48% 150 64001 0.48% 151 9245743 68.89% 13421079 reads passed initial QC criterion=sequence-density sequence-density=0.56 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=23 prefix-density=0.57 prefix-fanout=2.0 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTTCGAGCGAAGAAGGT criterion=fanout-score sequence-density=0.03 sequence-density-rank=27 fanout-score=111.23 fanout-score-rank=1 prefix-density=0.27 prefix-fanout=12.8 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTC criterion=sequence-density sequence-density=0.73 sequence-density-rank=1 fanout-score=2.10 fanout-score-rank=24 prefix-density=0.74 prefix-fanout=2.1 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=40.40 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=1.9 sequence=GGAACTCAAACGCATAGCTTCCTACAAATACCCCAGCTAGCCAATACTCTCCACCACTAAACCCAAAGCTCAAAAAAAATCTTAACTGCACCCGCTCATCCAGCAATGGCAGCAGCAACAATGGCCCTCTC SRR12670135 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 01:04:36 Started mapping on | Feb 11 01:04:37 Finished on | Feb 11 01:06:53 Mapping speed, Million of reads per hour | 355.26 Number of input reads | 13421079 Average input read length | 280 UNIQUE READS: Uniquely mapped reads number | 12517585 Uniquely mapped reads % | 93.27% Average mapped length | 279.34 Number of splices: Total | 11583358 Number of splices: Annotated (sjdb) | 11339912 Number of splices: GT/AG | 11342024 Number of splices: GC/AG | 193382 Number of splices: AT/AC | 6890 Number of splices: Non-canonical | 41062 Mismatch rate per base, % | 0.34% Deletion rate per base | 0.03% Deletion average length | 2.82 Insertion rate per base | 0.02% Insertion average length | 2.34 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 311038 % of reads mapped to multiple loci | 2.32% Number of reads mapped to too many loci | 49933 % of reads mapped to too many loci | 0.37% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.91% % of reads unmapped: other | 0.13% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 592456 592456 592456 N_multimapping 311038 311038 311038 N_noFeature 420540 12325380 507251 N_ambiguous 183296 727 77345 UnstrandedReadsAssigned:11913749 PositiveStrandReadsAssigned:191478 NegativeStrandReadsAssigned:11932989 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=128 echo kmer=123 SRR12670135 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: SRR12670135-trimmed-pair1.fastq SRR12670135-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,421,079 reads, 12,002,357 reads pseudoaligned [quant] estimated average fragment length: 198.367 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,111 rounds 52401 SRR12670135.ke.tsv 34699 SRR12670135.se.tsv 87100 total ==> SRR12670135.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1820.63 423 19.6561 Potri.005G024800.1.v4.1 1035 837.633 141 14.2411 Potri.004G059700.1.v4.1 961 763.667 5 0.553918 Potri.007G009000.2.v4.1 1416 1218.63 0 0 Potri.003G141000.2.v4.1 2943 2745.63 739.422 22.784 Potri.016G087400.1.v4.1 270 115.657 485 354.771 Potri.015G069301.1.v4.1 564 373.837 0 0 Potri.010G195200.1.v4.1 1773 1575.63 39 2.09406 Potri.012G127500.1.v4.1 977 779.643 95 10.3088 ==> SRR12670135.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 312 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 170 Potri.001G212900.v4.1 6 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 6 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR12670135 completed mapping pipeline successfully