Starting /dee2/code/volunteer_pipeline.sh SRR12951294 current disk space = 1543369342976 free memory = 1601271216 SRR12951294 SRAfilesize e521ad7b1edb5fb2ee2fdd9631e0e495 SRR12951294.sra SRR12951294.sra file validated SRR12951294 is paired end SRR12951294 is conventional basespace SRR12951294 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951294_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.4865 37.0 37.0 37.0 37.0 37.0 2 36.184 37.0 37.0 37.0 37.0 37.0 3 36.5815 37.0 37.0 37.0 37.0 37.0 4 36.511 37.0 37.0 37.0 37.0 37.0 5 36.518 37.0 37.0 37.0 37.0 37.0 6 36.658 37.0 37.0 37.0 37.0 37.0 7 36.595 37.0 37.0 37.0 37.0 37.0 8 36.601 37.0 37.0 37.0 37.0 37.0 9 36.576 37.0 37.0 37.0 37.0 37.0 10-14 36.5611 37.0 37.0 37.0 37.0 37.0 15-19 36.58670000000001 37.0 37.0 37.0 37.0 37.0 20-24 36.57860000000001 37.0 37.0 37.0 37.0 37.0 25-29 36.5415 37.0 37.0 37.0 37.0 37.0 30-34 36.534200000000006 37.0 37.0 37.0 37.0 37.0 35-39 36.5216 37.0 37.0 37.0 37.0 37.0 40-44 36.4385 37.0 37.0 37.0 37.0 37.0 45-49 36.4462 37.0 37.0 37.0 37.0 37.0 50-54 36.443599999999996 37.0 37.0 37.0 37.0 37.0 55-59 36.3806 37.0 37.0 37.0 37.0 37.0 60-64 36.339 37.0 37.0 37.0 37.0 37.0 65-69 36.2818 37.0 37.0 37.0 37.0 37.0 70-74 36.2742 37.0 37.0 37.0 37.0 37.0 75-79 36.263999999999996 37.0 37.0 37.0 37.0 37.0 80-84 36.287 37.0 37.0 37.0 37.0 37.0 85-89 36.216899999999995 37.0 37.0 37.0 37.0 37.0 90-94 36.24830000000001 37.0 37.0 37.0 37.0 37.0 95-99 36.173899999999996 37.0 37.0 37.0 37.0 37.0 100-104 36.1798 37.0 37.0 37.0 37.0 37.0 105-109 36.2585 37.0 37.0 37.0 37.0 37.0 110-114 36.1077 37.0 37.0 37.0 37.0 37.0 115-119 36.1778 37.0 37.0 37.0 37.0 37.0 120-124 36.1004 37.0 37.0 37.0 37.0 37.0 125-129 36.0243 37.0 37.0 37.0 37.0 37.0 130-134 36.0295 37.0 37.0 37.0 37.0 37.0 135-139 35.932900000000004 37.0 37.0 37.0 37.0 37.0 140-144 35.845699999999994 37.0 37.0 37.0 37.0 37.0 145-149 35.8166 37.0 37.0 37.0 37.0 37.0 150-151 35.60575 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 3.0 23 1.0 24 1.0 25 1.0 26 2.0 27 5.0 28 13.0 29 17.0 30 27.0 31 26.0 32 37.0 33 100.0 34 130.0 35 316.0 36 2850.0 37 470.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 42.699999999999996 12.275 5.45 39.574999999999996 2 22.035175879396984 11.331658291457286 34.07035175879397 32.562814070351756 3 20.025000000000002 15.0 25.624999999999996 39.35 4 24.2 21.025 22.475 32.300000000000004 5 26.825 27.55 23.200000000000003 22.425 6 24.6 30.575000000000003 22.3 22.525000000000002 7 18.95 27.250000000000004 33.675 20.125 8 21.8 24.725 28.275 25.2 9 22.0 22.1 30.5 25.4 10-14 23.145 26.295 24.535 26.025 15-19 23.62 24.905 25.4 26.075 20-24 23.105 25.86 24.715 26.32 25-29 23.53 25.72 24.79 25.96 30-34 23.365 25.045 25.255 26.334999999999997 35-39 23.625 25.259999999999998 24.465 26.650000000000002 40-44 24.365000000000002 24.685000000000002 25.074999999999996 25.874999999999996 45-49 24.095 25.069999999999997 24.705 26.13 50-54 23.59 24.88 25.0 26.529999999999998 55-59 23.815 25.369999999999997 23.990000000000002 26.825 60-64 23.89 24.39 24.8 26.919999999999998 65-69 24.005000000000003 25.275 25.174999999999997 25.545 70-74 24.965 24.135 24.19 26.71 75-79 24.95 24.47 24.279999999999998 26.3 80-84 24.705 24.79 24.245 26.26 85-89 24.205 24.73 24.705 26.36 90-94 25.319999999999997 24.349999999999998 24.315 26.015 95-99 24.98 24.525 24.654999999999998 25.840000000000003 100-104 24.705 24.995 24.38 25.919999999999998 105-109 24.474999999999998 24.815 24.834999999999997 25.874999999999996 110-114 24.855 24.884999999999998 23.745 26.515 115-119 25.005 24.6 24.099999999999998 26.295 120-124 25.83 24.82 23.225 26.125 125-129 25.069999999999997 25.34 23.39 26.200000000000003 130-134 25.25 24.610000000000003 23.685000000000002 26.455000000000002 135-139 25.180000000000003 25.045 23.275000000000002 26.5 140-144 25.169999999999998 24.775 23.419999999999998 26.634999999999998 145-149 25.785000000000004 24.4 23.535 26.279999999999998 150-151 25.95 24.7875 23.925 25.337500000000002 >>END_MODULE >>Per sequence GC content fail #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 0.0 22 0.0 23 0.0 24 0.5 25 0.5 26 0.5 27 1.0 28 4.0 29 5.0 30 4.0 31 7.0 32 13.0 33 18.5 34 19.0 35 29.0 36 50.5 37 68.5 38 78.0 39 100.5 40 119.0 41 126.0 42 154.5 43 166.5 44 168.0 45 190.5 46 187.0 47 183.5 48 189.0 49 175.0 50 159.5 51 150.0 52 144.5 53 121.5 54 94.5 55 93.5 56 97.0 57 76.5 58 70.5 59 71.0 60 59.0 61 71.5 62 73.0 63 65.5 64 63.0 65 63.5 66 67.0 67 55.5 68 54.0 69 57.5 70 46.5 71 38.0 72 30.5 73 24.0 74 21.0 75 15.5 76 16.5 77 12.5 78 8.0 79 7.0 80 4.0 81 1.5 82 1.5 83 3.5 84 2.5 85 0.0 86 0.5 87 0.5 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 0.5 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 78.925 #Duplication Level Percentage of deduplicated Percentage of total 1 80.32942667089009 63.4 2 14.82420019005385 23.400000000000002 3 3.4209692746278115 8.1 4 1.0769718086791258 3.4000000000000004 5 0.19005384859043395 0.75 6 0.06335128286347799 0.3 7 0.06335128286347799 0.35000000000000003 8 0.0 0.0 9 0.0 0.0 >10 0.031675641431738996 0.3 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCTGGATTATCTCGTAT 12 0.3 TruSeq Adapter, Index 25 (97% over 37bp) GCATGTTGATGGTGGCTTTGTTGACCTTCAGGAACACTCCATTGAAGATC 7 0.17500000000000002 No Hit GCTACCTGCTTCTGGTGCAACAAACTCCCATGGTGTGACGGGCGGTGTGT 7 0.17500000000000002 No Hit GTCGGCAATGGCGACGCCGCTCCAAGAGATCGCCGTGGTGAAGGTTGGAC 6 0.15 No Hit GTAGAATTTAGCTTCCTTTCTGTTGTACTGCTTGACCGTCTCCTTTAGCC 6 0.15 No Hit GCTCCAGCTCCGCCTCCGCGCCCACCTTCCCACGGTTCCCATTGTTGGTG 5 0.125 No Hit CTCCAGCTCCTTACCAGATCGCCTGTCGATCTTGGTCACCAGCTCCGCAA 5 0.125 No Hit GCTGGTATCTTGCGGAACCAAGTGATTAAAGGAAGTTGTTCAAATCATCT 5 0.125 No Hit ATCGAATTATTCACTCCGATGTTCAAAAAACCGTGGCGCAAAATGATGTG 5 0.125 No Hit GCCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTT 5 0.125 No Hit GCCGAAAAGAGGCGCCTCTCCGGGCCGACGCCCCAGGAGGCCGGGGAGGT 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 0.0125 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.037500000000000006 0.0 0.0 0.0 0.0 64-65 0.0875 0.0 0.0 0.0 0.0 66-67 0.1125 0.0 0.0 0.0 0.0 68-69 0.125 0.0 0.0 0.0 0.0 70-71 0.15 0.0 0.0 0.0 0.0 72-73 0.175 0.0 0.0 0.0 0.0 74-75 0.2375 0.0 0.0 0.0 0.0 76-77 0.3125 0.0 0.0 0.0 0.0 78-79 0.375 0.0 0.0 0.0 0.0 80-81 0.45 0.0 0.0 0.0 0.0 82-83 0.55 0.0 0.0 0.0 0.0 84-85 0.6625 0.0 0.0 0.0 0.0 86-87 0.8 0.0 0.0 0.0 0.0 88-89 1.0125 0.0 0.0 0.0 0.0 90-91 1.275 0.0 0.0 0.0 0.0 92-93 1.425 0.0 0.0 0.0 0.0 94-95 1.7125 0.0 0.0 0.0 0.0 96-97 1.9625 0.0 0.0 0.0 0.0 98-99 2.2375 0.0 0.0 0.0 0.0 100-101 2.7375 0.0 0.0 0.0 0.0 102-103 3.0625 0.0 0.0 0.0 0.0 104-105 3.35 0.0 0.0 0.0 0.0 106-107 3.8375 0.0 0.0 0.0 0.0 108-109 4.2875 0.0 0.0 0.0 0.0 110-111 5.0375 0.0 0.0 0.0 0.0125 112-113 5.5625 0.0 0.0 0.0 0.025 114-115 5.9625 0.0 0.0 0.0 0.025 116-117 6.85 0.0 0.0 0.0 0.025 118-119 7.637499999999999 0.0 0.0 0.0 0.025 120-121 8.425 0.0 0.0 0.0 0.025 122-123 8.825 0.0 0.0 0.0 0.025 124-125 9.375 0.0 0.0 0.0 0.025 126-127 9.9 0.0 0.0 0.0 0.025 128-129 10.725 0.0 0.0 0.0 0.025 130-131 11.4875 0.0 0.0 0.0 0.025 132-133 12.45 0.0 0.0 0.0 0.025 134-135 13.337499999999999 0.0 0.0 0.0 0.025 136-137 14.037500000000001 0.0 0.0 0.0 0.025 138-139 14.775 0.0 0.0 0.0 0.025 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCAGGAA 10 0.006830828 145.0 2 CACGCAG 10 0.006830828 145.0 9 GCCTGGT 10 0.006830828 145.0 1 >>END_MODULE SRR12951294 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951294_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.2565 37.0 37.0 37.0 37.0 37.0 2 36.12 37.0 37.0 37.0 37.0 37.0 3 36.1805 37.0 37.0 37.0 37.0 37.0 4 36.204 37.0 37.0 37.0 37.0 37.0 5 36.342 37.0 37.0 37.0 37.0 37.0 6 36.2995 37.0 37.0 37.0 37.0 37.0 7 36.2255 37.0 37.0 37.0 37.0 37.0 8 36.3125 37.0 37.0 37.0 37.0 37.0 9 36.2905 37.0 37.0 37.0 37.0 37.0 10-14 36.1866 37.0 37.0 37.0 37.0 37.0 15-19 36.2008 37.0 37.0 37.0 37.0 37.0 20-24 36.1569 37.0 37.0 37.0 37.0 37.0 25-29 36.0891 37.0 37.0 37.0 37.0 37.0 30-34 36.0518 37.0 37.0 37.0 37.0 37.0 35-39 35.9933 37.0 37.0 37.0 37.0 37.0 40-44 36.03529999999999 37.0 37.0 37.0 37.0 37.0 45-49 35.9726 37.0 37.0 37.0 37.0 37.0 50-54 35.931900000000006 37.0 37.0 37.0 37.0 37.0 55-59 35.9285 37.0 37.0 37.0 37.0 37.0 60-64 35.8865 37.0 37.0 37.0 37.0 37.0 65-69 35.8745 37.0 37.0 37.0 37.0 37.0 70-74 35.8414 37.0 37.0 37.0 37.0 37.0 75-79 35.817099999999996 37.0 37.0 37.0 37.0 37.0 80-84 35.819100000000006 37.0 37.0 37.0 37.0 37.0 85-89 35.786 37.0 37.0 37.0 37.0 37.0 90-94 35.840799999999994 37.0 37.0 37.0 37.0 37.0 95-99 35.809900000000006 37.0 37.0 37.0 37.0 37.0 100-104 35.764599999999994 37.0 37.0 37.0 37.0 37.0 105-109 35.6673 37.0 37.0 37.0 37.0 37.0 110-114 35.6991 37.0 37.0 37.0 37.0 37.0 115-119 35.706500000000005 37.0 37.0 37.0 37.0 37.0 120-124 35.591699999999996 37.0 37.0 37.0 37.0 37.0 125-129 35.55030000000001 37.0 37.0 37.0 37.0 37.0 130-134 35.3986 37.0 37.0 37.0 34.6 37.0 135-139 35.3042 37.0 37.0 37.0 37.0 37.0 140-144 35.2048 37.0 37.0 37.0 32.2 37.0 145-149 35.0539 37.0 37.0 37.0 29.8 37.0 150-151 34.64625 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 11 1.0 12 3.0 13 8.0 14 2.0 15 5.0 16 1.0 17 0.0 18 1.0 19 2.0 20 5.0 21 5.0 22 5.0 23 9.0 24 8.0 25 6.0 26 12.0 27 12.0 28 18.0 29 14.0 30 34.0 31 38.0 32 60.0 33 113.0 34 181.0 35 506.0 36 2592.0 37 359.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.475 22.0 9.4 30.125 2 28.1 22.975 26.900000000000002 22.025 3 24.125 24.3 28.349999999999998 23.225 4 27.474999999999998 28.525 19.7 24.3 5 29.049999999999997 31.7 18.875 20.375 6 23.925 35.5 17.424999999999997 23.150000000000002 7 24.099999999999998 21.475 32.225 22.2 8 23.925 23.35 23.925 28.799999999999997 9 25.025 21.375 26.275 27.325 10-14 26.665 25.8 22.29 25.245 15-19 27.41 24.779999999999998 22.66 25.15 20-24 26.33 25.06 23.335 25.275 25-29 26.745 24.14 24.095 25.019999999999996 30-34 27.400000000000002 24.51 23.26 24.83 35-39 28.065 25.025 22.755 24.154999999999998 40-44 26.68 24.89 23.39 25.040000000000003 45-49 26.965 24.240000000000002 23.95 24.845 50-54 26.479999999999997 24.310000000000002 24.68 24.529999999999998 55-59 26.784999999999997 24.955 23.855 24.404999999999998 60-64 27.445000000000004 24.709999999999997 23.724999999999998 24.12 65-69 26.834999999999997 24.445 23.91 24.81 70-74 27.37 24.39 24.104999999999997 24.135 75-79 27.245 25.355 22.884999999999998 24.515 80-84 26.85 24.82 23.635 24.695 85-89 28.02 24.185000000000002 23.599999999999998 24.195 90-94 27.384999999999998 25.290000000000003 24.265 23.06 95-99 28.015 25.355 22.759999999999998 23.87 100-104 27.655 24.625 23.630000000000003 24.09 105-109 27.875 24.795 23.41 23.919999999999998 110-114 28.15 25.36 23.615 22.875 115-119 28.294999999999998 24.945 23.72 23.04 120-124 28.37 24.345 23.355 23.93 125-129 29.415000000000003 25.490000000000002 22.34 22.755 130-134 29.360000000000003 24.715 23.325000000000003 22.6 135-139 29.744999999999997 24.685000000000002 23.04 22.53 140-144 30.964999999999996 25.055 22.71 21.27 145-149 30.805 23.945 23.51 21.740000000000002 150-151 32.175 23.3375 23.35 21.1375 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 1.0 5 1.0 6 0.5 7 0.0 8 1.0 9 1.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 1.0 17 1.0 18 0.0 19 0.0 20 0.5 21 1.0 22 0.5 23 0.0 24 0.0 25 0.5 26 1.5 27 2.0 28 4.0 29 3.5 30 6.0 31 9.0 32 9.5 33 12.5 34 17.0 35 25.0 36 35.0 37 54.0 38 70.5 39 90.5 40 111.5 41 121.5 42 125.0 43 149.0 44 171.0 45 177.0 46 184.0 47 179.0 48 173.0 49 156.0 50 143.0 51 134.0 52 122.0 53 120.5 54 119.0 55 114.0 56 106.5 57 95.5 58 89.5 59 85.0 60 77.5 61 73.0 62 75.5 63 84.0 64 81.0 65 73.0 66 62.5 67 49.0 68 53.0 69 53.5 70 45.0 71 40.0 72 37.5 73 31.5 74 22.5 75 21.0 76 21.5 77 15.0 78 8.5 79 8.5 80 7.0 81 3.0 82 2.0 83 3.0 84 2.0 85 1.0 86 1.0 87 0.5 88 0.0 89 1.0 90 1.0 91 0.5 92 0.5 93 0.5 94 0.5 95 0.5 96 0.5 97 1.5 98 2.0 99 2.5 100 6.5 >>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 79.60000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 81.18718592964824 64.625 2 14.03894472361809 22.35 3 3.4547738693467336 8.25 4 0.9736180904522613 3.1 5 0.18844221105527637 0.75 6 0.06281407035175879 0.3 7 0.06281407035175879 0.35000000000000003 8 0.0 0.0 9 0.0 0.0 >10 0.031407035175879394 0.27499999999999997 >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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 11 0.27499999999999997 No Hit GTGGGGATGACGTCAAGTCATCATGGCCCTTACGGCCAGGGCTACACACG 7 0.17500000000000002 No Hit TGGGCCGCCGAGAAGAAGACCAAGGCCGTCGAGGAGAAGAAGAAGTCGAG 7 0.17500000000000002 No Hit CTCATGGATATGCAGCTCCAGAGTATATTGCAACAGGTCGCCTATCTGCA 6 0.15 No Hit CAGCCGTCCAGAGCTCTCAAGGTGAGCTGCAAGCTCAACAATGCTGCTTG 6 0.15 No Hit GACGCAACGAACCAAAGGATTAGAAGAAGAATCCCCAAGAGGTCGAAACC 5 0.125 No Hit TAATAGAAGCTCGATGCTTTGAGCCGAGTGAATTCGCGGTGTTGTTTTTA 5 0.125 No Hit AGTGAACACAAGCACGCTTAATCGAGGTGCGCTAGCTAGTAGCTACTGAT 5 0.125 No Hit CTTGGAGAAAGCTGTCGCCATGGACAGCGTGCAGAACCTCGCTGCCGTGC 5 0.125 No Hit ATCTCTGGTTTTGAGGGTGACAACATGATTGAGAGGTCCACCAACCTTGA 5 0.125 No Hit GGCAGCTTTGCGCGGAAATCTAAGAAGCAACGATGAAGAGCAGCACGCTC 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 0.0125 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.037500000000000006 0.0 0.0 0.0 0.0 64-65 0.0875 0.0 0.0 0.0 0.0 66-67 0.1125 0.0 0.0 0.0 0.0 68-69 0.125 0.0 0.0 0.0 0.0 70-71 0.15 0.0 0.0 0.0 0.0 72-73 0.175 0.0 0.0 0.0 0.0 74-75 0.2375 0.0 0.0 0.0 0.0 76-77 0.3125 0.0 0.0 0.0 0.0 78-79 0.375 0.0 0.0 0.0 0.0 80-81 0.45 0.0 0.0 0.0 0.0 82-83 0.5375 0.0 0.0 0.0 0.0 84-85 0.6375 0.0 0.0 0.0 0.0 86-87 0.7749999999999999 0.0 0.0 0.0 0.0 88-89 0.9875 0.0 0.0 0.0 0.0 90-91 1.2625000000000002 0.0 0.0 0.0 0.0 92-93 1.425 0.0 0.0 0.0 0.0 94-95 1.7125 0.0 0.0 0.0 0.0 96-97 1.9749999999999999 0.0 0.0 0.0 0.0 98-99 2.2874999999999996 0.0 0.0 0.0 0.0 100-101 2.7625 0.0 0.0 0.0 0.0 102-103 3.0875 0.0 0.0 0.0 0.0 104-105 3.3875 0.0 0.0 0.0 0.0 106-107 3.8875 0.0 0.0 0.0 0.0 108-109 4.35 0.0 0.0 0.0 0.0 110-111 5.1125 0.0 0.0 0.0 0.0 112-113 5.6125 0.0 0.0 0.0 0.0 114-115 6.025 0.0 0.0 0.0 0.0 116-117 6.925000000000001 0.0 0.0 0.0 0.0 118-119 7.725 0.0 0.0 0.0 0.0 120-121 8.525 0.0 0.0 0.0 0.0 122-123 8.912500000000001 0.0 0.0 0.0 0.0 124-125 9.5 0.0 0.0 0.0 0.0 126-127 10.075 0.0 0.0 0.0 0.0 128-129 10.9375 0.0 0.0 0.0 0.0 130-131 11.7125 0.0 0.0 0.0 0.0 132-133 12.6625 0.0 0.0 0.0 0.0 134-135 13.525 0.0 0.0 0.0 0.0 136-137 14.212499999999999 0.0 0.0 0.0 0.0 138-139 14.95 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGAGACA 10 0.006830828 145.0 3 ACAAAGG 10 0.006830828 145.0 7 CTGAGAC 10 0.006830828 145.0 2 GACAAAG 10 0.006830828 145.0 6 TAGGGTT 10 0.006830828 145.0 8 AGACAAA 10 0.006830828 145.0 5 GAGACAA 10 0.006830828 145.0 4 >>END_MODULE Read 1503232 spots for SRR12951294.sra Written 1503232 spots for SRR12951294.sra Read 1503232 spots for SRR12951294.sra Written 1503232 spots for SRR12951294.sra Read 1503232 spots for SRR12951294.sra Written 1503232 spots for SRR12951294.sra Read 1503232 spots for SRR12951294.sra Written 1503232 spots for SRR12951294.sra Read 1503232 spots for SRR12951294.sra Written 1503232 spots for SRR12951294.sra Read 1503232 spots for SRR12951294.sra Written 1503232 spots for SRR12951294.sra Read 1503232 spots for SRR12951294.sra Written 1503232 spots for SRR12951294.sra Read 1503232 spots for SRR12951294.sra Written 1503232 spots for SRR12951294.sra Read 1503232 spots for SRR12951294.sra Written 1503232 spots for SRR12951294.sra Read 1503232 spots for SRR12951294.sra Written 1503232 spots for SRR12951294.sra Read 1503232 spots for SRR12951294.sra Written 1503232 spots for SRR12951294.sra Read 1503232 spots for SRR12951294.sra Written 1503232 spots for SRR12951294.sra Read 1503232 spots for SRR12951294.sra Written 1503232 spots for SRR12951294.sra Read 1503232 spots for SRR12951294.sra Written 1503232 spots for SRR12951294.sra Read 1503232 spots for SRR12951294.sra Written 1503232 spots for SRR12951294.sra Read 1503232 spots for SRR12951294.sra Written 1503232 spots for SRR12951294.sra Read 1503232 spots for SRR12951294.sra Written 1503232 spots for SRR12951294.sra Read 1503232 spots for SRR12951294.sra Written 1503232 spots for SRR12951294.sra Read 1503232 spots for SRR12951294.sra Written 1503232 spots for SRR12951294.sra Read 1503232 spots for SRR12951294.sra Written 1503232 spots for SRR12951294.sra SRR ids: ['SRR12951294.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_gjrlkpve SRR12951294.sra spots: 30064640 blocks: [[1, 1503232], [1503233, 3006464], [3006465, 4509696], [4509697, 6012928], [6012929, 7516160], [7516161, 9019392], [9019393, 10522624], [10522625, 12025856], [12025857, 13529088], [13529089, 15032320], [15032321, 16535552], [16535553, 18038784], [18038785, 19542016], [19542017, 21045248], [21045249, 22548480], [22548481, 24051712], [24051713, 25554944], [25554945, 27058176], [27058177, 28561408], [28561409, 30064640]] SRR12951294 file size 10195579 SRR12951294 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 SRR12951294 SRR12951294_1.fastq SRR12951294_2.fastq Input file: SRR12951294_1.fastq Paired file: SRR12951294_2.fastq trimmed: SRR12951294-trimmed-pair1.fastq, SRR12951294-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 Sat Dec 7 10:49:37 2024 >> started Sat Dec 7 10:50:08 2024 >> done (31.612s) 30064640 read pairs processed; of these: 220 ( 0.00%) short read pairs filtered out after trimming by size control 116565 ( 0.39%) empty read pairs filtered out after trimming by size control 29947855 (99.61%) read pairs available; of these: 5950788 (19.87%) trimmed read pairs available after processing 23997067 (80.13%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 12 0.00% 19 12 0.00% 20 28 0.00% 21 37 0.00% 22 40 0.00% 23 28 0.00% 24 55 0.00% 25 52 0.00% 26 75 0.00% 27 79 0.00% 28 64 0.00% 29 71 0.00% 30 106 0.00% 31 98 0.00% 32 99 0.00% 33 119 0.00% 34 121 0.00% 35 119 0.00% 36 133 0.00% 37 126 0.00% 38 159 0.00% 39 144 0.00% 40 169 0.00% 41 169 0.00% 42 208 0.00% 43 187 0.00% 44 195 0.00% 45 196 0.00% 46 272 0.00% 47 252 0.00% 48 317 0.00% 49 391 0.00% 50 417 0.00% 51 502 0.00% 52 565 0.00% 53 559 0.00% 54 598 0.00% 55 725 0.00% 56 749 0.00% 57 930 0.00% 58 940 0.00% 59 1138 0.00% 60 1464 0.00% 61 1569 0.01% 62 1869 0.01% 63 2006 0.01% 64 2314 0.01% 65 2434 0.01% 66 2830 0.01% 67 3031 0.01% 68 3464 0.01% 69 4024 0.01% 70 4607 0.02% 71 5247 0.02% 72 6156 0.02% 73 7104 0.02% 74 7808 0.03% 75 8569 0.03% 76 9399 0.03% 77 10397 0.03% 78 11427 0.04% 79 12874 0.04% 80 14257 0.05% 81 15271 0.05% 82 17811 0.06% 83 19669 0.07% 84 21377 0.07% 85 23423 0.08% 86 24990 0.08% 87 27154 0.09% 88 28330 0.09% 89 30388 0.10% 90 32304 0.11% 91 35069 0.12% 92 37557 0.13% 93 40279 0.13% 94 43963 0.15% 95 45890 0.15% 96 48139 0.16% 97 50243 0.17% 98 51717 0.17% 99 53422 0.18% 100 56025 0.19% 101 57557 0.19% 102 60647 0.20% 103 63941 0.21% 104 66322 0.22% 105 69069 0.23% 106 71096 0.24% 107 72546 0.24% 108 74003 0.25% 109 76147 0.25% 110 76668 0.26% 111 78491 0.26% 112 83074 0.28% 113 83478 0.28% 114 87447 0.29% 115 89959 0.30% 116 91867 0.31% 117 93643 0.31% 118 95714 0.32% 119 95734 0.32% 120 95731 0.32% 121 98613 0.33% 122 99888 0.33% 123 102224 0.34% 124 105747 0.35% 125 106973 0.36% 126 107893 0.36% 127 110038 0.37% 128 111126 0.37% 129 112509 0.38% 130 113002 0.38% 131 113275 0.38% 132 114121 0.38% 133 116408 0.39% 134 117664 0.39% 135 118889 0.40% 136 121341 0.41% 137 121208 0.40% 138 122367 0.41% 139 122885 0.41% 140 123583 0.41% 141 123606 0.41% 142 124724 0.42% 143 124434 0.42% 144 126868 0.42% 145 128134 0.43% 146 127713 0.43% 147 127407 0.43% 148 129145 0.43% 149 129287 0.43% 150 129455 0.43% 151 23997067 80.13% 29947855 reads passed initial QC criterion=sequence-density sequence-density=0.35 sequence-density-rank=1 fanout-score=3.17 fanout-score-rank=33 prefix-density=0.40 prefix-fanout=2.7 sequence=GTGATGGTCTTGCC criterion=fanout-score sequence-density=0.05 sequence-density-rank=33 fanout-score=256.39 fanout-score-rank=1 prefix-density=0.68 prefix-fanout=17.5 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.62 sequence-density-rank=1 fanout-score=2.07 fanout-score-rank=28 prefix-density=0.62 prefix-fanout=2.1 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.13 sequence-density-rank=14 fanout-score=151.19 fanout-score-rank=1 prefix-density=0.93 prefix-fanout=21.0 sequence=CGCCGCCGCCGC SRR12951294 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 10:50:44 Started mapping on | Dec 07 10:50:45 Finished on | Dec 07 10:53:01 Mapping speed, Million of reads per hour | 792.74 Number of input reads | 29947855 Average input read length | 290 UNIQUE READS: Uniquely mapped reads number | 28581374 Uniquely mapped reads % | 95.44% Average mapped length | 290.18 Number of splices: Total | 24537758 Number of splices: Annotated (sjdb) | 22660868 Number of splices: GT/AG | 24216156 Number of splices: GC/AG | 278011 Number of splices: AT/AC | 17005 Number of splices: Non-canonical | 26586 Mismatch rate per base, % | 0.11% Deletion rate per base | 0.00% Deletion average length | 1.54 Insertion rate per base | 0.00% Insertion average length | 1.12 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 242256 % of reads mapped to multiple loci | 0.81% Number of reads mapped to too many loci | 79014 % of reads mapped to too many loci | 0.26% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.23% % of reads unmapped: other | 1.26% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1124225 1124225 1124225 N_multimapping 242256 242256 242256 N_noFeature 1268023 27765251 1539708 N_ambiguous 631903 3843 87759 UnstrandedReadsAssigned:26681448 PositiveStrandReadsAssigned:812280 NegativeStrandReadsAssigned:26953907 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=149 echo kmer=145 SRR12951294 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: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in paired-end mode [quant] will process pair 1: SRR12951294-trimmed-pair1.fastq SRR12951294-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 29,947,855 reads, 27,285,231 reads pseudoaligned [quant] estimated average fragment length: 235.872 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,183 rounds 52973 SRR12951294.ke.tsv 35125 SRR12951294.se.tsv 88098 total ==> SRR12951294.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 701.625 0 0 PNS24247 1044 809.128 200.655 13.5225 PNS24249 1928 1693.13 506.491 16.312 PNS24246 1044 809.128 200.655 13.5225 PNS24248 1044 809.128 200.655 13.5225 PNS24244 1471 1236.13 278.545 12.2873 PNS24243 293 111.566 0 0 KQK14069 1603 1368.13 21986.5 876.303 KQK14071 474 257.45 745.836 157.97 ==> SRR12951294.se.tsv <== BRADI_1g14170v3 25260 BRADI_1g53295v3 200 BRADI_1g59795v3 973 BRADI_1g07683v3 0 BRADI_1g00485v3 25 BRADI_1g20270v3 982 BRADI_1g74790v3 2622 BRADI_1g09890v3 0 BRADI_1g77505v3 230 BRADI_1g48960v3 0 SRR12951294 completed mapping pipeline successfully