Starting /dee2/code/volunteer_pipeline.sh SRR12951285 current disk space = 1543570108416 free memory = 1598320672 SRR12951285 SRAfilesize b4f49a5237b4042ff6db9bc39f044aee SRR12951285.sra SRR12951285.sra file validated SRR12951285 is paired end SRR12951285 is conventional basespace SRR12951285 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951285_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.502 37.0 37.0 37.0 37.0 37.0 2 36.19525 37.0 37.0 37.0 37.0 37.0 3 36.466 37.0 37.0 37.0 37.0 37.0 4 36.545 37.0 37.0 37.0 37.0 37.0 5 36.6025 37.0 37.0 37.0 37.0 37.0 6 36.719 37.0 37.0 37.0 37.0 37.0 7 36.619 37.0 37.0 37.0 37.0 37.0 8 36.5225 37.0 37.0 37.0 37.0 37.0 9 36.6265 37.0 37.0 37.0 37.0 37.0 10-14 36.6056 37.0 37.0 37.0 37.0 37.0 15-19 36.597300000000004 37.0 37.0 37.0 37.0 37.0 20-24 36.5402 37.0 37.0 37.0 37.0 37.0 25-29 36.525800000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.4976 37.0 37.0 37.0 37.0 37.0 35-39 36.4877 37.0 37.0 37.0 37.0 37.0 40-44 36.4322 37.0 37.0 37.0 37.0 37.0 45-49 36.434000000000005 37.0 37.0 37.0 37.0 37.0 50-54 36.45139999999999 37.0 37.0 37.0 37.0 37.0 55-59 36.3683 37.0 37.0 37.0 37.0 37.0 60-64 36.3267 37.0 37.0 37.0 37.0 37.0 65-69 36.278200000000005 37.0 37.0 37.0 37.0 37.0 70-74 36.257 37.0 37.0 37.0 37.0 37.0 75-79 36.26369999999999 37.0 37.0 37.0 37.0 37.0 80-84 36.2678 37.0 37.0 37.0 37.0 37.0 85-89 36.2069 37.0 37.0 37.0 37.0 37.0 90-94 36.2173 37.0 37.0 37.0 37.0 37.0 95-99 36.195100000000004 37.0 37.0 37.0 37.0 37.0 100-104 36.175799999999995 37.0 37.0 37.0 37.0 37.0 105-109 36.238099999999996 37.0 37.0 37.0 37.0 37.0 110-114 36.1122 37.0 37.0 37.0 37.0 37.0 115-119 36.1637 37.0 37.0 37.0 37.0 37.0 120-124 36.0322 37.0 37.0 37.0 37.0 37.0 125-129 36.0377 37.0 37.0 37.0 37.0 37.0 130-134 35.9754 37.0 37.0 37.0 37.0 37.0 135-139 35.968599999999995 37.0 37.0 37.0 37.0 37.0 140-144 35.7803 37.0 37.0 37.0 37.0 37.0 145-149 35.82639999999999 37.0 37.0 37.0 37.0 37.0 150-151 35.6035 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 0.0 21 0.0 22 3.0 23 4.0 24 4.0 25 2.0 26 10.0 27 4.0 28 13.0 29 11.0 30 27.0 31 36.0 32 47.0 33 60.0 34 142.0 35 244.0 36 2887.0 37 505.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 48.275 10.625 4.65 36.449999999999996 2 19.72327044025157 11.19496855345912 36.65408805031446 32.42767295597484 3 18.099999999999998 14.499999999999998 25.974999999999998 41.425 4 24.925 20.65 23.65 30.775000000000002 5 25.650000000000002 26.224999999999998 22.400000000000002 25.724999999999998 6 25.05 29.2 21.825 23.925 7 20.200000000000003 25.0 36.15 18.65 8 19.1 24.575 31.1 25.224999999999998 9 21.95 20.599999999999998 30.975 26.474999999999998 10-14 23.885 25.405 25.095 25.615 15-19 23.865 24.435000000000002 25.014999999999997 26.685 20-24 23.69 25.055 25.06 26.195 25-29 24.845 24.285 24.345 26.525 30-34 24.13 24.09 24.485 27.295 35-39 24.445 23.955000000000002 25.335 26.265 40-44 24.41 24.585 24.82 26.185000000000002 45-49 24.265 23.89 25.14 26.705000000000002 50-54 24.435000000000002 24.43 24.610000000000003 26.525 55-59 24.705 24.18 24.285 26.83 60-64 24.34 23.875 24.759999999999998 27.025 65-69 24.605 24.775 24.425 26.195 70-74 24.55 23.945 24.13 27.375 75-79 24.72 24.175 24.455 26.650000000000002 80-84 24.775 24.03 24.8 26.395000000000003 85-89 25.215 23.965 24.63 26.19 90-94 25.3 23.925 24.39 26.384999999999998 95-99 25.679999999999996 24.81 24.085 25.424999999999997 100-104 24.86 24.645 24.395 26.1 105-109 25.3 24.23 24.275 26.195 110-114 25.1 24.805 24.235 25.86 115-119 25.35 24.305 23.775 26.57 120-124 25.035 24.46 24.455 26.05 125-129 24.515 24.625 23.93 26.93 130-134 25.605 24.21 24.365000000000002 25.82 135-139 25.035 24.795 23.455000000000002 26.715 140-144 25.290000000000003 24.77 23.22 26.72 145-149 26.25 24.165 23.565 26.02 150-151 24.712500000000002 24.7375 24.025 26.525 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 1.0 4 1.5 5 0.5 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 0.5 19 0.5 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.5 26 0.5 27 0.0 28 2.0 29 2.5 30 4.0 31 9.0 32 14.5 33 21.0 34 20.5 35 21.5 36 37.5 37 61.5 38 72.0 39 86.0 40 116.0 41 123.5 42 136.0 43 164.0 44 178.0 45 203.0 46 191.5 47 168.0 48 158.5 49 145.0 50 157.0 51 151.5 52 137.0 53 123.5 54 105.5 55 95.5 56 92.5 57 89.5 58 81.5 59 66.5 60 67.0 61 76.0 62 71.0 63 75.5 64 73.5 65 72.0 66 69.5 67 67.0 68 63.5 69 50.0 70 51.0 71 51.5 72 38.0 73 29.0 74 25.0 75 19.5 76 17.0 77 11.5 78 6.0 79 5.5 80 4.0 81 1.0 82 4.0 83 6.5 84 4.0 85 1.0 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 0.625 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 80.05 #Duplication Level Percentage of deduplicated Percentage of total 1 80.88694565896316 64.75 2 14.86570893191755 23.799999999999997 3 3.1230480949406623 7.5 4 0.8432229856339788 2.7 5 0.21861336664584632 0.8750000000000001 6 0.03123048094940662 0.15 7 0.0 0.0 8 0.0 0.0 9 0.03123048094940662 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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACACGGTCTTATCTCGTAT 9 0.22499999999999998 TruSeq Adapter, Index 5 (97% over 38bp) CAGTATCCATGAGTACCAGCTCTTGTGTTTGTCGTATTTGAGTGAATAGA 6 0.15 No Hit GGTGCCGTTGTCCGCGGTTTTACCTGGGGTGTGGCTGAAGGTGTCCCAAG 5 0.125 No Hit GCCGAAGCTCCAGGCGATGCCCTGGATCCCCACGGTGCCGCACTTGGAGG 5 0.125 No Hit TCATGGAAGTGGAGGCGGATGAGCCCGGCGGCGATGCCGGAATTGTTGGC 5 0.125 No Hit GGCACATGAGAGCAGAATAGAAGAGATGGTGGAAATATAGAAGGGCTTCA 5 0.125 No Hit GGAGGTCCCTGTCGGAGACGACGCAGAAGTCGCCGCCCGTCTTGCCGTGG 5 0.125 No Hit GCCCCGTCGCGTATTTAAGTCGTCTGCAAAGGATTCAGCCCGCCGCCCGT 5 0.125 No Hit CGCCAGCACAAATCTTTAAGCATGTGGCGATCGCCGATCGGAACGATCGG 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.037500000000000006 0.0 0.0 0.0 0.0 70-71 0.0625 0.0 0.0 0.0 0.0 72-73 0.1375 0.0 0.0 0.0 0.0 74-75 0.1875 0.0 0.0 0.0 0.0 76-77 0.225 0.0 0.0 0.0 0.0 78-79 0.275 0.0 0.0 0.0 0.0 80-81 0.3125 0.0 0.0 0.0 0.0 82-83 0.35 0.0 0.0 0.0 0.0 84-85 0.3875 0.0 0.0 0.0 0.0 86-87 0.6375 0.0 0.0 0.0 0.0 88-89 0.775 0.0 0.0 0.0 0.0 90-91 0.9 0.0 0.0 0.0 0.0 92-93 1.05 0.0 0.0 0.0 0.0 94-95 1.2375 0.0 0.0 0.0 0.0 96-97 1.3875 0.0 0.0 0.0 0.0 98-99 1.5 0.0 0.0 0.0 0.0 100-101 1.65 0.0 0.0 0.0 0.0 102-103 1.85 0.0 0.0 0.0 0.0 104-105 2.225 0.0 0.0 0.0 0.0 106-107 2.525 0.0 0.0 0.0 0.0 108-109 2.7750000000000004 0.0 0.0 0.0 0.0 110-111 3.1624999999999996 0.0 0.0 0.0 0.0 112-113 3.4875 0.0 0.0 0.0 0.0 114-115 3.775 0.0 0.0 0.0 0.0 116-117 4.3375 0.0 0.0 0.0 0.0 118-119 5.0125 0.0 0.0 0.0 0.0 120-121 5.4375 0.0 0.0 0.0 0.0 122-123 5.9125 0.0 0.0 0.0 0.0 124-125 6.425 0.0 0.0 0.0 0.0 126-127 6.9125 0.0 0.0 0.0 0.0 128-129 7.25 0.0 0.0 0.0 0.0 130-131 7.8999999999999995 0.0 0.0 0.0 0.0 132-133 8.6875 0.0 0.0 0.0 0.0 134-135 9.1625 0.0 0.0 0.0 0.0 136-137 9.8125 0.0 0.0 0.0 0.0 138-139 10.412500000000001 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCGACAG 10 0.006830828 145.0 9 AAACAAA 10 0.006830828 145.0 145 GAGTTAT 10 0.006830828 145.0 5 TCTGCTC 10 0.006830828 145.0 2 TATCATG 10 0.006830828 145.0 9 CGAGTTA 10 0.006830828 145.0 4 AGCGACA 10 0.006830828 145.0 8 TCGAGTT 10 0.006830828 145.0 3 GGGCCAG 10 0.006830828 145.0 3 >>END_MODULE SRR12951285 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951285_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 36.2915 37.0 37.0 37.0 37.0 37.0 2 36.1545 37.0 37.0 37.0 37.0 37.0 3 36.1455 37.0 37.0 37.0 37.0 37.0 4 36.1765 37.0 37.0 37.0 37.0 37.0 5 36.3 37.0 37.0 37.0 37.0 37.0 6 36.229 37.0 37.0 37.0 37.0 37.0 7 36.1575 37.0 37.0 37.0 37.0 37.0 8 36.204 37.0 37.0 37.0 37.0 37.0 9 36.204 37.0 37.0 37.0 37.0 37.0 10-14 36.2298 37.0 37.0 37.0 37.0 37.0 15-19 36.1853 37.0 37.0 37.0 37.0 37.0 20-24 36.0652 37.0 37.0 37.0 37.0 37.0 25-29 36.0432 37.0 37.0 37.0 37.0 37.0 30-34 35.9641 37.0 37.0 37.0 37.0 37.0 35-39 35.996 37.0 37.0 37.0 37.0 37.0 40-44 35.9385 37.0 37.0 37.0 37.0 37.0 45-49 35.9303 37.0 37.0 37.0 37.0 37.0 50-54 35.8667 37.0 37.0 37.0 37.0 37.0 55-59 35.9029 37.0 37.0 37.0 37.0 37.0 60-64 35.89219999999999 37.0 37.0 37.0 37.0 37.0 65-69 35.909800000000004 37.0 37.0 37.0 37.0 37.0 70-74 35.8264 37.0 37.0 37.0 37.0 37.0 75-79 35.8587 37.0 37.0 37.0 37.0 37.0 80-84 35.742200000000004 37.0 37.0 37.0 37.0 37.0 85-89 35.785399999999996 37.0 37.0 37.0 37.0 37.0 90-94 35.7313 37.0 37.0 37.0 37.0 37.0 95-99 35.7478 37.0 37.0 37.0 37.0 37.0 100-104 35.6986 37.0 37.0 37.0 37.0 37.0 105-109 35.6914 37.0 37.0 37.0 37.0 37.0 110-114 35.5917 37.0 37.0 37.0 37.0 37.0 115-119 35.7163 37.0 37.0 37.0 37.0 37.0 120-124 35.6628 37.0 37.0 37.0 37.0 37.0 125-129 35.6082 37.0 37.0 37.0 37.0 37.0 130-134 35.53869999999999 37.0 37.0 37.0 37.0 37.0 135-139 35.420700000000004 37.0 37.0 37.0 37.0 37.0 140-144 35.487199999999994 37.0 37.0 37.0 37.0 37.0 145-149 35.2604 37.0 37.0 37.0 34.6 37.0 150-151 35.007 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 2.0 13 7.0 14 6.0 15 5.0 16 3.0 17 1.0 18 3.0 19 7.0 20 4.0 21 7.0 22 11.0 23 11.0 24 11.0 25 9.0 26 8.0 27 12.0 28 13.0 29 26.0 30 20.0 31 28.0 32 50.0 33 62.0 34 145.0 35 469.0 36 2746.0 37 334.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.675 23.525 5.8999999999999995 30.9 2 31.6 23.525 26.6 18.275 3 22.25 24.0 28.999999999999996 24.75 4 27.125 29.475 20.5 22.900000000000002 5 26.1 34.075 18.8 21.025 6 25.874999999999996 34.150000000000006 18.325 21.65 7 24.75 20.775 30.425 24.05 8 22.575 23.849999999999998 22.875 30.7 9 24.875 21.05 25.275 28.799999999999997 10-14 25.735000000000003 24.95 22.99 26.325 15-19 26.840000000000003 24.765 23.135 25.259999999999998 20-24 25.685000000000002 24.81 23.82 25.685000000000002 25-29 26.275 24.37 23.16 26.195 30-34 25.924999999999997 25.535000000000004 23.555 24.985 35-39 26.650000000000002 25.365 22.81 25.174999999999997 40-44 26.224999999999998 25.305 23.825 24.645 45-49 26.655 24.21 23.945 25.19 50-54 27.105 24.955 23.735 24.205 55-59 27.165 24.97 23.31 24.555 60-64 27.52 25.240000000000002 22.465 24.775 65-69 27.195000000000004 25.245 23.369999999999997 24.19 70-74 27.505000000000003 24.745 23.965 23.785 75-79 27.224999999999998 24.68 22.95 25.145 80-84 26.5 24.37 23.755000000000003 25.374999999999996 85-89 26.87 24.3 23.82 25.009999999999998 90-94 26.93 24.2 23.585 25.285000000000004 95-99 27.87 25.14 22.675 24.315 100-104 27.825 24.745 23.715 23.715 105-109 27.215 24.925 23.145 24.715 110-114 27.045 25.130000000000003 23.96 23.865 115-119 28.444999999999997 24.435000000000002 23.200000000000003 23.919999999999998 120-124 28.78 25.235000000000003 22.89 23.095 125-129 29.225 24.560000000000002 22.745 23.47 130-134 29.099999999999998 24.525 22.7 23.674999999999997 135-139 29.59 25.074999999999996 22.465 22.869999999999997 140-144 30.165 24.865000000000002 22.175 22.795 145-149 30.615 24.060000000000002 22.73 22.595000000000002 150-151 30.2875 23.962500000000002 22.425 23.325000000000003 >>END_MODULE >>Per sequence GC content fail #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 0.5 8 1.5 9 1.0 10 0.5 11 0.5 12 1.5 13 3.0 14 2.5 15 1.5 16 0.5 17 0.0 18 0.5 19 0.5 20 0.5 21 0.5 22 0.5 23 0.5 24 2.0 25 2.5 26 2.0 27 2.0 28 4.0 29 9.5 30 7.5 31 6.5 32 7.5 33 9.0 34 17.5 35 24.5 36 38.5 37 52.0 38 70.0 39 85.5 40 104.5 41 125.0 42 138.0 43 159.0 44 187.5 45 182.5 46 168.0 47 179.0 48 168.5 49 148.5 50 124.5 51 123.5 52 131.0 53 130.0 54 118.5 55 84.0 56 70.5 57 78.0 58 78.5 59 88.0 60 88.0 61 74.0 62 72.5 63 68.5 64 68.0 65 74.5 66 74.5 67 66.0 68 72.5 69 71.0 70 55.5 71 55.0 72 51.5 73 38.0 74 24.5 75 18.0 76 17.0 77 15.5 78 9.5 79 5.5 80 4.5 81 1.5 82 0.5 83 1.5 84 2.0 85 2.0 86 1.0 87 0.0 88 0.5 89 1.0 90 1.5 91 1.0 92 0.5 93 1.5 94 1.0 95 0.5 96 0.5 97 1.0 98 4.0 99 4.0 100 3.5 >>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 80.30000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 81.60024906600249 65.525 2 14.04109589041096 22.55 3 3.1755915317559156 7.6499999999999995 4 0.8405977584059776 2.7 5 0.24906600249066002 1.0 6 0.031133250311332503 0.15 7 0.031133250311332503 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.031133250311332503 0.25 >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 10 0.25 No Hit CAGCAAGCCGGGGTTCGAGAGAAGAACCATCCAATCCAGGCTCGACCTGG 7 0.17500000000000002 No Hit ATAAGAACAAGTCCATGGAAGGTCTATCAGCAAAATCCGTTGTTCTGAAC 6 0.15 No Hit GTAGCTTTCAAGCCTACAGCAACTATTGGGAAAAAGCAAAATACTGTATC 5 0.125 No Hit AGCTAGCAAAAACAACACTCGATCTGAGCGCAATAATGGCGAGGCGCGTG 5 0.125 No Hit AGAAGAACCATCCAATCCAGGCTCGACCTGGGAATGAGTGTCAGTGCTGG 5 0.125 No Hit GCTCATCATCTTGTTTAATACCAAAGCTCTTCATATTCTCCTCCTTGATT 5 0.125 No Hit CCCACGTTGGAGCAGCAGCAGAGAGCCGGAGCGCCACCAGCCATCCGATC 5 0.125 No Hit CCATGGCCGCGCCTGGCTCTTGTTCTTGACGACGTGCCTTTGGCTTCTGC 5 0.125 No Hit CGATAAGACAATCACATATACCAGCTGCTAGCTAGCTCGAACTAACCATG 5 0.125 No Hit ATCACCTCCTCCTCGATCCCCCAATCAACCATCAAGAAAAGAAACTAGCT 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.037500000000000006 0.0 0.0 0.0 0.0 70-71 0.0625 0.0 0.0 0.0 0.0 72-73 0.15 0.0 0.0 0.0 0.0 74-75 0.21250000000000002 0.0 0.0 0.0 0.0 76-77 0.275 0.0 0.0 0.0 0.0 78-79 0.32499999999999996 0.0 0.0 0.0 0.0 80-81 0.3625 0.0 0.0 0.0 0.0 82-83 0.4 0.0 0.0 0.0 0.0 84-85 0.4375 0.0 0.0 0.0 0.0 86-87 0.6875 0.0 0.0 0.0 0.0 88-89 0.825 0.0 0.0 0.0 0.0 90-91 0.95 0.0 0.0 0.0 0.0 92-93 1.1 0.0 0.0 0.0 0.0 94-95 1.2875 0.0 0.0 0.0 0.0 96-97 1.4375 0.0 0.0 0.0 0.0 98-99 1.55 0.0 0.0 0.0 0.0 100-101 1.7 0.0 0.0 0.0 0.0 102-103 1.9 0.0 0.0 0.0 0.0 104-105 2.2625 0.0 0.0 0.0 0.0 106-107 2.55 0.0 0.0 0.0 0.0 108-109 2.8 0.0 0.0 0.0 0.0 110-111 3.1875 0.0 0.0 0.0 0.0 112-113 3.5125 0.0 0.0 0.0 0.0 114-115 3.8 0.0 0.0 0.0 0.0 116-117 4.35 0.0 0.0 0.0 0.0 118-119 5.0125 0.0 0.0 0.0 0.0 120-121 5.4375 0.0 0.0 0.0 0.0 122-123 5.9125 0.0 0.0 0.0 0.0 124-125 6.387499999999999 0.0 0.0 0.0 0.0 126-127 6.9 0.0 0.0 0.0 0.0 128-129 7.300000000000001 0.0 0.0 0.0 0.0 130-131 7.9625 0.0 0.0 0.0 0.0 132-133 8.712499999999999 0.0 0.0 0.0 0.0 134-135 9.1875 0.0 0.0 0.0 0.0 136-137 9.8375 0.0 0.0 0.0 0.0 138-139 10.462499999999999 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TAAATCA 10 0.006830828 145.0 8 AAATCAG 10 0.006830828 145.0 9 CGAAGGT 10 0.006830828 145.0 3 AAGGTGG 10 0.006830828 145.0 5 CTCATTA 10 0.006830828 145.0 3 GCTCATT 10 0.006830828 145.0 2 >>END_MODULE Read 1874805 spots for SRR12951285.sra Written 1874805 spots for SRR12951285.sra Read 1874805 spots for SRR12951285.sra Written 1874805 spots for SRR12951285.sra Read 1874805 spots for SRR12951285.sra Written 1874805 spots for SRR12951285.sra Read 1874805 spots for SRR12951285.sra Written 1874805 spots for SRR12951285.sra Read 1874805 spots for SRR12951285.sra Written 1874805 spots for SRR12951285.sra Read 1874805 spots for SRR12951285.sra Written 1874805 spots for SRR12951285.sra Read 1874805 spots for SRR12951285.sra Written 1874805 spots for SRR12951285.sra Read 1874805 spots for SRR12951285.sra Written 1874805 spots for SRR12951285.sra Read 1874805 spots for SRR12951285.sra Written 1874805 spots for SRR12951285.sra Read 1874805 spots for SRR12951285.sra Written 1874805 spots for SRR12951285.sra Read 1874805 spots for SRR12951285.sra Written 1874805 spots for SRR12951285.sra Read 1874805 spots for SRR12951285.sra Written 1874805 spots for SRR12951285.sra Read 1874805 spots for SRR12951285.sra Written 1874805 spots for SRR12951285.sra Read 1874806 spots for SRR12951285.sra Written 1874806 spots for SRR12951285.sra Read 1874805 spots for SRR12951285.sra Written 1874805 spots for SRR12951285.sra Read 1874805 spots for SRR12951285.sra Written 1874805 spots for SRR12951285.sra Read 1874805 spots for SRR12951285.sra Written 1874805 spots for SRR12951285.sra Read 1874805 spots for SRR12951285.sra Written 1874805 spots for SRR12951285.sra Read 1874805 spots for SRR12951285.sra Written 1874805 spots for SRR12951285.sra Read 1874805 spots for SRR12951285.sra Written 1874805 spots for SRR12951285.sra SRR ids: ['SRR12951285.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_cccs9sz_ SRR12951285.sra spots: 37496101 blocks: [[1, 1874805], [1874806, 3749610], [3749611, 5624415], [5624416, 7499220], [7499221, 9374025], [9374026, 11248830], [11248831, 13123635], [13123636, 14998440], [14998441, 16873245], [16873246, 18748050], [18748051, 20622855], [20622856, 22497660], [22497661, 24372465], [24372466, 26247270], [26247271, 28122075], [28122076, 29996880], [29996881, 31871685], [31871686, 33746490], [33746491, 35621295], [35621296, 37496101]] SRR12951285 file size 12721115 SRR12951285 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 SRR12951285 SRR12951285_1.fastq SRR12951285_2.fastq Input file: SRR12951285_1.fastq Paired file: SRR12951285_2.fastq trimmed: SRR12951285-trimmed-pair1.fastq, SRR12951285-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 10:30:11 2024 >> started Sat Dec 7 10:30:50 2024 >> done (39.014s) 37496101 read pairs processed; of these: 271 ( 0.00%) short read pairs filtered out after trimming by size control 92020 ( 0.25%) empty read pairs filtered out after trimming by size control 37403810 (99.75%) read pairs available; of these: 5352367 (14.31%) trimmed read pairs available after processing 32051443 (85.69%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 32 0.00% 19 19 0.00% 20 29 0.00% 21 45 0.00% 22 35 0.00% 23 36 0.00% 24 63 0.00% 25 97 0.00% 26 75 0.00% 27 81 0.00% 28 89 0.00% 29 92 0.00% 30 98 0.00% 31 131 0.00% 32 107 0.00% 33 117 0.00% 34 112 0.00% 35 142 0.00% 36 97 0.00% 37 113 0.00% 38 142 0.00% 39 136 0.00% 40 164 0.00% 41 175 0.00% 42 170 0.00% 43 184 0.00% 44 183 0.00% 45 195 0.00% 46 199 0.00% 47 211 0.00% 48 291 0.00% 49 303 0.00% 50 316 0.00% 51 364 0.00% 52 451 0.00% 53 406 0.00% 54 462 0.00% 55 578 0.00% 56 550 0.00% 57 581 0.00% 58 720 0.00% 59 811 0.00% 60 946 0.00% 61 1094 0.00% 62 1251 0.00% 63 1386 0.00% 64 1472 0.00% 65 1648 0.00% 66 1743 0.00% 67 1977 0.01% 68 2198 0.01% 69 2643 0.01% 70 3173 0.01% 71 3726 0.01% 72 3890 0.01% 73 4593 0.01% 74 4850 0.01% 75 5705 0.02% 76 6127 0.02% 77 6743 0.02% 78 7493 0.02% 79 8565 0.02% 80 9472 0.03% 81 10447 0.03% 82 11931 0.03% 83 13416 0.04% 84 14707 0.04% 85 15886 0.04% 86 17054 0.05% 87 18567 0.05% 88 19441 0.05% 89 21277 0.06% 90 22552 0.06% 91 24946 0.07% 92 27057 0.07% 93 29334 0.08% 94 31296 0.08% 95 33236 0.09% 96 35105 0.09% 97 37028 0.10% 98 38165 0.10% 99 39905 0.11% 100 41614 0.11% 101 43695 0.12% 102 46150 0.12% 103 48885 0.13% 104 52634 0.14% 105 54491 0.15% 106 56935 0.15% 107 57828 0.15% 108 59642 0.16% 109 61772 0.17% 110 62935 0.17% 111 65463 0.18% 112 68485 0.18% 113 71050 0.19% 114 74635 0.20% 115 76737 0.21% 116 78397 0.21% 117 81400 0.22% 118 82650 0.22% 119 82592 0.22% 120 84972 0.23% 121 87596 0.23% 122 89370 0.24% 123 91701 0.25% 124 95559 0.26% 125 96946 0.26% 126 99930 0.27% 127 101937 0.27% 128 103743 0.28% 129 105363 0.28% 130 105721 0.28% 131 107186 0.29% 132 109489 0.29% 133 111419 0.30% 134 113658 0.30% 135 117278 0.31% 136 119975 0.32% 137 120004 0.32% 138 122528 0.33% 139 122444 0.33% 140 122533 0.33% 141 125401 0.34% 142 125885 0.34% 143 127553 0.34% 144 128760 0.34% 145 129616 0.35% 146 130639 0.35% 147 131405 0.35% 148 134220 0.36% 149 134233 0.36% 150 136066 0.36% 151 32051443 85.69% 37403810 reads passed initial QC criterion=sequence-density sequence-density=0.27 sequence-density-rank=1 fanout-score=4.42 fanout-score-rank=27 prefix-density=0.38 prefix-fanout=3.1 sequence=GAACCGGAACCG criterion=fanout-score sequence-density=0.03 sequence-density-rank=35 fanout-score=412.45 fanout-score-rank=1 prefix-density=0.70 prefix-fanout=15.9 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=1.12 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=36 prefix-density=1.13 prefix-fanout=2.0 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.13 sequence-density-rank=11 fanout-score=168.17 fanout-score-rank=1 prefix-density=1.06 prefix-fanout=21.2 sequence=GCGGCGGCGGCGA SRR12951285 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 10:31:32 Started mapping on | Dec 07 10:31:32 Finished on | Dec 07 10:34:49 Mapping speed, Million of reads per hour | 683.52 Number of input reads | 37403810 Average input read length | 294 UNIQUE READS: Uniquely mapped reads number | 35497698 Uniquely mapped reads % | 94.90% Average mapped length | 293.50 Number of splices: Total | 33898054 Number of splices: Annotated (sjdb) | 31517830 Number of splices: GT/AG | 33419652 Number of splices: GC/AG | 401771 Number of splices: AT/AC | 20864 Number of splices: Non-canonical | 55767 Mismatch rate per base, % | 0.24% Deletion rate per base | 0.01% Deletion average length | 2.18 Insertion rate per base | 0.01% Insertion average length | 2.48 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 432481 % of reads mapped to multiple loci | 1.16% Number of reads mapped to too many loci | 48827 % of reads mapped to too many loci | 0.13% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.09% % of reads unmapped: other | 0.72% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1473631 1473631 1473631 N_multimapping 432481 432481 432481 N_noFeature 1349928 34560628 1675050 N_ambiguous 722887 4696 111417 UnstrandedReadsAssigned:33424883 PositiveStrandReadsAssigned:932374 NegativeStrandReadsAssigned:33711231 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12951285 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: SRR12951285-trimmed-pair1.fastq SRR12951285-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 37,403,810 reads, 34,340,999 reads pseudoaligned [quant] estimated average fragment length: 258.901 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,205 rounds 52973 SRR12951285.ke.tsv 35125 SRR12951285.se.tsv 88098 total ==> SRR12951285.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 678.695 0 0 PNS24247 1044 786.099 149.776 7.89777 PNS24249 1928 1670.1 416.158 10.3289 PNS24246 1044 786.099 149.776 7.89777 PNS24248 1044 786.099 149.776 7.89777 PNS24244 1471 1213.1 230.513 7.8766 PNS24243 293 104.4 1 0.397042 KQK14069 1603 1345.1 67777.7 2088.68 KQK14071 474 243.272 382.148 65.1148 ==> SRR12951285.se.tsv <== BRADI_1g14170v3 68935 BRADI_1g53295v3 374 BRADI_1g59795v3 1009 BRADI_1g07683v3 0 BRADI_1g00485v3 44 BRADI_1g20270v3 1198 BRADI_1g74790v3 2844 BRADI_1g09890v3 0 BRADI_1g77505v3 512 BRADI_1g48960v3 0 SRR12951285 completed mapping pipeline successfully