Starting /dee2/code/volunteer_pipeline.sh SRR13695436 current disk space = 3049236340736 free memory = 1298170916 SRR13695436 SRAfilesize 9491c20c07e90435dedfc5fb74e8e07d SRR13695436.sra SRR13695436.sra file validated SRR13695436 is paired end SRR13695436 is conventional basespace SRR13695436 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13695436_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 36.4775 37.0 37.0 37.0 37.0 37.0 2 36.44925 37.0 37.0 37.0 37.0 37.0 3 36.5675 37.0 37.0 37.0 37.0 37.0 4 36.592 37.0 37.0 37.0 37.0 37.0 5 36.5495 37.0 37.0 37.0 37.0 37.0 6 36.596 37.0 37.0 37.0 37.0 37.0 7 36.5445 37.0 37.0 37.0 37.0 37.0 8 36.5155 37.0 37.0 37.0 37.0 37.0 9 36.5425 37.0 37.0 37.0 37.0 37.0 10-14 36.5709 37.0 37.0 37.0 37.0 37.0 15-19 36.5356 37.0 37.0 37.0 37.0 37.0 20-24 36.5009 37.0 37.0 37.0 37.0 37.0 25-29 36.4867 37.0 37.0 37.0 37.0 37.0 30-34 36.4947 37.0 37.0 37.0 37.0 37.0 35-39 36.41459999999999 37.0 37.0 37.0 37.0 37.0 40-44 36.4045 37.0 37.0 37.0 37.0 37.0 45-49 36.3169 37.0 37.0 37.0 37.0 37.0 50-54 36.4051 37.0 37.0 37.0 37.0 37.0 55-59 36.3097 37.0 37.0 37.0 37.0 37.0 60-64 36.324799999999996 37.0 37.0 37.0 37.0 37.0 65-69 36.314499999999995 37.0 37.0 37.0 37.0 37.0 70-74 36.275 37.0 37.0 37.0 37.0 37.0 75-79 36.3399 37.0 37.0 37.0 37.0 37.0 80-84 36.3224 37.0 37.0 37.0 37.0 37.0 85-89 36.245400000000004 37.0 37.0 37.0 37.0 37.0 90-94 36.176300000000005 37.0 37.0 37.0 37.0 37.0 95-99 36.164500000000004 37.0 37.0 37.0 37.0 37.0 100-104 36.0555 37.0 37.0 37.0 37.0 37.0 105-109 36.13440000000001 37.0 37.0 37.0 37.0 37.0 110-114 36.201 37.0 37.0 37.0 37.0 37.0 115-119 36.2402 37.0 37.0 37.0 37.0 37.0 120-124 36.1605 37.0 37.0 37.0 37.0 37.0 125-129 36.073299999999996 37.0 37.0 37.0 37.0 37.0 130-134 36.0732 37.0 37.0 37.0 37.0 37.0 135-139 35.9633 37.0 37.0 37.0 37.0 37.0 140-144 35.7877 37.0 37.0 37.0 37.0 37.0 145-149 35.6616 37.0 37.0 37.0 37.0 37.0 150-151 34.903999999999996 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 0.0 21 1.0 22 5.0 23 3.0 24 3.0 25 1.0 26 5.0 27 13.0 28 7.0 29 9.0 30 20.0 31 20.0 32 52.0 33 67.0 34 111.0 35 331.0 36 3079.0 37 272.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 44.425 13.575000000000001 8.6 33.4 2 22.39179384538404 13.435076307230423 31.548661496122094 32.624468351263445 3 19.45 17.474999999999998 26.325 36.75 4 22.85 21.5 23.799999999999997 31.85 5 23.625 28.599999999999998 25.25 22.525000000000002 6 21.099999999999998 31.15 25.75 22.0 7 16.375 28.349999999999998 38.1 17.175 8 18.4 27.500000000000004 31.85 22.25 9 17.275 24.975 34.599999999999994 23.150000000000002 10-14 20.625 29.18 27.029999999999998 23.165 15-19 20.745 28.389999999999997 27.310000000000002 23.555 20-24 20.575 28.000000000000004 27.73 23.695 25-29 20.5 28.64 27.315 23.544999999999998 30-34 21.075 28.999999999999996 26.955000000000002 22.97 35-39 20.62 28.475 27.279999999999998 23.625 40-44 20.7 28.79 26.634999999999998 23.875 45-49 21.055 27.779999999999998 27.505000000000003 23.66 50-54 21.535 28.415000000000003 26.540000000000003 23.51 55-59 21.785 28.175 26.415 23.625 60-64 20.79 28.175 26.924999999999997 24.11 65-69 20.94 29.13 26.305 23.625 70-74 21.005 28.365000000000002 26.640000000000004 23.990000000000002 75-79 20.615 27.845 26.88 24.66 80-84 21.245 28.375 26.63 23.75 85-89 21.905 27.755000000000003 26.66 23.68 90-94 21.065 27.560000000000002 27.16 24.215 95-99 21.29 27.534999999999997 27.24 23.935000000000002 100-104 21.615000000000002 27.689999999999998 26.63 24.065 105-109 21.41 27.644999999999996 26.784999999999997 24.16 110-114 21.83 27.525 26.6 24.044999999999998 115-119 22.11 28.139999999999997 26.14 23.61 120-124 21.645 27.72 25.874999999999996 24.759999999999998 125-129 21.884999999999998 27.67 26.83 23.615 130-134 21.09 27.13 26.669999999999998 25.11 135-139 22.470000000000002 27.485 26.57 23.474999999999998 140-144 22.37 27.16 26.22 24.25 145-149 22.13 27.595 26.06 24.215 150-151 21.925 27.450000000000003 26.0375 24.587500000000002 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 1.5 3 2.5 4 1.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.5 11 0.5 12 0.5 13 0.5 14 0.5 15 1.0 16 0.5 17 0.0 18 0.0 19 0.0 20 0.5 21 2.0 22 2.5 23 1.5 24 2.0 25 4.5 26 7.0 27 7.5 28 11.5 29 19.5 30 20.5 31 21.5 32 27.5 33 45.0 34 65.5 35 83.0 36 96.0 37 109.0 38 122.5 39 120.0 40 129.0 41 152.0 42 171.5 43 191.0 44 221.0 45 229.0 46 222.5 47 245.0 48 257.5 49 230.0 50 202.5 51 177.0 52 138.0 53 121.5 54 117.5 55 100.0 56 80.5 57 64.0 58 41.5 59 30.5 60 29.5 61 18.5 62 11.5 63 13.5 64 9.5 65 4.5 66 4.0 67 2.0 68 2.5 69 2.0 70 0.5 71 0.5 72 0.0 73 0.5 74 1.0 75 0.5 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 0.075 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 84.55 #Duplication Level Percentage of deduplicated Percentage of total 1 85.36369012418687 72.175 2 11.916026020106447 20.150000000000002 3 2.069781194559432 5.25 4 0.4139562389118865 1.4000000000000001 5 0.20697811945594324 0.8750000000000001 6 0.029568302779420463 0.15 7 0.0 0.0 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 GCCTTATGTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGA 6 0.15 No Hit CTTGGTATACGGACAACTGATGGACCCACGTTGCGAGTCCAGTAAATCAG 5 0.125 No Hit GGGAGATTTTCTTACAGAGAATTACAAAAGAGCTTTTCACACCAATGGTT 5 0.125 No Hit GCATTTAGATTATGAGTAGGGAACATCAAGAAAAGTAAAATCACAGAGAA 5 0.125 No Hit GCCAGAACCGAATCGGATCGGGCTAGGTCAGATCCGTCTCTGCGAAGGCA 5 0.125 No Hit CACCAAGAGATGGAATCGTGTTCTGAAATATCAGCAATTTCCCACCAAGC 5 0.125 No Hit TGCATTTAACGTTCATGTAAATGAGTATTAGTAGAAGACAATATGTTGAA 5 0.125 No Hit GCCATTCGGACCTACCGTAAGCCTATATTTCGTTTTTCTGAGACCTATCC 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #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 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 82-83 0.037500000000000006 0.0 0.0 0.0 0.0 84-85 0.05 0.0 0.0 0.0 0.0 86-87 0.075 0.0 0.0 0.0 0.0 88-89 0.1 0.0 0.0 0.0 0.0 90-91 0.1 0.0 0.0 0.0 0.0 92-93 0.175 0.0 0.0 0.0 0.0 94-95 0.25 0.0 0.0 0.0 0.0 96-97 0.375 0.0 0.0 0.0 0.0 98-99 0.5 0.0 0.0 0.0 0.0 100-101 0.675 0.0 0.0 0.0 0.0 102-103 0.7625 0.0 0.0 0.0 0.0 104-105 0.85 0.0 0.0 0.0 0.0 106-107 1.0875 0.0 0.0 0.0 0.0 108-109 1.4125 0.0 0.0 0.0 0.0 110-111 1.6 0.0 0.0 0.0 0.0 112-113 1.75 0.0 0.0 0.0 0.0 114-115 2.0 0.0 0.0 0.0 0.0 116-117 2.3125 0.0 0.0 0.0 0.0 118-119 2.55 0.0 0.0 0.0 0.0 120-121 2.8125 0.0 0.0 0.0 0.0 122-123 3.025 0.0 0.0 0.0 0.0 124-125 3.2875 0.0 0.0 0.0 0.0 126-127 3.5375 0.0 0.0 0.0 0.0 128-129 3.875 0.0 0.0 0.0 0.0 130-131 4.35 0.0 0.0 0.0 0.0 132-133 4.887499999999999 0.0 0.0 0.0 0.0 134-135 5.225 0.0 0.0 0.0 0.0 136-137 5.612500000000001 0.0 0.0 0.0 0.0 138-139 6.1125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR13695436 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13695436_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.71075 37.0 37.0 37.0 11.0 37.0 2 34.5215 37.0 37.0 37.0 25.0 37.0 3 35.3035 37.0 37.0 37.0 25.0 37.0 4 35.3015 37.0 37.0 37.0 37.0 37.0 5 35.5105 37.0 37.0 37.0 37.0 37.0 6 35.2415 37.0 37.0 37.0 25.0 37.0 7 35.4255 37.0 37.0 37.0 37.0 37.0 8 35.6405 37.0 37.0 37.0 37.0 37.0 9 35.5835 37.0 37.0 37.0 37.0 37.0 10-14 35.52479999999999 37.0 37.0 37.0 37.0 37.0 15-19 35.518899999999995 37.0 37.0 37.0 37.0 37.0 20-24 35.3779 37.0 37.0 37.0 32.2 37.0 25-29 35.4307 37.0 37.0 37.0 37.0 37.0 30-34 35.386 37.0 37.0 37.0 37.0 37.0 35-39 35.401799999999994 37.0 37.0 37.0 37.0 37.0 40-44 35.3293 37.0 37.0 37.0 37.0 37.0 45-49 35.365199999999994 37.0 37.0 37.0 37.0 37.0 50-54 35.34179999999999 37.0 37.0 37.0 37.0 37.0 55-59 35.368700000000004 37.0 37.0 37.0 32.2 37.0 60-64 35.366 37.0 37.0 37.0 34.6 37.0 65-69 35.44669999999999 37.0 37.0 37.0 37.0 37.0 70-74 35.4165 37.0 37.0 37.0 34.6 37.0 75-79 35.2995 37.0 37.0 37.0 27.4 37.0 80-84 35.185 37.0 37.0 37.0 25.0 37.0 85-89 34.824 37.0 37.0 37.0 25.0 37.0 90-94 34.7663 37.0 37.0 37.0 25.0 37.0 95-99 34.933 37.0 37.0 37.0 25.0 37.0 100-104 35.1937 37.0 37.0 37.0 27.4 37.0 105-109 35.3019 37.0 37.0 37.0 29.8 37.0 110-114 35.406099999999995 37.0 37.0 37.0 37.0 37.0 115-119 35.47 37.0 37.0 37.0 37.0 37.0 120-124 35.432100000000005 37.0 37.0 37.0 34.6 37.0 125-129 35.324400000000004 37.0 37.0 37.0 32.2 37.0 130-134 35.3214 37.0 37.0 37.0 32.2 37.0 135-139 35.2496 37.0 37.0 37.0 29.8 37.0 140-144 35.2213 37.0 37.0 37.0 32.2 37.0 145-149 34.9762 37.0 37.0 37.0 25.0 37.0 150-151 34.23725 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 5.0 14 8.0 15 8.0 16 6.0 17 3.0 18 1.0 19 9.0 20 7.0 21 6.0 22 8.0 23 6.0 24 9.0 25 12.0 26 8.0 27 14.0 28 12.0 29 27.0 30 40.0 31 43.0 32 99.0 33 165.0 34 362.0 35 995.0 36 2108.0 37 39.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.535633908477124 23.305826456614152 10.05251312828207 24.10602650662666 2 28.999999999999996 25.85 27.250000000000004 17.9 3 23.225 27.500000000000004 29.349999999999998 19.925 4 26.05 33.35 21.95 18.65 5 24.9 37.375 20.375 17.349999999999998 6 22.45 37.724999999999994 21.775 18.05 7 23.025000000000002 22.325 34.599999999999994 20.05 8 22.875 25.324999999999996 27.525 24.275 9 24.099999999999998 24.25 26.625 25.025 10-14 24.68 28.060000000000002 24.834999999999997 22.425 15-19 24.44 27.615000000000002 26.150000000000002 21.795 20-24 24.325 28.175 26.474999999999998 21.025 25-29 24.64 27.060000000000002 26.26 22.040000000000003 30-34 24.22 27.744999999999997 26.619999999999997 21.415 35-39 24.415 26.834999999999997 26.22 22.53 40-44 24.65 26.83 26.58 21.94 45-49 23.705000000000002 27.555000000000003 26.985 21.755 50-54 23.98 27.57 26.619999999999997 21.83 55-59 24.044999999999998 27.384999999999998 26.44 22.13 60-64 23.965 27.72 26.05 22.264999999999997 65-69 24.6 27.52 26.290000000000003 21.59 70-74 25.009999999999998 27.095000000000002 25.900000000000002 21.995 75-79 24.19 27.71 25.735000000000003 22.365 80-84 24.16 27.224999999999998 26.775 21.84 85-89 24.610000000000003 26.905 27.155 21.33 90-94 24.735 26.93 25.979999999999997 22.355 95-99 23.735 28.345 26.284999999999997 21.634999999999998 100-104 24.72 27.22 26.33 21.73 105-109 24.925 27.37 26.305 21.4 110-114 24.41 27.169999999999998 26.455000000000002 21.965 115-119 25.240000000000002 27.315 26.290000000000003 21.154999999999998 120-124 24.93 27.205000000000002 26.855 21.01 125-129 25.155 27.175 26.615 21.055 130-134 25.825 26.75 26.61 20.815 135-139 25.89 27.134999999999998 26.295 20.68 140-144 25.2 27.839999999999996 26.400000000000002 20.560000000000002 145-149 26.145000000000003 27.68 26.31 19.865 150-151 26.950000000000003 27.537499999999998 25.937500000000004 19.575 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.5 3 0.5 4 0.5 5 0.5 6 0.5 7 0.5 8 0.0 9 0.0 10 0.5 11 1.0 12 1.0 13 0.5 14 0.0 15 0.0 16 0.0 17 1.5 18 1.5 19 0.0 20 0.5 21 0.5 22 0.0 23 0.5 24 2.5 25 2.5 26 2.5 27 4.5 28 6.5 29 9.0 30 11.0 31 12.0 32 17.0 33 20.0 34 27.0 35 45.0 36 49.0 37 66.5 38 106.0 39 130.0 40 153.0 41 174.5 42 189.5 43 230.5 44 253.0 45 256.0 46 245.5 47 239.0 48 252.0 49 232.0 50 193.0 51 175.5 52 160.5 53 141.5 54 129.5 55 100.5 56 77.0 57 56.5 58 42.5 59 40.5 60 31.5 61 19.5 62 14.0 63 9.5 64 5.5 65 4.5 66 3.0 67 2.0 68 3.5 69 3.5 70 1.0 71 0.5 72 1.0 73 1.0 74 1.5 75 2.0 76 1.5 77 0.5 78 0.5 79 0.5 80 1.0 81 1.5 82 0.5 83 2.0 84 2.5 85 0.5 86 0.5 87 0.5 88 0.5 89 1.5 90 1.0 91 1.5 92 2.0 93 1.5 94 1.5 95 1.0 96 1.0 97 0.5 98 1.0 99 1.0 100 3.5 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.025 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 85.625 #Duplication Level Percentage of deduplicated Percentage of total 1 86.71532846715328 74.25 2 10.91970802919708 18.7 3 1.8102189781021898 4.65 4 0.32116788321167883 1.0999999999999999 5 0.145985401459854 0.625 6 0.029197080291970805 0.15 7 0.029197080291970805 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.029197080291970805 0.35000000000000003 >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 14 0.35000000000000003 No Hit CATTAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAAT 7 0.17500000000000002 No Hit AGAACACATTCATACCCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 6 0.15 No Hit GGAGGACAATCCCCTGGTAGACTTTGTTGAACTTCCAGACACATGTCAAG 5 0.125 No Hit GGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTC 5 0.125 No Hit GCAATGTCTGCCGAGGTTGAGTACAGGTGCTTTGTTGGCGGCCTCGCTTG 5 0.125 No Hit CTTGATGACATATTTGTTCCCTTGCCTGATGATCTCCTTGTTAACTTGTC 5 0.125 No Hit ATTACTTCCATTTCCGCCCAAGCTGCTCACAGTATACGGGCGTCGGCATC 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #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 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 82-83 0.037500000000000006 0.0 0.0 0.0 0.0 84-85 0.05 0.0 0.0 0.0 0.0 86-87 0.075 0.0 0.0 0.0 0.0 88-89 0.1 0.0 0.0 0.0 0.0 90-91 0.1 0.0 0.0 0.0 0.0 92-93 0.175 0.0 0.0 0.0 0.0 94-95 0.25 0.0 0.0 0.0 0.0 96-97 0.375 0.0 0.0 0.0 0.0 98-99 0.5 0.0 0.0 0.0 0.0 100-101 0.675 0.0 0.0 0.0 0.0 102-103 0.7625 0.0 0.0 0.0 0.0 104-105 0.85 0.0 0.0 0.0 0.0 106-107 1.1 0.0 0.0 0.0 0.0 108-109 1.4375 0.0 0.0 0.0 0.0 110-111 1.625 0.0 0.0 0.0 0.0 112-113 1.775 0.0 0.0 0.0 0.0 114-115 2.0250000000000004 0.0 0.0 0.0 0.0 116-117 2.35 0.0 0.0 0.0 0.0 118-119 2.5999999999999996 0.0 0.0 0.0 0.0 120-121 2.8625 0.0 0.0 0.0 0.0 122-123 3.075 0.0 0.0 0.0 0.0 124-125 3.3375 0.0 0.0 0.0 0.0 126-127 3.6125 0.0 0.0 0.0 0.0 128-129 3.95 0.0 0.0 0.0 0.0 130-131 4.425000000000001 0.0 0.0 0.0 0.0 132-133 4.975 0.0 0.0 0.0 0.0 134-135 5.35 0.0 0.0 0.0 0.0 136-137 5.737500000000001 0.0 0.0 0.0 0.0 138-139 6.2125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 421557 spots for SRR13695436.sra Written 421557 spots for SRR13695436.sra Read 421557 spots for SRR13695436.sra Written 421557 spots for SRR13695436.sra Read 421557 spots for SRR13695436.sra Written 421557 spots for SRR13695436.sra Read 421557 spots for SRR13695436.sra Written 421557 spots for SRR13695436.sra Read 421557 spots for SRR13695436.sra Written 421557 spots for SRR13695436.sra Read 421557 spots for SRR13695436.sra Written 421557 spots for SRR13695436.sra Read 421557 spots for SRR13695436.sra Written 421557 spots for SRR13695436.sra Read 421557 spots for SRR13695436.sra Written 421557 spots for SRR13695436.sra Read 421557 spots for SRR13695436.sra Written 421557 spots for SRR13695436.sra Read 421557 spots for SRR13695436.sra Written 421557 spots for SRR13695436.sra Read 421557 spots for SRR13695436.sra Written 421557 spots for SRR13695436.sra Read 421557 spots for SRR13695436.sra Written 421557 spots for SRR13695436.sra Read 421557 spots for SRR13695436.sra Written 421557 spots for SRR13695436.sra Read 421557 spots for SRR13695436.sra Written 421557 spots for SRR13695436.sra Read 421557 spots for SRR13695436.sra Written 421557 spots for SRR13695436.sra Read 421557 spots for SRR13695436.sra Written 421557 spots for SRR13695436.sra Read 421557 spots for SRR13695436.sra Written 421557 spots for SRR13695436.sra Read 421557 spots for SRR13695436.sra Written 421557 spots for SRR13695436.sra Read 421557 spots for SRR13695436.sra Written 421557 spots for SRR13695436.sra Read 421565 spots for SRR13695436.sra Written 421565 spots for SRR13695436.sra SRR ids: ['SRR13695436.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_44aajtjt SRR13695436.sra spots: 8431148 blocks: [[1, 421557], [421558, 843114], [843115, 1264671], [1264672, 1686228], [1686229, 2107785], [2107786, 2529342], [2529343, 2950899], [2950900, 3372456], [3372457, 3794013], [3794014, 4215570], [4215571, 4637127], [4637128, 5058684], [5058685, 5480241], [5480242, 5901798], [5901799, 6323355], [6323356, 6744912], [6744913, 7166469], [7166470, 7588026], [7588027, 8009583], [8009584, 8431148]] SRR13695436 file size 2846636 SRR13695436 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 SRR13695436 SRR13695436_1.fastq SRR13695436_2.fastq Input file: SRR13695436_1.fastq Paired file: SRR13695436_2.fastq trimmed: SRR13695436-trimmed-pair1.fastq, SRR13695436-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 Wed Feb 12 02:29:44 2025 >> started Wed Feb 12 02:29:54 2025 >> done (9.972s) 8431148 read pairs processed; of these: 22 ( 0.00%) short read pairs filtered out after trimming by size control 13104 ( 0.16%) empty read pairs filtered out after trimming by size control 8418022 (99.84%) read pairs available; of these: 831398 ( 9.88%) trimmed read pairs available after processing 7586624 (90.12%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 2 0.00% 20 2 0.00% 21 0 0.00% 22 0 0.00% 23 4 0.00% 24 3 0.00% 25 3 0.00% 26 2 0.00% 27 3 0.00% 28 1 0.00% 29 2 0.00% 30 2 0.00% 31 9 0.00% 32 3 0.00% 33 5 0.00% 34 4 0.00% 35 4 0.00% 36 6 0.00% 37 5 0.00% 38 9 0.00% 39 8 0.00% 40 9 0.00% 41 13 0.00% 42 10 0.00% 43 15 0.00% 44 5 0.00% 45 13 0.00% 46 28 0.00% 47 9 0.00% 48 23 0.00% 49 27 0.00% 50 26 0.00% 51 31 0.00% 52 33 0.00% 53 32 0.00% 54 46 0.00% 55 30 0.00% 56 57 0.00% 57 52 0.00% 58 57 0.00% 59 86 0.00% 60 98 0.00% 61 101 0.00% 62 138 0.00% 63 131 0.00% 64 131 0.00% 65 155 0.00% 66 175 0.00% 67 190 0.00% 68 212 0.00% 69 238 0.00% 70 334 0.00% 71 349 0.00% 72 355 0.00% 73 440 0.01% 74 488 0.01% 75 544 0.01% 76 600 0.01% 77 692 0.01% 78 783 0.01% 79 947 0.01% 80 983 0.01% 81 1057 0.01% 82 1234 0.01% 83 1377 0.02% 84 1579 0.02% 85 1710 0.02% 86 1786 0.02% 87 1928 0.02% 88 2153 0.03% 89 2366 0.03% 90 2542 0.03% 91 2758 0.03% 92 3085 0.04% 93 3362 0.04% 94 3545 0.04% 95 3889 0.05% 96 4110 0.05% 97 4125 0.05% 98 4550 0.05% 99 4912 0.06% 100 5225 0.06% 101 5466 0.06% 102 5620 0.07% 103 6114 0.07% 104 6396 0.08% 105 6681 0.08% 106 7078 0.08% 107 7451 0.09% 108 7815 0.09% 109 8231 0.10% 110 8421 0.10% 111 8845 0.11% 112 9317 0.11% 113 9669 0.11% 114 10138 0.12% 115 10341 0.12% 116 10772 0.13% 117 11268 0.13% 118 11560 0.14% 119 11780 0.14% 120 12230 0.15% 121 12825 0.15% 122 13162 0.16% 123 13885 0.16% 124 14104 0.17% 125 14359 0.17% 126 15252 0.18% 127 15377 0.18% 128 15833 0.19% 129 16425 0.20% 130 16839 0.20% 131 17265 0.21% 132 17902 0.21% 133 18470 0.22% 134 19207 0.23% 135 19485 0.23% 136 19585 0.23% 137 20258 0.24% 138 20667 0.25% 139 21514 0.26% 140 21232 0.25% 141 21918 0.26% 142 23050 0.27% 143 23464 0.28% 144 24304 0.29% 145 24232 0.29% 146 25101 0.30% 147 25135 0.30% 148 26338 0.31% 149 25997 0.31% 150 26963 0.32% 151 7586624 90.12% 8418022 reads passed initial QC criterion=sequence-density sequence-density=0.82 sequence-density-rank=1 fanout-score=3.14 fanout-score-rank=10 prefix-density=0.98 prefix-fanout=2.6 sequence=TGAGATGCCTCAGTGCATCCAAACATGGGTAG criterion=fanout-score sequence-density=0.01 sequence-density-rank=26 fanout-score=55.07 fanout-score-rank=1 prefix-density=0.08 prefix-fanout=8.3 sequence=GTTTCATCAATGGCACTCTCTCACAGCCAATAACTTCAACAACTTCCCTATCTTTAATCCTCTCACTCCACAAATTCATAAGCTTCACCATTTTACTTCACCAATTCCTTAGAGATGTAATAGCCCATAACAATAGGAAATATCAGAAATCCAATAAGAATCAGCAATTCAGGAAGAAATATGACAAGGAGTAGTAGTGTGGATGTTGTTGTTAGACACTTCTTTTTGTCTTTAAATATAAGGCGTGGTAGAATTACTGGCACTCCAATGATTCCATATAACGGCCATAATGGAGCTATAGAATACAACACCAACGTCGCAAAAAACCAGCAAAAATTCTTAACATTATTTTTAGAAATCCCATACTGCCACCGAATATTCAGTCCTTTAAGAAATCGAACAGCATACCCAACATAGTAAAAACCA criterion=sequence-density sequence-density=1.33 sequence-density-rank=1 fanout-score=2.44 fanout-score-rank=12 prefix-density=1.42 prefix-fanout=2.3 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTG criterion=fanout-score sequence-density=0.10 sequence-density-rank=24 fanout-score=8.60 fanout-score-rank=1 prefix-density=0.57 prefix-fanout=1.5 sequence=TTACTTCCATTTCCGCCCAAGCTGCTCACAGTATACGGGCGTCGGCATCCAGACCGTCGGCTGATCGTGGTTTTACTAGGCTAGACTAGCGTACGAGCACTATGGTCAGTAATTCCTGGAGGAATAGGTACCAAGAAAAAAACGAACCTTTGGGTTCCAGAGCTGTACGGTCGCACTGAACTCGGATAGGTCTCAGAAAAACGAAATATAGGCTTACGGTAGGTCCGAATGGCACAAAGCTTGTTCCGTTAGCTGGCATAAGATTCCATGCCTAGATGTGATACACGTTTCTGGAAACTGCCTCGTCATGCGACTGTTCCCCGGGGTCAGGGCCGCTGGTATTTGCTGTAAAGAGGGGCGTTGAGTCCGTCCGACTTCACTGCCCCCTTTCAGCCTTTTGGGTCCTGTATCCCAATTCTCAGAGGTCCCGCCGTACGCTGAGGACCACCTGAAACGGGCATCGTCGCTCTTCGTTGTTCGTCGACTTCTAGTGTGGAGACGAATTGCCAGA SRR13695436 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 12 02:30:46 Started mapping on | Feb 12 02:30:46 Finished on | Feb 12 02:33:24 Mapping speed, Million of reads per hour | 191.80 Number of input reads | 8418022 Average input read length | 297 UNIQUE READS: Uniquely mapped reads number | 7031406 Uniquely mapped reads % | 83.53% Average mapped length | 296.20 Number of splices: Total | 6778369 Number of splices: Annotated (sjdb) | 6662815 Number of splices: GT/AG | 6632861 Number of splices: GC/AG | 125688 Number of splices: AT/AC | 4086 Number of splices: Non-canonical | 15734 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.02% Deletion average length | 2.92 Insertion rate per base | 0.02% Insertion average length | 2.42 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 169592 % of reads mapped to multiple loci | 2.01% Number of reads mapped to too many loci | 82615 % of reads mapped to too many loci | 0.98% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 13.07% % of reads unmapped: other | 0.41% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1217024 1217024 1217024 N_multimapping 169592 169592 169592 N_noFeature 179640 6884164 210415 N_ambiguous 162220 407 45594 UnstrandedReadsAssigned:6689546 PositiveStrandReadsAssigned:146835 NegativeStrandReadsAssigned:6775397 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR13695436 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: SRR13695436-trimmed-pair1.fastq SRR13695436-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 8,418,022 reads, 6,904,529 reads pseudoaligned [quant] estimated average fragment length: 244.283 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 996 rounds 52401 SRR13695436.ke.tsv 34699 SRR13695436.se.tsv 87100 total ==> SRR13695436.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1774.72 129 6.80449 Potri.005G024800.1.v4.1 1035 791.717 68 8.04032 Potri.004G059700.1.v4.1 961 717.733 0 0 Potri.007G009000.2.v4.1 1416 1172.72 0 0 Potri.003G141000.2.v4.1 2943 2699.72 302 10.4719 Potri.016G087400.1.v4.1 270 78.9706 325 385.259 Potri.015G069301.1.v4.1 564 324.972 0 0 Potri.010G195200.1.v4.1 1773 1529.72 15 0.917941 Potri.012G127500.1.v4.1 977 733.723 22 2.80689 ==> SRR13695436.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 69 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 153 Potri.001G212900.v4.1 3 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 1 SRR13695436 completed mapping pipeline successfully