Starting /dee2/code/volunteer_pipeline.sh SRR12667005 current disk space = 1540721143808 free memory = 1602351620 SRR12667005 SRAfilesize 282e91f6d8dd3fa7c505aa0b3f867c42 SRR12667005.sra SRR12667005.sra file validated SRR12667005 is paired end SRR12667005 is conventional basespace SRR12667005 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12667005_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.475 37.0 37.0 37.0 37.0 37.0 2 36.28975 37.0 37.0 37.0 37.0 37.0 3 36.4405 37.0 37.0 37.0 37.0 37.0 4 36.499 37.0 37.0 37.0 37.0 37.0 5 36.5285 37.0 37.0 37.0 37.0 37.0 6 36.501 37.0 37.0 37.0 37.0 37.0 7 36.432 37.0 37.0 37.0 37.0 37.0 8 36.5205 37.0 37.0 37.0 37.0 37.0 9 36.5095 37.0 37.0 37.0 37.0 37.0 10-14 36.51950000000001 37.0 37.0 37.0 37.0 37.0 15-19 36.55 37.0 37.0 37.0 37.0 37.0 20-24 36.537800000000004 37.0 37.0 37.0 37.0 37.0 25-29 36.4645 37.0 37.0 37.0 37.0 37.0 30-34 36.395700000000005 37.0 37.0 37.0 37.0 37.0 35-39 36.41029999999999 37.0 37.0 37.0 37.0 37.0 40-44 36.378499999999995 37.0 37.0 37.0 37.0 37.0 45-49 36.3361 37.0 37.0 37.0 37.0 37.0 50-54 36.35960000000001 37.0 37.0 37.0 37.0 37.0 55-59 36.3009 37.0 37.0 37.0 37.0 37.0 60-64 36.313599999999994 37.0 37.0 37.0 37.0 37.0 65-69 36.2745 37.0 37.0 37.0 37.0 37.0 70-74 36.273900000000005 37.0 37.0 37.0 37.0 37.0 75-79 36.2425 37.0 37.0 37.0 37.0 37.0 80-84 36.2244 37.0 37.0 37.0 37.0 37.0 85-89 36.22370000000001 37.0 37.0 37.0 37.0 37.0 90-94 36.171099999999996 37.0 37.0 37.0 37.0 37.0 95-99 36.10339999999999 37.0 37.0 37.0 37.0 37.0 100-104 36.1332 37.0 37.0 37.0 37.0 37.0 105-109 36.1704 37.0 37.0 37.0 37.0 37.0 110-114 36.028499999999994 37.0 37.0 37.0 37.0 37.0 115-119 35.948899999999995 37.0 37.0 37.0 37.0 37.0 120-124 35.9376 37.0 37.0 37.0 37.0 37.0 125-129 35.896 37.0 37.0 37.0 37.0 37.0 130-134 35.925 37.0 37.0 37.0 37.0 37.0 135-139 35.9764 37.0 37.0 37.0 37.0 37.0 140-144 35.7398 37.0 37.0 37.0 37.0 37.0 145-149 35.6733 37.0 37.0 37.0 37.0 37.0 150-151 35.512 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 4.0 24 1.0 25 4.0 26 2.0 27 9.0 28 15.0 29 16.0 30 30.0 31 49.0 32 60.0 33 96.0 34 144.0 35 277.0 36 2827.0 37 465.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 50.925 13.025 6.875000000000001 29.175 2 23.14235676757568 15.386539904928698 34.550913184888664 26.920190142606952 3 20.549999999999997 23.7 27.05 28.7 4 24.725 29.775000000000002 21.05 24.45 5 24.75 33.375 22.625 19.25 6 21.575 33.175 23.849999999999998 21.4 7 16.825000000000003 21.45 39.825 21.9 8 19.375 22.400000000000002 28.4 29.825000000000003 9 18.575 20.150000000000002 32.775 28.499999999999996 10-14 23.23 26.145000000000003 25.085 25.540000000000003 15-19 23.1 25.825 25.655 25.419999999999998 20-24 22.715 26.185000000000002 25.34 25.759999999999998 25-29 22.919999999999998 26.040000000000003 25.019999999999996 26.02 30-34 22.645 26.029999999999998 25.34 25.985000000000003 35-39 23.505000000000003 26.02 25.369999999999997 25.105 40-44 23.3 26.015 25.35 25.335 45-49 22.86 26.14 25.15 25.85 50-54 23.175 26.340000000000003 25.009999999999998 25.474999999999998 55-59 23.005 26.075 25.1 25.82 60-64 22.86 26.695 25.295 25.15 65-69 23.169999999999998 26.25 24.675 25.905 70-74 23.34 25.185000000000002 25.75 25.724999999999998 75-79 23.705000000000002 25.314999999999998 25.335 25.645 80-84 23.185 25.590000000000003 25.259999999999998 25.965 85-89 23.21 25.540000000000003 25.424999999999997 25.825 90-94 23.49 26.0 25.11 25.4 95-99 23.5 25.16 25.45 25.89 100-104 23.765 25.715 24.88 25.64 105-109 24.09 25.490000000000002 25.055 25.365 110-114 24.2 25.825 24.945 25.03 115-119 23.985 25.715 24.8 25.5 120-124 24.0 25.89 24.755 25.355 125-129 23.669999999999998 25.6 24.745 25.985000000000003 130-134 23.57 25.71 25.35 25.369999999999997 135-139 23.75 25.629999999999995 24.44 26.179999999999996 140-144 23.830000000000002 25.72 24.884999999999998 25.564999999999998 145-149 23.845 25.94 24.325 25.89 150-151 24.05 24.775 24.25 26.924999999999997 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 2.0 1 1.0 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 0.5 22 0.5 23 0.0 24 0.0 25 1.0 26 2.5 27 3.5 28 5.5 29 5.0 30 4.5 31 10.0 32 15.0 33 19.0 34 30.0 35 36.5 36 50.5 37 62.5 38 76.5 39 97.5 40 121.5 41 142.5 42 155.5 43 188.5 44 201.5 45 195.0 46 199.0 47 209.5 48 194.0 49 180.0 50 190.5 51 172.0 52 153.5 53 146.0 54 131.5 55 121.5 56 97.5 57 78.5 58 77.0 59 68.5 60 60.0 61 58.5 62 52.5 63 49.5 64 52.0 65 44.0 66 42.0 67 46.0 68 35.0 69 21.5 70 20.5 71 19.0 72 13.5 73 11.5 74 8.5 75 7.0 76 5.0 77 2.5 78 3.5 79 2.0 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 92.175 #Duplication Level Percentage of deduplicated Percentage of total 1 92.35150528885274 85.125 2 6.889069704366693 12.7 3 0.6780580417683754 1.875 4 0.08136696501220504 0.3 5 0.0 0.0 6 0.0 0.0 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 pass >>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 0.0125 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 0.05 0.0 0.0 0.0 0.0 84-85 0.05 0.0 0.0 0.0 0.0 86-87 0.05 0.0 0.0 0.0 0.0 88-89 0.05 0.0 0.0 0.0 0.0 90-91 0.05 0.0 0.0 0.0 0.0 92-93 0.1125 0.0 0.0 0.0 0.0 94-95 0.15 0.0 0.0 0.0 0.0 96-97 0.15 0.0 0.0 0.0 0.0 98-99 0.22499999999999998 0.0 0.0 0.0 0.0 100-101 0.36250000000000004 0.0 0.0 0.0 0.0 102-103 0.5 0.0 0.0 0.0 0.0 104-105 0.6375 0.0 0.0 0.0 0.0 106-107 0.7375 0.0 0.0 0.0 0.0 108-109 0.875 0.0 0.0 0.0 0.0 110-111 1.1625 0.0 0.0 0.0 0.0 112-113 1.3375 0.0 0.0 0.0 0.0 114-115 1.575 0.0 0.0 0.0 0.0 116-117 1.8624999999999998 0.0 0.0 0.0 0.0 118-119 2.1875 0.0 0.0 0.0 0.0 120-121 2.5999999999999996 0.0 0.0 0.0 0.0 122-123 2.8875 0.0 0.0 0.0 0.0 124-125 3.2125000000000004 0.0 0.0 0.0 0.0 126-127 3.55 0.0 0.0 0.0 0.0 128-129 3.9125 0.0 0.0 0.0 0.0 130-131 4.3375 0.0 0.0 0.0 0.0 132-133 4.7625 0.0 0.0 0.0 0.0 134-135 5.1625 0.0 0.0 0.0 0.0 136-137 5.4375 0.0 0.0 0.0 0.0 138-139 5.8625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12667005 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12667005_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.966 37.0 37.0 37.0 37.0 37.0 2 36.0325 37.0 37.0 37.0 37.0 37.0 3 36.1595 37.0 37.0 37.0 37.0 37.0 4 36.207 37.0 37.0 37.0 37.0 37.0 5 36.201 37.0 37.0 37.0 37.0 37.0 6 36.149 37.0 37.0 37.0 37.0 37.0 7 35.927 37.0 37.0 37.0 37.0 37.0 8 36.227 37.0 37.0 37.0 37.0 37.0 9 36.117 37.0 37.0 37.0 37.0 37.0 10-14 36.1274 37.0 37.0 37.0 37.0 37.0 15-19 36.1271 37.0 37.0 37.0 37.0 37.0 20-24 36.0829 37.0 37.0 37.0 37.0 37.0 25-29 36.089299999999994 37.0 37.0 37.0 37.0 37.0 30-34 36.0036 37.0 37.0 37.0 37.0 37.0 35-39 36.018 37.0 37.0 37.0 37.0 37.0 40-44 35.9553 37.0 37.0 37.0 37.0 37.0 45-49 35.938100000000006 37.0 37.0 37.0 37.0 37.0 50-54 35.9043 37.0 37.0 37.0 37.0 37.0 55-59 35.9322 37.0 37.0 37.0 37.0 37.0 60-64 35.819399999999995 37.0 37.0 37.0 37.0 37.0 65-69 35.8729 37.0 37.0 37.0 37.0 37.0 70-74 35.8534 37.0 37.0 37.0 37.0 37.0 75-79 35.8292 37.0 37.0 37.0 37.0 37.0 80-84 35.8387 37.0 37.0 37.0 37.0 37.0 85-89 35.8182 37.0 37.0 37.0 37.0 37.0 90-94 35.783300000000004 37.0 37.0 37.0 37.0 37.0 95-99 35.775 37.0 37.0 37.0 37.0 37.0 100-104 35.7462 37.0 37.0 37.0 37.0 37.0 105-109 35.703700000000005 37.0 37.0 37.0 37.0 37.0 110-114 35.6683 37.0 37.0 37.0 37.0 37.0 115-119 35.636 37.0 37.0 37.0 37.0 37.0 120-124 35.7238 37.0 37.0 37.0 37.0 37.0 125-129 35.682900000000004 37.0 37.0 37.0 37.0 37.0 130-134 35.7219 37.0 37.0 37.0 37.0 37.0 135-139 35.5377 37.0 37.0 37.0 37.0 37.0 140-144 35.4616 37.0 37.0 37.0 37.0 37.0 145-149 35.39169999999999 37.0 37.0 37.0 34.6 37.0 150-151 35.12625 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 3.0 13 7.0 14 8.0 15 6.0 16 3.0 17 4.0 18 4.0 19 3.0 20 1.0 21 10.0 22 10.0 23 10.0 24 9.0 25 8.0 26 8.0 27 12.0 28 15.0 29 19.0 30 27.0 31 30.0 32 49.0 33 88.0 34 159.0 35 398.0 36 2662.0 37 447.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 51.449999999999996 16.375 9.15 23.025000000000002 2 28.725 20.424999999999997 28.325 22.525000000000002 3 25.25 23.1 27.975 23.674999999999997 4 27.975 30.775000000000002 18.65 22.6 5 26.924999999999997 32.975 19.275000000000002 20.825 6 24.349999999999998 33.725 19.475 22.45 7 22.2 17.925 36.275 23.599999999999998 8 22.3 19.8 23.825 34.075 9 23.150000000000002 21.425 25.95 29.475 10-14 26.040000000000003 25.145 23.225 25.590000000000003 15-19 26.169999999999998 25.185000000000002 23.89 24.755 20-24 25.915 25.66 23.82 24.605 25-29 26.125 25.14 24.345 24.39 30-34 25.924999999999997 25.22 24.33 24.525 35-39 25.995 25.465 23.525 25.014999999999997 40-44 26.314999999999998 25.240000000000002 24.315 24.13 45-49 25.240000000000002 25.535000000000004 24.08 25.145 50-54 25.91 25.655 24.215 24.22 55-59 26.16 25.455 24.035 24.349999999999998 60-64 25.900000000000002 26.25 23.985 23.865 65-69 25.629999999999995 25.915 24.5 23.955000000000002 70-74 26.229999999999997 26.39 23.630000000000003 23.75 75-79 26.26 25.45 24.11 24.18 80-84 25.445 25.55 24.065 24.94 85-89 26.484999999999996 26.145000000000003 24.025 23.345 90-94 25.540000000000003 25.575 24.82 24.065 95-99 26.05 25.71 24.525 23.715 100-104 25.990000000000002 25.69 24.125 24.195 105-109 26.229999999999997 25.324999999999996 24.92 23.525 110-114 25.990000000000002 25.16 25.155 23.695 115-119 25.485000000000003 25.990000000000002 24.474999999999998 24.05 120-124 26.58 25.745 24.93 22.745 125-129 26.375 26.35 24.25 23.025000000000002 130-134 26.455000000000002 26.645000000000003 24.295 22.605 135-139 26.985 26.015 24.85 22.15 140-144 26.275 26.41 24.610000000000003 22.705000000000002 145-149 27.47 26.009999999999998 24.485 22.035 150-151 26.85 26.700000000000003 24.212500000000002 22.237499999999997 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 1.5 3 1.5 4 0.5 5 0.5 6 0.5 7 0.5 8 1.5 9 2.0 10 1.5 11 2.0 12 2.5 13 1.0 14 0.0 15 0.5 16 1.0 17 1.0 18 1.0 19 1.5 20 1.5 21 1.0 22 1.0 23 0.5 24 1.5 25 1.5 26 0.0 27 0.5 28 2.0 29 4.0 30 5.5 31 4.5 32 7.5 33 12.5 34 18.5 35 22.5 36 26.5 37 44.0 38 54.5 39 81.5 40 119.5 41 135.5 42 150.0 43 165.0 44 169.5 45 181.0 46 197.5 47 188.0 48 184.5 49 190.0 50 171.0 51 154.5 52 141.0 53 127.0 54 118.0 55 113.0 56 104.5 57 85.5 58 74.0 59 89.0 60 94.5 61 79.5 62 80.5 63 76.5 64 64.0 65 59.5 66 67.0 67 66.0 68 53.5 69 42.0 70 31.0 71 26.0 72 26.0 73 19.0 74 10.0 75 6.0 76 5.0 77 4.0 78 1.5 79 2.5 80 2.5 81 0.5 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.5 88 0.5 89 0.5 90 1.0 91 0.5 92 1.0 93 1.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.5 99 1.5 100 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 92.225 #Duplication Level Percentage of deduplicated Percentage of total 1 92.46408240715641 85.275 2 6.776904310111141 12.5 3 0.6776904310111141 1.875 4 0.05421523448088912 0.2 5 0.0 0.0 6 0.02710761724044456 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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 6 0.15 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 0.0125 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 0.05 0.0 0.0 0.0 0.0 84-85 0.05 0.0 0.0 0.0 0.0 86-87 0.05 0.0 0.0 0.0 0.0 88-89 0.05 0.0 0.0 0.0 0.0 90-91 0.05 0.0 0.0 0.0 0.0 92-93 0.1125 0.0 0.0 0.0 0.0 94-95 0.15 0.0 0.0 0.0 0.0 96-97 0.15 0.0 0.0 0.0 0.0 98-99 0.22499999999999998 0.0 0.0 0.0 0.0 100-101 0.36250000000000004 0.0 0.0 0.0 0.0 102-103 0.5 0.0 0.0 0.0 0.0 104-105 0.6375 0.0 0.0 0.0 0.0 106-107 0.7625 0.0 0.0 0.0 0.0 108-109 0.9125 0.0 0.0 0.0 0.0 110-111 1.2125 0.0 0.0 0.0 0.0 112-113 1.3875000000000002 0.0 0.0 0.0 0.0 114-115 1.625 0.0 0.0 0.0 0.0 116-117 1.9125 0.0 0.0 0.0 0.0 118-119 2.2625 0.0 0.0 0.0 0.0 120-121 2.6500000000000004 0.0 0.0 0.0 0.0 122-123 2.9375 0.0 0.0 0.0 0.0 124-125 3.2625 0.0 0.0 0.0 0.0 126-127 3.5999999999999996 0.0 0.0 0.0 0.0 128-129 3.9375 0.0 0.0 0.0 0.0 130-131 4.362500000000001 0.0 0.0 0.0 0.0 132-133 4.7875 0.0 0.0 0.0 0.0 134-135 5.1875 0.0 0.0 0.0 0.0 136-137 5.4625 0.0 0.0 0.0 0.0 138-139 5.8875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAGATTT 10 0.006830828 145.0 8 TGAGATT 10 0.006830828 145.0 7 >>END_MODULE Read 1449631 spots for SRR12667005.sra Written 1449631 spots for SRR12667005.sra Read 1449631 spots for SRR12667005.sra Written 1449631 spots for SRR12667005.sra Read 1449631 spots for SRR12667005.sra Written 1449631 spots for SRR12667005.sra Read 1449631 spots for SRR12667005.sra Written 1449631 spots for SRR12667005.sra Read 1449631 spots for SRR12667005.sra Written 1449631 spots for SRR12667005.sra Read 1449631 spots for SRR12667005.sra Written 1449631 spots for SRR12667005.sra Read 1449631 spots for SRR12667005.sra Written 1449631 spots for SRR12667005.sra Read 1449631 spots for SRR12667005.sra Written 1449631 spots for SRR12667005.sra Read 1449631 spots for SRR12667005.sra Written 1449631 spots for SRR12667005.sra Read 1449631 spots for SRR12667005.sra Written 1449631 spots for SRR12667005.sra Read 1449631 spots for SRR12667005.sra Written 1449631 spots for SRR12667005.sra Read 1449631 spots for SRR12667005.sra Written 1449631 spots for SRR12667005.sra Read 1449631 spots for SRR12667005.sra Written 1449631 spots for SRR12667005.sra Read 1449631 spots for SRR12667005.sra Written 1449631 spots for SRR12667005.sra Read 1449631 spots for SRR12667005.sra Written 1449631 spots for SRR12667005.sra Read 1449631 spots for SRR12667005.sra Written 1449631 spots for SRR12667005.sra Read 1449631 spots for SRR12667005.sra Written 1449631 spots for SRR12667005.sra Read 1449631 spots for SRR12667005.sra Written 1449631 spots for SRR12667005.sra Read 1449631 spots for SRR12667005.sra Written 1449631 spots for SRR12667005.sra Read 1449631 spots for SRR12667005.sra Written 1449631 spots for SRR12667005.sra SRR ids: ['SRR12667005.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_a9ps_ndm SRR12667005.sra spots: 28992620 blocks: [[1, 1449631], [1449632, 2899262], [2899263, 4348893], [4348894, 5798524], [5798525, 7248155], [7248156, 8697786], [8697787, 10147417], [10147418, 11597048], [11597049, 13046679], [13046680, 14496310], [14496311, 15945941], [15945942, 17395572], [17395573, 18845203], [18845204, 20294834], [20294835, 21744465], [21744466, 23194096], [23194097, 24643727], [24643728, 26093358], [26093359, 27542989], [27542990, 28992620]] SRR12667005 file size 9831260 SRR12667005 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 SRR12667005 SRR12667005_1.fastq SRR12667005_2.fastq Input file: SRR12667005_1.fastq Paired file: SRR12667005_2.fastq trimmed: SRR12667005-trimmed-pair1.fastq, SRR12667005-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 18:04:41 2024 >> started Sat Dec 7 18:05:15 2024 >> done (33.905s) 28992620 read pairs processed; of these: 90 ( 0.00%) short read pairs filtered out after trimming by size control 8184 ( 0.03%) empty read pairs filtered out after trimming by size control 28984346 (99.97%) read pairs available; of these: 2544399 ( 8.78%) trimmed read pairs available after processing 26439947 (91.22%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 12 0.00% 19 16 0.00% 20 14 0.00% 21 16 0.00% 22 15 0.00% 23 19 0.00% 24 13 0.00% 25 28 0.00% 26 23 0.00% 27 34 0.00% 28 47 0.00% 29 36 0.00% 30 25 0.00% 31 40 0.00% 32 42 0.00% 33 44 0.00% 34 47 0.00% 35 41 0.00% 36 46 0.00% 37 50 0.00% 38 54 0.00% 39 53 0.00% 40 46 0.00% 41 48 0.00% 42 87 0.00% 43 70 0.00% 44 55 0.00% 45 68 0.00% 46 87 0.00% 47 79 0.00% 48 71 0.00% 49 103 0.00% 50 98 0.00% 51 91 0.00% 52 93 0.00% 53 120 0.00% 54 101 0.00% 55 139 0.00% 56 146 0.00% 57 157 0.00% 58 143 0.00% 59 173 0.00% 60 182 0.00% 61 266 0.00% 62 266 0.00% 63 256 0.00% 64 315 0.00% 65 368 0.00% 66 367 0.00% 67 419 0.00% 68 456 0.00% 69 569 0.00% 70 633 0.00% 71 730 0.00% 72 860 0.00% 73 1024 0.00% 74 1111 0.00% 75 1164 0.00% 76 1374 0.00% 77 1505 0.01% 78 1704 0.01% 79 2030 0.01% 80 2171 0.01% 81 2446 0.01% 82 2889 0.01% 83 3315 0.01% 84 3752 0.01% 85 4067 0.01% 86 4571 0.02% 87 4910 0.02% 88 5350 0.02% 89 5876 0.02% 90 6670 0.02% 91 7417 0.03% 92 8300 0.03% 93 9085 0.03% 94 9948 0.03% 95 10840 0.04% 96 11444 0.04% 97 12215 0.04% 98 12872 0.04% 99 13754 0.05% 100 14800 0.05% 101 15981 0.06% 102 17517 0.06% 103 18798 0.06% 104 20405 0.07% 105 21055 0.07% 106 22330 0.08% 107 23037 0.08% 108 24081 0.08% 109 24774 0.09% 110 25800 0.09% 111 27159 0.09% 112 29009 0.10% 113 30471 0.11% 114 32565 0.11% 115 34103 0.12% 116 34865 0.12% 117 36046 0.12% 118 36140 0.12% 119 37518 0.13% 120 38861 0.13% 121 39837 0.14% 122 41638 0.14% 123 44338 0.15% 124 46164 0.16% 125 48087 0.17% 126 49188 0.17% 127 49394 0.17% 128 49964 0.17% 129 50981 0.18% 130 51825 0.18% 131 52554 0.18% 132 55161 0.19% 133 57509 0.20% 134 59154 0.20% 135 61747 0.21% 136 62826 0.22% 137 63753 0.22% 138 64291 0.22% 139 64697 0.22% 140 65141 0.22% 141 66015 0.23% 142 67959 0.23% 143 70909 0.24% 144 72717 0.25% 145 74996 0.26% 146 76593 0.26% 147 77536 0.27% 148 77420 0.27% 149 77675 0.27% 150 78834 0.27% 151 26439947 91.22% 28984346 reads passed initial QC criterion=sequence-density sequence-density=0.20 sequence-density-rank=1 fanout-score=4.32 fanout-score-rank=23 prefix-density=0.24 prefix-fanout=3.7 sequence=GTGATGGTCTTGCC criterion=fanout-score sequence-density=0.03 sequence-density-rank=31 fanout-score=189.38 fanout-score-rank=1 prefix-density=0.36 prefix-fanout=16.6 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.39 sequence-density-rank=1 fanout-score=2.25 fanout-score-rank=36 prefix-density=0.40 prefix-fanout=2.2 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.02 sequence-density-rank=36 fanout-score=567.95 fanout-score-rank=1 prefix-density=0.74 prefix-fanout=17.6 sequence=GCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGCTGAGATGAACAAGAGGTCATTCAAGTACGCGTGGGTGCTTGACAAGCTGAAGGCTGAGCGTGAGAGAGGTATCACCATCGATATTGCCTTGTGGAAGTTCGAGACCACCAAGTACTACTGCACCGTCATTGATGCCCCTGGACACCGTGACTTCATCAAGAACATGATTACCGGTACCTCCCAGGCTGACTGTGCCGTGCTTATCATTGACTCCACGACTGGAGGTTTTGAGGCTGGTATCTCCAAGGATGGCCAGACCCGTGAGCATGCCCTCCTTGCTTTCACTCTTGGAGTGAAGCAGATGATCTGCTGCTGCAACAAGATGGA SRR12667005 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 18:06:07 Started mapping on | Dec 07 18:06:08 Finished on | Dec 07 18:09:22 Mapping speed, Million of reads per hour | 537.85 Number of input reads | 28984346 Average input read length | 298 UNIQUE READS: Uniquely mapped reads number | 27191175 Uniquely mapped reads % | 93.81% Average mapped length | 296.82 Number of splices: Total | 29411473 Number of splices: Annotated (sjdb) | 27635973 Number of splices: GT/AG | 28978913 Number of splices: GC/AG | 334229 Number of splices: AT/AC | 20070 Number of splices: Non-canonical | 78261 Mismatch rate per base, % | 0.30% Deletion rate per base | 0.02% Deletion average length | 2.57 Insertion rate per base | 0.02% Insertion average length | 2.26 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 410282 % of reads mapped to multiple loci | 1.42% Number of reads mapped to too many loci | 34033 % of reads mapped to too many loci | 0.12% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.97% % of reads unmapped: other | 0.69% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1382889 1382889 1382889 N_multimapping 410282 410282 410282 N_noFeature 922336 26532846 1123802 N_ambiguous 549352 4276 94140 UnstrandedReadsAssigned:25719487 PositiveStrandReadsAssigned:654053 NegativeStrandReadsAssigned:25973233 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12667005 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: SRR12667005-trimmed-pair1.fastq SRR12667005-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 28,984,346 reads, 26,409,433 reads pseudoaligned [quant] estimated average fragment length: 286.008 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,170 rounds 52973 SRR12667005.ke.tsv 35125 SRR12667005.se.tsv 88098 total ==> SRR12667005.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 651.981 0 0 PNS24247 1044 758.992 114.898 9.00716 PNS24249 1928 1642.99 114.782 4.15671 PNS24246 1044 758.992 114.898 9.00716 PNS24248 1044 758.992 114.898 9.00716 PNS24244 1471 1185.99 272.523 13.672 PNS24243 293 91.5558 0 0 KQK14069 1603 1317.99 6043.47 272.826 KQK14071 474 224.245 93.4294 24.7898 ==> SRR12667005.se.tsv <== BRADI_1g14170v3 6613 BRADI_1g53295v3 269 BRADI_1g59795v3 600 BRADI_1g07683v3 0 BRADI_1g00485v3 128 BRADI_1g20270v3 1476 BRADI_1g74790v3 58 BRADI_1g09890v3 0 BRADI_1g77505v3 204 BRADI_1g48960v3 0 SRR12667005 completed mapping pipeline successfully