Starting /dee2/code/volunteer_pipeline.sh ERR9452517 current disk space = 1547593170944 free memory = 1599975876 ERR9452517 SRAfilesize 9cafbd17beacad6c24028f5f6a239e8d ERR9452517.sra ERR9452517.sra file validated ERR9452517 is paired end ERR9452517 is conventional basespace ERR9452517 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452517_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 55 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.57275 37.0 37.0 37.0 37.0 37.0 2 35.64775 37.0 37.0 37.0 37.0 37.0 3 36.031 37.0 37.0 37.0 37.0 37.0 4 35.939 37.0 37.0 37.0 37.0 37.0 5 36.0155 37.0 37.0 37.0 37.0 37.0 6 36.236 37.0 37.0 37.0 37.0 37.0 7 36.0595 37.0 37.0 37.0 37.0 37.0 8 36.1435 37.0 37.0 37.0 37.0 37.0 9 36.161 37.0 37.0 37.0 37.0 37.0 10-14 36.180499999999995 37.0 37.0 37.0 37.0 37.0 15-19 36.1702 37.0 37.0 37.0 37.0 37.0 20-24 36.1163 37.0 37.0 37.0 37.0 37.0 25-29 36.033 37.0 37.0 37.0 37.0 37.0 30-34 35.99210000000001 37.0 37.0 37.0 37.0 37.0 35-39 35.995799999999996 37.0 37.0 37.0 37.0 37.0 40-44 35.804 37.0 37.0 37.0 37.0 37.0 45-49 35.77589999999999 37.0 37.0 37.0 37.0 37.0 50-54 35.8862 37.0 37.0 37.0 37.0 37.0 55-59 35.8871 37.0 37.0 37.0 37.0 37.0 60-64 35.9079 37.0 37.0 37.0 37.0 37.0 65-69 35.8411 37.0 37.0 37.0 37.0 37.0 70-74 35.8143 37.0 37.0 37.0 37.0 37.0 75-79 35.6957 37.0 37.0 37.0 37.0 37.0 80-84 35.7595 37.0 37.0 37.0 37.0 37.0 85-89 35.7804 37.0 37.0 37.0 37.0 37.0 90-94 35.6919 37.0 37.0 37.0 37.0 37.0 95-99 35.708999999999996 37.0 37.0 37.0 37.0 37.0 100-104 35.6065 37.0 37.0 37.0 37.0 37.0 105-109 35.6023 37.0 37.0 37.0 37.0 37.0 110-114 35.5787 37.0 37.0 37.0 37.0 37.0 115-119 35.4813 37.0 37.0 37.0 37.0 37.0 120-124 35.556999999999995 37.0 37.0 37.0 37.0 37.0 125-129 35.6023 37.0 37.0 37.0 37.0 37.0 130-134 35.358 37.0 37.0 37.0 34.6 37.0 135-139 35.391799999999996 37.0 37.0 37.0 37.0 37.0 140-144 35.2385 37.0 37.0 37.0 32.2 37.0 145-149 35.3395 37.0 37.0 37.0 34.6 37.0 150 35.466 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 1.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 1.0 22 2.0 23 4.0 24 2.0 25 7.0 26 13.0 27 23.0 28 23.0 29 51.0 30 55.0 31 82.0 32 113.0 33 164.0 34 195.0 35 390.0 36 2571.0 37 303.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 28.796597448086064 13.710282712034024 15.236427320490368 42.256692519389546 2 27.9459594696022 21.165874405804352 29.522141606204656 21.36602451838879 3 26.525 26.5 19.0 27.975 4 30.2 28.475 16.25 25.074999999999996 5 27.750000000000004 30.575000000000003 18.425 23.25 6 21.8 32.45 19.625 26.125 7 22.2 13.700000000000001 37.05 27.05 8 23.9 17.224999999999998 25.474999999999998 33.4 9 23.375 17.849999999999998 27.750000000000004 31.025000000000002 10-14 25.945 23.96 21.82 28.275 15-19 26.200000000000003 22.825 22.869999999999997 28.105000000000004 20-24 26.93 22.725 22.56 27.785 25-29 26.36 22.71 22.45 28.48 30-34 26.69 23.715 21.87 27.725 35-39 26.615 22.650000000000002 22.865 27.87 40-44 26.400000000000002 22.695 22.41 28.494999999999997 45-49 26.845000000000002 22.445 22.015 28.694999999999997 50-54 26.945000000000004 22.255 22.755 28.044999999999998 55-59 27.325 22.37 22.13 28.175 60-64 27.055 21.945 22.435 28.565 65-69 27.35 22.205 22.105 28.34 70-74 27.834999999999997 22.02 22.634999999999998 27.51 75-79 26.924999999999997 22.425 22.18 28.470000000000002 80-84 27.57 21.985 22.07 28.375 85-89 27.42 22.07 22.14 28.37 90-94 27.089999999999996 21.7 23.465 27.744999999999997 95-99 26.99 22.375 22.3 28.335 100-104 27.465 21.795 22.55 28.189999999999998 105-109 27.62 22.3 21.9 28.18 110-114 28.189999999999998 23.0 21.55 27.26 115-119 28.175 21.88 22.2 27.744999999999997 120-124 28.035 21.349999999999998 22.505 28.110000000000003 125-129 27.855 22.63 22.02 27.495000000000005 130-134 27.54 21.94 22.365 28.155 135-139 27.72 22.994999999999997 22.505 26.779999999999998 140-144 28.23 22.52 21.975 27.275 145-149 27.47 22.355 22.285 27.889999999999997 150 29.075 21.2 23.400000000000002 26.325 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.5 4 0.5 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 0.5 21 0.5 22 0.0 23 0.0 24 0.0 25 1.0 26 1.0 27 0.5 28 1.0 29 2.5 30 5.0 31 8.5 32 10.5 33 15.0 34 21.5 35 20.0 36 22.5 37 34.5 38 52.5 39 69.5 40 81.5 41 91.5 42 110.5 43 126.5 44 129.0 45 131.0 46 128.0 47 132.5 48 136.5 49 137.5 50 128.0 51 112.5 52 99.5 53 98.5 54 102.5 55 100.5 56 92.0 57 83.5 58 80.5 59 76.5 60 83.0 61 99.5 62 104.0 63 104.5 64 109.0 65 108.5 66 103.0 67 93.0 68 86.5 69 80.0 70 78.5 71 73.0 72 71.0 73 66.5 74 61.0 75 54.5 76 42.0 77 32.5 78 24.5 79 19.5 80 17.0 81 13.5 82 9.5 83 7.5 84 6.0 85 4.0 86 1.5 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 0.075 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 92.60000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 92.5755939524838 85.725 2 6.884449244060475 12.75 3 0.5129589632829373 1.425 4 0.02699784017278618 0.1 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 pass #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 0.0125 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.037500000000000006 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 82-83 0.1 0.0 0.0 0.0 0.0 84-85 0.1125 0.0 0.0 0.0 0.0 86-87 0.125 0.0 0.0 0.0 0.0 88-89 0.125 0.0 0.0 0.0 0.0 90-91 0.16249999999999998 0.0 0.0 0.0 0.0 92-93 0.175 0.0 0.0 0.0 0.0 94-95 0.2 0.0 0.0 0.0 0.0 96-97 0.25 0.0 0.0 0.0 0.0 98-99 0.25 0.0 0.0 0.0 0.0 100-101 0.3 0.0 0.0 0.0 0.0 102-103 0.325 0.0 0.0 0.0 0.0 104-105 0.325 0.0 0.0 0.0 0.0 106-107 0.325 0.0 0.0 0.0 0.0 108-109 0.3625 0.0 0.0 0.0 0.0 110-111 0.375 0.0 0.0 0.0 0.0 112-113 0.44999999999999996 0.0 0.0 0.0 0.0 114-115 0.5625 0.0 0.0 0.0 0.0 116-117 0.625 0.0 0.0 0.0 0.0 118-119 0.675 0.0 0.0 0.0 0.0 120-121 0.7124999999999999 0.0 0.0 0.0 0.0 122-123 0.725 0.0 0.0 0.0 0.0 124-125 0.725 0.0 0.0 0.0 0.0 126-127 0.8625 0.0 0.0 0.0 0.0 128-129 1.0 0.0 0.0 0.0 0.0 130-131 1.0375 0.0 0.0 0.0 0.0 132-133 1.175 0.0 0.0 0.0 0.0 134-135 1.275 0.0 0.0 0.0 0.0 136-137 1.4375 0.0 0.0 0.0 0.0 138 1.5 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR9452517 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452517_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 55 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.796 37.0 37.0 37.0 37.0 37.0 2 35.73 37.0 37.0 37.0 37.0 37.0 3 35.9405 37.0 37.0 37.0 37.0 37.0 4 35.8725 37.0 37.0 37.0 37.0 37.0 5 35.9115 37.0 37.0 37.0 37.0 37.0 6 35.9935 37.0 37.0 37.0 37.0 37.0 7 35.9735 37.0 37.0 37.0 37.0 37.0 8 35.8635 37.0 37.0 37.0 37.0 37.0 9 36.029 37.0 37.0 37.0 37.0 37.0 10-14 36.0255 37.0 37.0 37.0 37.0 37.0 15-19 35.9218 37.0 37.0 37.0 37.0 37.0 20-24 35.882799999999996 37.0 37.0 37.0 37.0 37.0 25-29 35.9383 37.0 37.0 37.0 37.0 37.0 30-34 35.8798 37.0 37.0 37.0 37.0 37.0 35-39 35.9166 37.0 37.0 37.0 37.0 37.0 40-44 35.9231 37.0 37.0 37.0 37.0 37.0 45-49 35.7742 37.0 37.0 37.0 37.0 37.0 50-54 35.7467 37.0 37.0 37.0 37.0 37.0 55-59 35.7988 37.0 37.0 37.0 37.0 37.0 60-64 35.7515 37.0 37.0 37.0 37.0 37.0 65-69 35.754999999999995 37.0 37.0 37.0 37.0 37.0 70-74 35.70989999999999 37.0 37.0 37.0 37.0 37.0 75-79 35.6665 37.0 37.0 37.0 37.0 37.0 80-84 35.5928 37.0 37.0 37.0 37.0 37.0 85-89 35.5031 37.0 37.0 37.0 37.0 37.0 90-94 35.4742 37.0 37.0 37.0 34.6 37.0 95-99 35.435 37.0 37.0 37.0 37.0 37.0 100-104 35.492 37.0 37.0 37.0 37.0 37.0 105-109 35.526399999999995 37.0 37.0 37.0 37.0 37.0 110-114 35.3801 37.0 37.0 37.0 32.2 37.0 115-119 35.386900000000004 37.0 37.0 37.0 34.6 37.0 120-124 35.247499999999995 37.0 37.0 37.0 29.8 37.0 125-129 35.259699999999995 37.0 37.0 37.0 34.6 37.0 130-134 35.1801 37.0 37.0 37.0 27.4 37.0 135-139 35.2727 37.0 37.0 37.0 34.6 37.0 140-144 35.189499999999995 37.0 37.0 37.0 27.4 37.0 145-149 34.9623 37.0 37.0 37.0 25.0 37.0 150 35.416 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 15 1.0 16 1.0 17 0.0 18 1.0 19 0.0 20 0.0 21 1.0 22 6.0 23 13.0 24 7.0 25 13.0 26 16.0 27 21.0 28 31.0 29 48.0 30 71.0 31 71.0 32 81.0 33 126.0 34 215.0 35 548.0 36 2512.0 37 217.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 27.200000000000003 13.450000000000001 15.55 43.8 2 29.049999999999997 20.75 27.500000000000004 22.7 3 27.775 26.0 18.075 28.15 4 30.975 29.075 15.1 24.85 5 27.725 31.6 18.75 21.925 6 22.1 32.45 19.025 26.424999999999997 7 21.099999999999998 13.925 37.35 27.625 8 22.45 17.75 25.224999999999998 34.575 9 24.5 18.25 25.95 31.3 10-14 25.4 24.099999999999998 22.205 28.294999999999998 15-19 25.705 22.725 23.115 28.455000000000002 20-24 26.525 23.395 22.335 27.744999999999997 25-29 26.064999999999998 23.105 22.715 28.115000000000002 30-34 26.240000000000002 23.380000000000003 22.295 28.084999999999997 35-39 26.590000000000003 22.735 22.425 28.249999999999996 40-44 26.834999999999997 22.81 22.215 28.139999999999997 45-49 26.375 22.505 22.830000000000002 28.29 50-54 26.865 23.24 22.215 27.68 55-59 26.355 22.715 22.615 28.315 60-64 27.015 22.88 22.345000000000002 27.76 65-69 26.529999999999998 22.835 22.75 27.884999999999998 70-74 27.22 23.085 21.705 27.99 75-79 27.415 22.805 21.959999999999997 27.82 80-84 27.49 22.830000000000002 22.0 27.68 85-89 27.175 22.845 21.61 28.37 90-94 27.0 23.27 21.89 27.839999999999996 95-99 27.644999999999996 21.905 22.07 28.38 100-104 27.97 22.775000000000002 22.1 27.155 105-109 28.01 22.43 22.09 27.47 110-114 27.54 22.405 21.825 28.23 115-119 27.85 22.75 21.755 27.644999999999996 120-124 27.325 22.314999999999998 22.435 27.925 125-129 27.92 21.95 21.915000000000003 28.215 130-134 28.27 22.005 22.07 27.655 135-139 28.32 22.17 22.175 27.334999999999997 140-144 28.449999999999996 22.400000000000002 21.695 27.455000000000002 145-149 28.89 22.375 21.255 27.48 150 29.099999999999998 23.275000000000002 21.05 26.575 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 5.0 1 2.5 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.5 10 0.5 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 1.0 23 0.5 24 0.5 25 1.0 26 0.5 27 1.0 28 1.0 29 3.0 30 5.0 31 5.0 32 8.0 33 11.0 34 20.0 35 28.5 36 34.5 37 40.5 38 55.5 39 71.0 40 74.0 41 99.5 42 117.0 43 108.0 44 123.0 45 140.0 46 137.5 47 140.0 48 136.0 49 122.5 50 120.0 51 123.0 52 113.0 53 107.0 54 105.0 55 89.5 56 91.5 57 93.0 58 85.0 59 94.5 60 96.0 61 89.0 62 86.0 63 84.0 64 96.0 65 101.5 66 94.0 67 89.0 68 87.5 69 86.5 70 80.5 71 80.5 72 74.5 73 61.5 74 56.0 75 49.5 76 44.0 77 35.5 78 25.0 79 18.5 80 12.0 81 10.0 82 7.0 83 4.5 84 5.0 85 5.0 86 3.0 87 1.0 88 0.5 89 0.0 90 0.5 91 0.5 92 0.0 93 0.5 94 0.5 95 0.0 96 0.0 97 0.5 98 1.0 99 0.5 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 92.825 #Duplication Level Percentage of deduplicated Percentage of total 1 92.88984648532185 86.225 2 6.544573121465122 12.15 3 0.5386479935362241 1.5 4 0.0 0.0 5 0.026932399676811204 0.125 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 warn #Sequence Count Percentage Possible Source TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #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 0.0125 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.037500000000000006 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 82-83 0.1 0.0 0.0 0.0 0.0 84-85 0.1 0.0 0.0 0.0 0.0 86-87 0.1 0.0 0.0 0.0 0.0 88-89 0.1 0.0 0.0 0.0 0.0 90-91 0.1375 0.0 0.0 0.0 0.0 92-93 0.15 0.0 0.0 0.0 0.0 94-95 0.175 0.0 0.0 0.0 0.0 96-97 0.225 0.0 0.0 0.0 0.0 98-99 0.225 0.0 0.0 0.0 0.0 100-101 0.275 0.0 0.0 0.0 0.0 102-103 0.3 0.0 0.0 0.0 0.0 104-105 0.3 0.0 0.0 0.0 0.0 106-107 0.3 0.0 0.0 0.0 0.0 108-109 0.325 0.0 0.0 0.0 0.0 110-111 0.325 0.0 0.0 0.0 0.0 112-113 0.4 0.0 0.0 0.0 0.0 114-115 0.5125 0.0 0.0 0.0 0.0 116-117 0.575 0.0 0.0 0.0 0.0 118-119 0.625 0.0 0.0 0.0 0.0 120-121 0.6625000000000001 0.0 0.0 0.0 0.0 122-123 0.675 0.0 0.0 0.0 0.0 124-125 0.675 0.0 0.0 0.0 0.0 126-127 0.8 0.0 0.0 0.0 0.0 128-129 0.925 0.0 0.0 0.0 0.0 130-131 0.9624999999999999 0.0 0.0 0.0 0.0 132-133 1.1 0.0 0.0 0.0 0.0 134-135 1.2 0.0 0.0 0.0 0.0 136-137 1.3375 0.0 0.0 0.0 0.0 138 1.375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCGATCT 10 0.006973645 144.0 3 AACACCA 10 0.006973645 144.0 5 >>END_MODULE Read 1226411 spots for ERR9452517.sra Written 1226411 spots for ERR9452517.sra Read 1226411 spots for ERR9452517.sra Written 1226411 spots for ERR9452517.sra Read 1226411 spots for ERR9452517.sra Written 1226411 spots for ERR9452517.sra Read 1226411 spots for ERR9452517.sra Written 1226411 spots for ERR9452517.sra Read 1226411 spots for ERR9452517.sra Written 1226411 spots for ERR9452517.sra Read 1226411 spots for ERR9452517.sra Written 1226411 spots for ERR9452517.sra Read 1226426 spots for ERR9452517.sra Written 1226426 spots for ERR9452517.sra Read 1226411 spots for ERR9452517.sra Written 1226411 spots for ERR9452517.sra Read 1226411 spots for ERR9452517.sra Written 1226411 spots for ERR9452517.sra Read 1226411 spots for ERR9452517.sra Written 1226411 spots for ERR9452517.sra Read 1226411 spots for ERR9452517.sra Written 1226411 spots for ERR9452517.sra Read 1226411 spots for ERR9452517.sra Written 1226411 spots for ERR9452517.sra Read 1226411 spots for ERR9452517.sra Written 1226411 spots for ERR9452517.sra Read 1226411 spots for ERR9452517.sra Written 1226411 spots for ERR9452517.sra Read 1226411 spots for ERR9452517.sra Written 1226411 spots for ERR9452517.sra Read 1226411 spots for ERR9452517.sra Written 1226411 spots for ERR9452517.sra Read 1226411 spots for ERR9452517.sra Written 1226411 spots for ERR9452517.sra Read 1226411 spots for ERR9452517.sra Written 1226411 spots for ERR9452517.sra Read 1226411 spots for ERR9452517.sra Written 1226411 spots for ERR9452517.sra Read 1226411 spots for ERR9452517.sra Written 1226411 spots for ERR9452517.sra SRR ids: ['ERR9452517.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ewqp9v65 ERR9452517.sra spots: 24528235 blocks: [[1, 1226411], [1226412, 2452822], [2452823, 3679233], [3679234, 4905644], [4905645, 6132055], [6132056, 7358466], [7358467, 8584877], [8584878, 9811288], [9811289, 11037699], [11037700, 12264110], [12264111, 13490521], [13490522, 14716932], [14716933, 15943343], [15943344, 17169754], [17169755, 18396165], [18396166, 19622576], [19622577, 20848987], [20848988, 22075398], [22075399, 23301809], [23301810, 24528235]] ERR9452517 file size 8242206 ERR9452517 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 ERR9452517 ERR9452517_1.fastq ERR9452517_2.fastq Input file: ERR9452517_1.fastq Paired file: ERR9452517_2.fastq trimmed: ERR9452517-trimmed-pair1.fastq, ERR9452517-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 Fri Dec 6 23:25:35 2024 >> started Fri Dec 6 23:26:00 2024 >> done (25.516s) 24528235 read pairs processed; of these: 307 ( 0.00%) short read pairs filtered out after trimming by size control 706 ( 0.00%) empty read pairs filtered out after trimming by size control 24527222 (100.00%) read pairs available; of these: 661989 ( 2.70%) trimmed read pairs available after processing 23865233 (97.30%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 30 0.00% 19 47 0.00% 20 6348 0.03% 21 73 0.00% 22 26 0.00% 23 21 0.00% 24 18 0.00% 25 21 0.00% 26 21 0.00% 27 20 0.00% 28 25 0.00% 29 47 0.00% 30 183 0.00% 31 52 0.00% 32 23 0.00% 33 26 0.00% 34 27 0.00% 35 30 0.00% 36 32 0.00% 37 29 0.00% 38 36 0.00% 39 32 0.00% 40 35 0.00% 41 40 0.00% 42 49 0.00% 43 49 0.00% 44 54 0.00% 45 47 0.00% 46 80 0.00% 47 90 0.00% 48 95 0.00% 49 121 0.00% 50 135 0.00% 51 159 0.00% 52 178 0.00% 53 157 0.00% 54 199 0.00% 55 211 0.00% 56 228 0.00% 57 292 0.00% 58 352 0.00% 59 354 0.00% 60 428 0.00% 61 478 0.00% 62 511 0.00% 63 573 0.00% 64 600 0.00% 65 641 0.00% 66 657 0.00% 67 743 0.00% 68 776 0.00% 69 829 0.00% 70 862 0.00% 71 931 0.00% 72 1046 0.00% 73 1059 0.00% 74 1106 0.00% 75 1190 0.00% 76 1249 0.01% 77 1370 0.01% 78 1441 0.01% 79 1464 0.01% 80 1578 0.01% 81 1610 0.01% 82 1702 0.01% 83 1872 0.01% 84 1901 0.01% 85 2219 0.01% 86 2087 0.01% 87 2132 0.01% 88 2290 0.01% 89 2277 0.01% 90 2436 0.01% 91 2539 0.01% 92 2674 0.01% 93 2905 0.01% 94 3134 0.01% 95 3019 0.01% 96 3207 0.01% 97 3398 0.01% 98 3526 0.01% 99 3749 0.02% 100 3642 0.01% 101 3999 0.02% 102 3973 0.02% 103 4344 0.02% 104 4423 0.02% 105 4776 0.02% 106 4772 0.02% 107 4905 0.02% 108 4945 0.02% 109 5366 0.02% 110 5519 0.02% 111 5735 0.02% 112 5864 0.02% 113 6445 0.03% 114 6553 0.03% 115 6951 0.03% 116 7072 0.03% 117 7242 0.03% 118 7595 0.03% 119 7734 0.03% 120 8150 0.03% 121 8370 0.03% 122 8693 0.04% 123 9371 0.04% 124 9873 0.04% 125 10273 0.04% 126 10623 0.04% 127 10782 0.04% 128 11286 0.05% 129 11748 0.05% 130 12158 0.05% 131 12733 0.05% 132 13080 0.05% 133 13899 0.06% 134 14938 0.06% 135 15562 0.06% 136 15917 0.06% 137 16630 0.07% 138 17075 0.07% 139 17237 0.07% 140 18338 0.07% 141 18913 0.08% 142 19773 0.08% 143 20830 0.08% 144 21366 0.09% 145 23127 0.09% 146 23453 0.10% 147 24979 0.10% 148 25662 0.10% 149 26994 0.11% 150 23865233 97.30% 24527222 reads passed initial QC criterion=sequence-density sequence-density=0.26 sequence-density-rank=1 fanout-score=1.95 fanout-score-rank=36 prefix-density=0.26 prefix-fanout=2.0 sequence=GTCCGCATCATCGGCTTCGACAACACCCGGCAGGTGCAGTGCATCAGCTTCATCGCCTTCAAGCCACCGGGCTGCGAGGAATCCGGCAAGGCATAAACAACCAAGGACAGCTCCGTATTAAGATGGACCATATATAAAGTGTCAGCTCAGTTTTGTCAACTCTGACATTGCTTTGAGTTTTCTATTTTTCATCCCCAAGATTGTTGTTGTGTGTAGCAACCTGGCTCTCGATCGAGGAGCTAGCTTGCATATGT criterion=fanout-score sequence-density=0.11 sequence-density-rank=27 fanout-score=182.00 fanout-score-rank=1 prefix-density=1.02 prefix-fanout=19.5 sequence=CCGCCGCCGCCG criterion=sequence-density sequence-density=0.26 sequence-density-rank=1 fanout-score=1.96 fanout-score-rank=37 prefix-density=0.26 prefix-fanout=2.0 sequence=GTCCGCATCATCGGCTTCGACAACACCCGGCAGGTGCAGTGCATCAGCTTCATCGCCTTCAAGCCACCGGGCTGCGAGGAATCCGGCAAGGCATAAACAACCAAGGACAGCTCCGTATTAAGATGGACCATATATAAAGTGTCAGCTCAGTTTTGTCAACTCTGACATTGCTTTGAGTTTTCTATTTTTCATCCCCAAGATTGTTGTTGTGTGTAGCAACCTGGCTCTCGATCGAGGAGCTAGCT criterion=fanout-score sequence-density=0.12 sequence-density-rank=22 fanout-score=164.19 fanout-score-rank=1 prefix-density=1.03 prefix-fanout=18.5 sequence=CCGCCGCCGCCA ERR9452517 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 23:27:21 Started mapping on | Dec 06 23:27:21 Finished on | Dec 06 23:30:27 Mapping speed, Million of reads per hour | 474.72 Number of input reads | 24527222 Average input read length | 298 UNIQUE READS: Uniquely mapped reads number | 22939888 Uniquely mapped reads % | 93.53% Average mapped length | 297.08 Number of splices: Total | 21406757 Number of splices: Annotated (sjdb) | 20206070 Number of splices: GT/AG | 21084555 Number of splices: GC/AG | 260657 Number of splices: AT/AC | 9677 Number of splices: Non-canonical | 51868 Mismatch rate per base, % | 0.44% Deletion rate per base | 0.03% Deletion average length | 2.86 Insertion rate per base | 0.02% Insertion average length | 2.85 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 342388 % of reads mapped to multiple loci | 1.40% Number of reads mapped to too many loci | 65482 % of reads mapped to too many loci | 0.27% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.31% % of reads unmapped: other | 2.50% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1244946 1244946 1244946 N_multimapping 342388 342388 342388 N_noFeature 765973 11589039 11682867 N_ambiguous 558476 65176 64412 UnstrandedReadsAssigned:21615439 PositiveStrandReadsAssigned:11285673 NegativeStrandReadsAssigned:11192609 Dataset is classified unstranded MeadianReadLen=150 20thPercentileLength=150 echo kmer=145 ERR9452517 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: ERR9452517-trimmed-pair1.fastq ERR9452517-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 24,527,222 reads, 22,486,012 reads pseudoaligned [quant] estimated average fragment length: 246.214 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,113 rounds 52973 ERR9452517.ke.tsv 35125 ERR9452517.se.tsv 88098 total ==> ERR9452517.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 691.021 0 0 PNS24247 1044 798.786 63.4404 4.49679 PNS24249 1928 1682.79 354.5 11.9277 PNS24246 1044 798.786 63.4404 4.49679 PNS24248 1044 798.786 63.4404 4.49679 PNS24244 1471 1225.79 54.1786 2.50254 PNS24243 293 68.6878 21 17.3104 KQK14069 1603 1357.79 10248.8 427.374 KQK14071 474 232.231 944.413 230.256 ==> ERR9452517.se.tsv <== BRADI_1g14170v3 12146 BRADI_1g53295v3 539 BRADI_1g59795v3 79 BRADI_1g07683v3 0 BRADI_1g00485v3 53 BRADI_1g20270v3 1064 BRADI_1g74790v3 439 BRADI_1g09890v3 13 BRADI_1g77505v3 505 BRADI_1g48960v3 0 ERR9452517 completed mapping pipeline successfully