Starting /dee2/code/volunteer_pipeline.sh SRR7814818 current disk space = 1551567142912 free memory = 1599143300 SRR7814818 SRAfilesize eaeeb99bc35ad46d396ea78e8c9accf0 SRR7814818.sra SRR7814818.sra file validated SRR7814818 is paired end SRR7814818 is conventional basespace SRR7814818 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7814818_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 36.36525 37.0 37.0 37.0 37.0 37.0 2 36.369 37.0 37.0 37.0 37.0 37.0 3 36.4655 37.0 37.0 37.0 37.0 37.0 4 36.521 37.0 37.0 37.0 37.0 37.0 5 36.4885 37.0 37.0 37.0 37.0 37.0 6 36.537 37.0 37.0 37.0 37.0 37.0 7 36.4375 37.0 37.0 37.0 37.0 37.0 8 36.5325 37.0 37.0 37.0 37.0 37.0 9 36.618 37.0 37.0 37.0 37.0 37.0 10-14 36.517500000000005 37.0 37.0 37.0 37.0 37.0 15-19 36.4499 37.0 37.0 37.0 37.0 37.0 20-24 36.4945 37.0 37.0 37.0 37.0 37.0 25-29 36.409800000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.175 37.0 37.0 37.0 37.0 37.0 35-39 36.1766 37.0 37.0 37.0 37.0 37.0 40-44 36.14450000000001 37.0 37.0 37.0 37.0 37.0 45-49 36.2551 37.0 37.0 37.0 37.0 37.0 50-54 36.277499999999996 37.0 37.0 37.0 37.0 37.0 55-59 36.2329 37.0 37.0 37.0 37.0 37.0 60-64 36.1762 37.0 37.0 37.0 37.0 37.0 65-69 36.06 37.0 37.0 37.0 37.0 37.0 70-74 36.0427 37.0 37.0 37.0 37.0 37.0 75-79 35.9901 37.0 37.0 37.0 37.0 37.0 80-84 36.0064 37.0 37.0 37.0 37.0 37.0 85-89 36.0184 37.0 37.0 37.0 37.0 37.0 90-94 35.9257 37.0 37.0 37.0 37.0 37.0 95-99 35.648 37.0 37.0 37.0 37.0 37.0 100-104 35.273700000000005 37.0 37.0 37.0 32.2 37.0 105-109 35.513999999999996 37.0 37.0 37.0 37.0 37.0 110-114 35.6581 37.0 37.0 37.0 37.0 37.0 115-119 35.4153 37.0 37.0 37.0 34.6 37.0 120-124 34.8258 37.0 37.0 37.0 25.0 37.0 125-129 34.57090000000001 37.0 37.0 37.0 25.0 37.0 130-134 35.1058 37.0 37.0 37.0 25.0 37.0 135-139 34.9244 37.0 37.0 37.0 25.0 37.0 140-144 35.0597 37.0 37.0 37.0 27.4 37.0 145-149 34.94500000000001 37.0 37.0 37.0 25.0 37.0 150-151 34.17575 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 4.0 24 6.0 25 2.0 26 4.0 27 10.0 28 21.0 29 29.0 30 40.0 31 48.0 32 72.0 33 172.0 34 303.0 35 604.0 36 2498.0 37 187.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 55.85359739283028 11.13060917523189 4.437202306342441 28.578591125595388 2 26.400000000000002 12.375 29.825000000000003 31.4 3 20.875 19.5 24.55 35.075 4 27.250000000000004 26.3 20.05 26.400000000000002 5 26.650000000000002 29.849999999999998 22.575 20.925 6 23.625 31.525 21.975 22.875 7 18.9 23.125 39.225 18.75 8 19.775000000000002 23.075000000000003 29.975 27.175 9 21.4 21.45 30.85 26.3 10-14 24.22 25.95 24.255 25.575 15-19 24.305 24.875 24.695 26.125 20-24 24.215 25.285000000000004 24.610000000000003 25.89 25-29 24.145 25.09 24.33 26.435 30-34 24.325 25.130000000000003 24.175 26.369999999999997 35-39 24.455 24.945 24.54 26.06 40-44 24.465 24.465 24.695 26.375 45-49 24.5 25.665 24.035 25.8 50-54 24.515 24.965 24.375 26.145000000000003 55-59 24.585 24.36 24.525 26.529999999999998 60-64 24.685000000000002 24.75 23.885 26.68 65-69 25.119999999999997 24.84 23.9 26.14 70-74 25.569999999999997 24.38 23.87 26.179999999999996 75-79 24.73 24.69 24.349999999999998 26.229999999999997 80-84 24.27 24.275 24.115000000000002 27.339999999999996 85-89 24.815 24.705 24.375 26.105 90-94 25.165 23.77 24.224999999999998 26.840000000000003 95-99 25.53 23.794999999999998 24.68 25.995 100-104 25.53 24.235 23.875 26.36 105-109 25.555 24.075 23.880000000000003 26.490000000000002 110-114 25.525 24.605 23.52 26.35 115-119 25.47 24.015 23.565 26.950000000000003 120-124 25.16 24.240000000000002 23.330000000000002 27.27 125-129 25.045 24.25 23.815 26.889999999999997 130-134 25.555 24.39 23.29 26.765 135-139 25.82 24.275 23.28 26.625 140-144 25.185000000000002 23.87 23.849999999999998 27.095000000000002 145-149 24.98 24.355 23.265 27.400000000000002 150-151 25.7 24.1375 23.2625 26.900000000000002 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.5 6 0.5 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 1.0 24 1.0 25 1.5 26 2.0 27 0.5 28 4.0 29 8.5 30 8.0 31 8.5 32 13.0 33 17.0 34 23.5 35 35.5 36 48.0 37 62.0 38 77.5 39 88.5 40 105.5 41 141.5 42 156.5 43 155.5 44 171.5 45 166.5 46 161.5 47 167.5 48 151.5 49 149.5 50 147.0 51 131.5 52 129.0 53 125.0 54 106.5 55 99.5 56 106.5 57 94.5 58 82.0 59 84.0 60 90.5 61 84.5 62 73.5 63 75.5 64 68.0 65 66.5 66 72.5 67 70.0 68 66.0 69 56.5 70 49.0 71 36.5 72 33.0 73 32.0 74 21.5 75 17.5 76 14.0 77 11.5 78 12.0 79 8.0 80 2.0 81 1.0 82 1.5 83 0.5 84 1.0 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 0.27499999999999997 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 90.45 #Duplication Level Percentage of deduplicated Percentage of total 1 91.04477611940298 82.35 2 7.739082365948037 14.000000000000002 3 1.077943615257048 2.9250000000000003 4 0.055279159756771695 0.2 5 0.0 0.0 6 0.055279159756771695 0.3 7 0.0 0.0 8 0.0 0.0 9 0.027639579878385848 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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTAACGACATCTCGTAT 9 0.22499999999999998 TruSeq Adapter, Index 19 (97% over 37bp) CACCTTTTTGCTAGCATCTCGCACGGCAAGAGCGATTGCCGAGCTTAGAG 6 0.15 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTAACGACATCGCGTAT 6 0.15 TruSeq Adapter, Index 19 (97% over 37bp) >>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 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.0625 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.125 0.0 0.0 0.0 0.0 82-83 0.1375 0.0 0.0 0.0 0.0 84-85 0.175 0.0 0.0 0.0 0.0 86-87 0.2 0.0 0.0 0.0 0.0 88-89 0.225 0.0 0.0 0.0 0.0 90-91 0.4 0.0 0.0 0.0 0.0 92-93 0.5125 0.0 0.0 0.0 0.0 94-95 0.575 0.0 0.0 0.0 0.0 96-97 0.675 0.0 0.0 0.0 0.0 98-99 0.8374999999999999 0.0 0.0 0.0 0.0 100-101 0.9375 0.0 0.0 0.0 0.0 102-103 1.125 0.0 0.0 0.0 0.0 104-105 1.3875 0.0 0.0 0.0 0.0 106-107 1.5875 0.0 0.0 0.0 0.0 108-109 1.8 0.0 0.0 0.0 0.0 110-111 2.0375 0.0 0.0 0.0 0.0 112-113 2.2249999999999996 0.0 0.0 0.0 0.0 114-115 2.4875 0.0 0.0 0.0 0.0 116-117 2.85 0.0 0.0 0.0 0.0 118-119 3.1625 0.0 0.0 0.0 0.0 120-121 3.475 0.0 0.0 0.0 0.0 122-123 3.725 0.0 0.0 0.0 0.0 124-125 4.0125 0.0 0.0 0.0 0.0 126-127 4.4125 0.0 0.0 0.0 0.0 128-129 4.85 0.0 0.0 0.0 0.0 130-131 5.3375 0.0 0.0 0.0 0.0 132-133 5.8 0.0 0.0 0.0 0.0 134-135 6.225 0.0 0.0 0.0 0.0 136-137 6.5375 0.0 0.0 0.0 0.0 138-139 7.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR7814818 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7814818_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 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.0615 37.0 37.0 37.0 37.0 37.0 2 35.825 37.0 37.0 37.0 37.0 37.0 3 35.4785 37.0 37.0 37.0 37.0 37.0 4 35.787 37.0 37.0 37.0 37.0 37.0 5 35.7935 37.0 37.0 37.0 37.0 37.0 6 35.6515 37.0 37.0 37.0 37.0 37.0 7 35.273 37.0 37.0 37.0 37.0 37.0 8 35.565 37.0 37.0 37.0 37.0 37.0 9 35.649 37.0 37.0 37.0 37.0 37.0 10-14 35.548 37.0 37.0 37.0 37.0 37.0 15-19 35.150400000000005 37.0 37.0 37.0 32.2 37.0 20-24 35.4406 37.0 37.0 37.0 37.0 37.0 25-29 35.248900000000006 37.0 37.0 37.0 34.6 37.0 30-34 35.0308 37.0 37.0 37.0 27.4 37.0 35-39 35.083600000000004 37.0 37.0 37.0 32.2 37.0 40-44 34.650400000000005 37.0 37.0 37.0 25.0 37.0 45-49 34.8257 37.0 37.0 37.0 25.0 37.0 50-54 34.176300000000005 37.0 37.0 37.0 25.0 37.0 55-59 34.0924 37.0 37.0 37.0 25.0 37.0 60-64 34.3374 37.0 37.0 37.0 25.0 37.0 65-69 34.2863 37.0 37.0 37.0 25.0 37.0 70-74 33.912099999999995 37.0 37.0 37.0 25.0 37.0 75-79 33.706 37.0 37.0 37.0 22.2 37.0 80-84 33.61900000000001 37.0 37.0 37.0 19.4 37.0 85-89 34.047999999999995 37.0 37.0 37.0 25.0 37.0 90-94 33.5972 37.0 37.0 37.0 25.0 37.0 95-99 32.721900000000005 37.0 37.0 37.0 11.0 37.0 100-104 33.052 37.0 37.0 37.0 13.8 37.0 105-109 32.6573 37.0 37.0 37.0 11.0 37.0 110-114 32.9906 37.0 37.0 37.0 11.0 37.0 115-119 33.1154 37.0 37.0 37.0 16.6 37.0 120-124 32.3817 37.0 37.0 37.0 11.0 37.0 125-129 32.5851 37.0 34.6 37.0 13.8 37.0 130-134 32.10980000000001 37.0 32.2 37.0 11.0 37.0 135-139 32.1022 37.0 29.8 37.0 11.0 37.0 140-144 32.2307 37.0 37.0 37.0 11.0 37.0 145-149 31.8416 37.0 27.4 37.0 11.0 37.0 150-151 31.602249999999998 37.0 31.0 37.0 11.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 6.0 15 9.0 16 4.0 17 2.0 18 3.0 19 10.0 20 13.0 21 19.0 22 19.0 23 43.0 24 56.0 25 71.0 26 80.0 27 95.0 28 101.0 29 113.0 30 130.0 31 149.0 32 156.0 33 204.0 34 309.0 35 702.0 36 1661.0 37 45.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 50.675000000000004 18.325 6.35 24.65 2 31.974999999999998 20.575 25.275 22.175 3 25.75 22.8 26.924999999999997 24.525 4 29.299999999999997 30.025000000000002 17.424999999999997 23.25 5 28.225 31.724999999999998 18.575 21.475 6 24.15 34.35 17.7 23.799999999999997 7 26.400000000000002 18.55 30.5 24.55 8 23.325000000000003 22.15 22.475 32.05 9 25.45 21.55 24.875 28.125 10-14 27.245 25.374999999999996 21.185000000000002 26.195 15-19 27.47 23.665 22.57 26.295 20-24 27.71 24.34 22.285 25.665 25-29 26.855 25.085 22.035 26.025 30-34 26.009999999999998 25.180000000000003 22.645 26.165 35-39 26.400000000000002 24.515 22.805 26.279999999999998 40-44 26.340000000000003 24.5 23.265 25.895000000000003 45-49 27.644999999999996 24.425 22.7 25.230000000000004 50-54 26.35 25.22 22.835 25.595000000000002 55-59 27.005000000000003 24.875 22.59 25.53 60-64 27.075 24.385 23.005 25.535000000000004 65-69 26.855 24.63 22.7 25.814999999999998 70-74 26.705000000000002 24.975 23.225 25.095 75-79 26.905 25.055 22.585 25.455 80-84 26.39 25.285000000000004 23.3 25.025 85-89 26.935 24.27 23.380000000000003 25.415 90-94 26.745 24.82 23.47 24.965 95-99 26.825 26.135 22.46 24.58 100-104 26.924999999999997 26.27 22.675 24.13 105-109 25.81 26.284999999999997 22.535 25.369999999999997 110-114 27.16 25.5 22.759999999999998 24.58 115-119 27.63 25.935000000000002 22.25 24.185000000000002 120-124 26.985 26.815 22.165000000000003 24.035 125-129 27.529999999999998 26.965 22.0 23.505000000000003 130-134 27.245 27.034999999999997 22.7 23.02 135-139 28.199999999999996 27.375 21.72 22.705000000000002 140-144 27.785 26.900000000000002 22.085 23.23 145-149 27.779999999999998 27.24 22.33 22.650000000000002 150-151 28.6875 25.624999999999996 22.3375 23.35 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.5 5 0.5 6 0.0 7 0.5 8 2.0 9 1.5 10 1.0 11 1.5 12 0.5 13 0.5 14 1.0 15 0.5 16 0.5 17 1.5 18 1.0 19 1.0 20 1.5 21 1.0 22 2.0 23 3.0 24 3.0 25 2.5 26 2.0 27 1.5 28 2.5 29 7.5 30 12.0 31 12.0 32 13.0 33 21.0 34 27.5 35 29.0 36 42.0 37 50.0 38 57.0 39 67.5 40 86.0 41 111.0 42 120.0 43 135.0 44 130.5 45 128.5 46 151.5 47 160.0 48 158.0 49 157.0 50 139.0 51 124.0 52 113.5 53 108.0 54 123.5 55 116.5 56 109.0 57 107.0 58 103.5 59 96.0 60 85.0 61 90.5 62 87.0 63 84.0 64 82.5 65 71.0 66 78.5 67 76.0 68 64.0 69 69.5 70 64.5 71 53.5 72 48.0 73 39.5 74 31.0 75 26.0 76 21.0 77 19.5 78 15.0 79 8.0 80 3.5 81 1.5 82 4.0 83 4.0 84 2.5 85 2.0 86 1.5 87 1.0 88 0.5 89 0.5 90 1.0 91 1.5 92 0.5 93 1.0 94 1.0 95 0.0 96 0.0 97 0.5 98 1.0 99 0.5 100 4.5 >>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 91.2 #Duplication Level Percentage of deduplicated Percentage of total 1 92.07785087719299 83.975 2 6.962719298245614 12.7 3 0.7949561403508772 2.175 4 0.027412280701754384 0.1 5 0.027412280701754384 0.125 6 0.05482456140350877 0.3 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.05482456140350877 0.625 >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 13 0.325 No Hit AGCACACACAAGCCTAGAAGCCTTCAGCTTAATCTTCTTCCTAAGCAAGT 12 0.3 No Hit CTGGTAGACGACCAGCGCTGACGAGCTGGCGCAATGACGACCTAATTGGC 6 0.15 No Hit GTGAGCACCACTGCTGCAGAGAGAGAGATCGAGATGGCAGCGTCCATGAT 6 0.15 No Hit GAAGCACACACAAGCCTAGAAGCCTTCAGCTTAATCTTCTTCCTAAGCAA 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 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.0625 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.125 0.0 0.0 0.0 0.0 82-83 0.1375 0.0 0.0 0.0 0.0 84-85 0.175 0.0 0.0 0.0 0.0 86-87 0.2 0.0 0.0 0.0 0.0 88-89 0.225 0.0 0.0 0.0 0.0 90-91 0.375 0.0 0.0 0.0 0.0 92-93 0.475 0.0 0.0 0.0 0.0 94-95 0.5 0.0 0.0 0.0 0.0 96-97 0.6000000000000001 0.0 0.0 0.0 0.0 98-99 0.7625 0.0 0.0 0.0 0.0 100-101 0.85 0.0 0.0 0.0 0.0 102-103 1.025 0.0 0.0 0.0 0.0 104-105 1.275 0.0 0.0 0.0 0.0 106-107 1.425 0.0 0.0 0.0 0.0 108-109 1.675 0.0 0.0 0.0 0.0 110-111 1.8875 0.0 0.0 0.0 0.0 112-113 2.05 0.0 0.0 0.0 0.0 114-115 2.3125 0.0 0.0 0.0 0.0 116-117 2.6625 0.0 0.0 0.0 0.0 118-119 2.9625 0.0 0.0 0.0 0.0 120-121 3.2375 0.0 0.0 0.0 0.0 122-123 3.4125 0.0 0.0 0.0 0.0 124-125 3.6500000000000004 0.0 0.0 0.0 0.0 126-127 3.9749999999999996 0.0 0.0 0.0 0.0 128-129 4.3375 0.0 0.0 0.0 0.0 130-131 4.6625 0.0 0.0 0.0 0.0 132-133 5.125 0.0 0.0 0.0 0.0 134-135 5.5 0.0 0.0 0.0 0.0 136-137 5.825 0.0 0.0 0.0 0.0 138-139 6.2375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CGTCAGA 10 0.006830828 145.0 145 CACACAA 10 0.006830828 145.0 5 ACACACA 15 1.1411342E-4 145.0 4 ACACAAG 10 0.006830828 145.0 6 AGCACAC 10 0.006830828 145.0 1 GCACACA 10 0.006830828 145.0 2 GAGATTT 10 0.006830828 145.0 1 CACACAC 20 3.5877043E-4 108.75 3 >>END_MODULE Read 1630338 spots for SRR7814818.sra Written 1630338 spots for SRR7814818.sra Read 1630338 spots for SRR7814818.sra Written 1630338 spots for SRR7814818.sra Read 1630338 spots for SRR7814818.sra Written 1630338 spots for SRR7814818.sra Read 1630338 spots for SRR7814818.sra Written 1630338 spots for SRR7814818.sra Read 1630338 spots for SRR7814818.sra Written 1630338 spots for SRR7814818.sra Read 1630338 spots for SRR7814818.sra Written 1630338 spots for SRR7814818.sra Read 1630338 spots for SRR7814818.sra Written 1630338 spots for SRR7814818.sra Read 1630338 spots for SRR7814818.sra Written 1630338 spots for SRR7814818.sra Read 1630338 spots for SRR7814818.sra Written 1630338 spots for SRR7814818.sra Read 1630343 spots for SRR7814818.sra Written 1630343 spots for SRR7814818.sra Read 1630338 spots for SRR7814818.sra Written 1630338 spots for SRR7814818.sra Read 1630338 spots for SRR7814818.sra Written 1630338 spots for SRR7814818.sra Read 1630338 spots for SRR7814818.sra Written 1630338 spots for SRR7814818.sra Read 1630338 spots for SRR7814818.sra Written 1630338 spots for SRR7814818.sra Read 1630338 spots for SRR7814818.sra Written 1630338 spots for SRR7814818.sra Read 1630338 spots for SRR7814818.sra Written 1630338 spots for SRR7814818.sra Read 1630338 spots for SRR7814818.sra Written 1630338 spots for SRR7814818.sra Read 1630338 spots for SRR7814818.sra Written 1630338 spots for SRR7814818.sra Read 1630338 spots for SRR7814818.sra Written 1630338 spots for SRR7814818.sra Read 1630338 spots for SRR7814818.sra Written 1630338 spots for SRR7814818.sra SRR ids: ['SRR7814818.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_bfa1h58r SRR7814818.sra spots: 32606765 blocks: [[1, 1630338], [1630339, 3260676], [3260677, 4891014], [4891015, 6521352], [6521353, 8151690], [8151691, 9782028], [9782029, 11412366], [11412367, 13042704], [13042705, 14673042], [14673043, 16303380], [16303381, 17933718], [17933719, 19564056], [19564057, 21194394], [21194395, 22824732], [22824733, 24455070], [24455071, 26085408], [26085409, 27715746], [27715747, 29346084], [29346085, 30976422], [30976423, 32606765]] SRR7814818 file size 11027662 SRR7814818 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 SRR7814818 SRR7814818_1.fastq SRR7814818_2.fastq Input file: SRR7814818_1.fastq Paired file: SRR7814818_2.fastq trimmed: SRR7814818-trimmed-pair1.fastq, SRR7814818-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 11:10:32 2024 >> started Fri Dec 6 11:11:10 2024 >> done (37.954s) 32606765 read pairs processed; of these: 208 ( 0.00%) short read pairs filtered out after trimming by size control 80134 ( 0.25%) empty read pairs filtered out after trimming by size control 32526423 (99.75%) read pairs available; of these: 3163354 ( 9.73%) trimmed read pairs available after processing 29363069 (90.27%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 10 0.00% 19 20 0.00% 20 20 0.00% 21 13 0.00% 22 18 0.00% 23 21 0.00% 24 26 0.00% 25 43 0.00% 26 23 0.00% 27 30 0.00% 28 52 0.00% 29 37 0.00% 30 47 0.00% 31 50 0.00% 32 55 0.00% 33 54 0.00% 34 60 0.00% 35 56 0.00% 36 54 0.00% 37 75 0.00% 38 80 0.00% 39 72 0.00% 40 85 0.00% 41 77 0.00% 42 89 0.00% 43 89 0.00% 44 78 0.00% 45 104 0.00% 46 105 0.00% 47 125 0.00% 48 116 0.00% 49 171 0.00% 50 149 0.00% 51 175 0.00% 52 176 0.00% 53 172 0.00% 54 179 0.00% 55 215 0.00% 56 229 0.00% 57 252 0.00% 58 300 0.00% 59 361 0.00% 60 420 0.00% 61 432 0.00% 62 528 0.00% 63 564 0.00% 64 589 0.00% 65 582 0.00% 66 721 0.00% 67 827 0.00% 68 884 0.00% 69 972 0.00% 70 1171 0.00% 71 1365 0.00% 72 1555 0.00% 73 1791 0.01% 74 1888 0.01% 75 2093 0.01% 76 2335 0.01% 77 2610 0.01% 78 2863 0.01% 79 3274 0.01% 80 3665 0.01% 81 4174 0.01% 82 4738 0.01% 83 5204 0.02% 84 5943 0.02% 85 6294 0.02% 86 6733 0.02% 87 7549 0.02% 88 8297 0.03% 89 8918 0.03% 90 10006 0.03% 91 11082 0.03% 92 12150 0.04% 93 13245 0.04% 94 14296 0.04% 95 15359 0.05% 96 16505 0.05% 97 17560 0.05% 98 18258 0.06% 99 19708 0.06% 100 21079 0.06% 101 22328 0.07% 102 24464 0.08% 103 25206 0.08% 104 26988 0.08% 105 28118 0.09% 106 29776 0.09% 107 30411 0.09% 108 31720 0.10% 109 32993 0.10% 110 34436 0.11% 111 36519 0.11% 112 37964 0.12% 113 39799 0.12% 114 41989 0.13% 115 43470 0.13% 116 44572 0.14% 117 46132 0.14% 118 46333 0.14% 119 47475 0.15% 120 49061 0.15% 121 50558 0.16% 122 51685 0.16% 123 54617 0.17% 124 57200 0.18% 125 58497 0.18% 126 60043 0.18% 127 60298 0.19% 128 61425 0.19% 129 63009 0.19% 130 63235 0.19% 131 64943 0.20% 132 67641 0.21% 133 69702 0.21% 134 71061 0.22% 135 73426 0.23% 136 74102 0.23% 137 73614 0.23% 138 75843 0.23% 139 76327 0.23% 140 78144 0.24% 141 79112 0.24% 142 81151 0.25% 143 82622 0.25% 144 86390 0.27% 145 88001 0.27% 146 89438 0.27% 147 92211 0.28% 148 90718 0.28% 149 92111 0.28% 150 94086 0.29% 151 29363069 90.27% 32526423 reads passed initial QC criterion=sequence-density sequence-density=0.90 sequence-density-rank=1 fanout-score=3.11 fanout-score-rank=15 prefix-density=0.97 prefix-fanout=2.9 sequence=GGTGTTGTCGAAGCCGATGATGCGGACATAGGCGTCAGGGTACTCCTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=27 fanout-score=18.63 fanout-score-rank=1 prefix-density=0.03 prefix-fanout=3.7 sequence=ACCAAATGAATATACTCAATATCTTTATATATGAACAAAAACTTTTCATGCCCAGCAATTGCTTGGATGCAATGCGGTACTTAGGTACAAAGAGTGAAACATCAGAATAATTAAAGTGGCATGCTTAAAAGGTGTAAAGGCAGCTGCCGTCGTCACTCCTTGCTGTTGGGTCGTAGTTCTCGGCATTCCGGTCAGTGCAACCTTCTGGGACGGGCAAATTACCTTGTTGTGCTCCTTTACCTCCTCCTATGCAGCTAGAGATGGTGTGTGTATGAAGAGTGTTCTAACCGTAGAAGGAACCAGTCTTCATGGCATCTGAGTTAGCATCTCCCAGAGCAGCCTCGCTCATGTACTTGTCAGCAAGCTGCACACGCTTGACATTGTCCTGCTCTTGGACGAGCATGTGGCCGTACTCCAGGAGCTTCTCGATTGTCATCTTTGGCTGCTCAAAGGACACCGGTCCATCCTTCGAGTTCACCAGCTTCTTGCCGATGTTCTCTATTCCGGTTGA criterion=sequence-density sequence-density=0.58 sequence-density-rank=1 fanout-score=4.94 fanout-score-rank=13 prefix-density=0.77 prefix-fanout=3.7 sequence=AAGGAGCTGGAGGAGGT criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=123.36 fanout-score-rank=1 prefix-density=0.26 prefix-fanout=6.0 sequence=GCAGCAGCCATTACTTGATCATCTGAAAAATCTTAATCCAGATCAGACCAAGCAGAGCAGAGATGTCTGCTACCTTCTCGTCCACCGTCGGAGCTCCGGCTTCTACGCCAACCAGCTTCCTTGGGAAGAAGCTCAAGAAGCAGGTGACCTCGGCCGTGAACTACCATGGCAAGAGCACCAAGGCCAACAGATTCACAGTCATGGCCAAGGAGGTGGACGAGTCAAAGCAGACTGACCAGGACAGGTGGAAGGGCCTCGCCTACGATATCTCCGACGACCAGCAGGACATCACCAGGGGGAAGGGTATCGTCGACTCGCTCTTCCAGGCGCCCATGGGCGACGGTACCCACGTGGCCGTCCTCAGCTCCCAAGAGTACATCAGCCAGGGCCTAAGGAAGTACGACTTCGACAACA SRR7814818 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 11:12:34 Started mapping on | Dec 06 11:12:35 Finished on | Dec 06 11:17:54 Mapping speed, Million of reads per hour | 367.07 Number of input reads | 32526423 Average input read length | 297 UNIQUE READS: Uniquely mapped reads number | 29444238 Uniquely mapped reads % | 90.52% Average mapped length | 295.40 Number of splices: Total | 28353725 Number of splices: Annotated (sjdb) | 26736453 Number of splices: GT/AG | 27930507 Number of splices: GC/AG | 345304 Number of splices: AT/AC | 12245 Number of splices: Non-canonical | 65669 Mismatch rate per base, % | 0.45% Deletion rate per base | 0.03% Deletion average length | 3.15 Insertion rate per base | 0.02% Insertion average length | 2.82 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 564459 % of reads mapped to multiple loci | 1.74% Number of reads mapped to too many loci | 37455 % of reads mapped to too many loci | 0.12% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.92% % of reads unmapped: other | 0.71% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2517726 2517726 2517726 N_multimapping 564459 564459 564459 N_noFeature 999484 28566947 1291777 N_ambiguous 707256 3824 124017 UnstrandedReadsAssigned:27737498 PositiveStrandReadsAssigned:873467 NegativeStrandReadsAssigned:28028444 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR7814818 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: SRR7814818-trimmed-pair1.fastq SRR7814818-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 32,526,423 reads, 28,822,722 reads pseudoaligned [quant] estimated average fragment length: 267.896 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,163 rounds 52973 SRR7814818.ke.tsv 35125 SRR7814818.se.tsv 88098 total ==> SRR7814818.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 669.565 0 0 PNS24247 1044 777.104 77.2238 4.34238 PNS24249 1928 1661.1 69.2645 1.82209 PNS24246 1044 777.104 77.2238 4.34238 PNS24248 1044 777.104 77.2238 4.34238 PNS24244 1471 1204.1 253.064 9.1838 PNS24243 293 93.8519 2 0.9312 KQK14069 1603 1336.1 353.126 11.549 KQK14071 474 231.272 3.78721 0.715569 ==> SRR7814818.se.tsv <== BRADI_1g14170v3 380 BRADI_1g53295v3 861 BRADI_1g59795v3 178 BRADI_1g07683v3 0 BRADI_1g00485v3 4 BRADI_1g20270v3 744 BRADI_1g74790v3 263 BRADI_1g09890v3 1 BRADI_1g77505v3 565 BRADI_1g48960v3 0 SRR7814818 completed mapping pipeline successfully