Starting /dee2/code/volunteer_pipeline.sh SRR18694443 current disk space = 1525905170432 free memory = 1405530080 SRR18694443 SRAfilesize d895c993b22e3dc5f286857917ec7202 SRR18694443.sra SRR18694443.sra file validated SRR18694443 is paired end SRR18694443 is conventional basespace SRR18694443 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR18694443_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 36.075 37.0 37.0 37.0 37.0 37.0 2 36.039 37.0 37.0 37.0 37.0 37.0 3 36.3705 37.0 37.0 37.0 37.0 37.0 4 36.4845 37.0 37.0 37.0 37.0 37.0 5 36.61 37.0 37.0 37.0 37.0 37.0 6 36.537 37.0 37.0 37.0 37.0 37.0 7 36.556 37.0 37.0 37.0 37.0 37.0 8 36.5235 37.0 37.0 37.0 37.0 37.0 9 36.6265 37.0 37.0 37.0 37.0 37.0 10-14 36.6309 37.0 37.0 37.0 37.0 37.0 15-19 36.6069 37.0 37.0 37.0 37.0 37.0 20-24 36.6348 37.0 37.0 37.0 37.0 37.0 25-29 36.59739999999999 37.0 37.0 37.0 37.0 37.0 30-34 36.532399999999996 37.0 37.0 37.0 37.0 37.0 35-39 36.700599999999994 37.0 37.0 37.0 37.0 37.0 40-44 36.583600000000004 37.0 37.0 37.0 37.0 37.0 45-49 36.4172 37.0 37.0 37.0 37.0 37.0 50-54 36.549 37.0 37.0 37.0 37.0 37.0 55-59 36.5526 37.0 37.0 37.0 37.0 37.0 60-64 36.5156 37.0 37.0 37.0 37.0 37.0 65-69 36.303000000000004 37.0 37.0 37.0 37.0 37.0 70-74 36.4224 37.0 37.0 37.0 37.0 37.0 75-79 36.50429999999999 37.0 37.0 37.0 37.0 37.0 80-84 36.4028 37.0 37.0 37.0 37.0 37.0 85-89 36.1606 37.0 37.0 37.0 37.0 37.0 90-94 35.40350000000001 37.0 37.0 37.0 29.8 37.0 95-99 36.1499 37.0 37.0 37.0 37.0 37.0 100-104 36.17230000000001 37.0 37.0 37.0 37.0 37.0 105-109 36.1568 37.0 37.0 37.0 37.0 37.0 110-114 36.233799999999995 37.0 37.0 37.0 37.0 37.0 115-119 36.5041 37.0 37.0 37.0 37.0 37.0 120-124 36.5752 37.0 37.0 37.0 37.0 37.0 125-129 36.559999999999995 37.0 37.0 37.0 37.0 37.0 130-134 36.5068 37.0 37.0 37.0 37.0 37.0 135-139 36.3979 37.0 37.0 37.0 37.0 37.0 140-144 36.2815 37.0 37.0 37.0 37.0 37.0 145-149 36.2453 37.0 37.0 37.0 37.0 37.0 150-151 33.775 37.0 31.0 37.0 24.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 17 2.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 1.0 24 1.0 25 1.0 26 1.0 27 2.0 28 3.0 29 4.0 30 6.0 31 15.0 32 27.0 33 60.0 34 97.0 35 302.0 36 3316.0 37 162.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 46.475 10.0 4.625 38.9 2 21.098845960863024 10.336176618163574 38.71048670346212 29.85449071751129 3 20.349999999999998 13.55 24.525 41.575 4 26.924999999999997 20.275000000000002 21.725 31.075000000000003 5 25.75 27.400000000000002 23.775 23.075000000000003 6 24.0 30.125 22.675 23.200000000000003 7 19.05 24.725 38.35 17.875 8 18.9 23.724999999999998 32.475 24.9 9 20.025000000000002 20.775 35.449999999999996 23.75 10-14 23.215 26.625 26.040000000000003 24.12 15-19 24.075 25.25 26.029999999999998 24.645 20-24 23.22 24.855 26.435 25.490000000000002 25-29 22.845 25.624999999999996 25.424999999999997 26.105 30-34 23.775 24.47 25.5 26.255 35-39 22.884999999999998 25.705 26.13 25.28 40-44 23.235 25.85 25.814999999999998 25.1 45-49 23.265 25.674999999999997 25.169999999999998 25.89 50-54 22.79 26.215 25.130000000000003 25.865 55-59 22.93 26.1 25.085 25.885 60-64 23.01 25.419999999999998 25.679999999999996 25.89 65-69 22.895 25.69 26.369999999999997 25.045 70-74 23.080000000000002 24.915000000000003 26.150000000000002 25.855 75-79 23.865 25.14 25.595000000000002 25.4 80-84 23.71 24.925 25.979999999999997 25.385 85-89 23.965 25.82 24.43 25.785000000000004 90-94 24.245 25.545 25.09 25.119999999999997 95-99 23.7 24.815 25.615 25.869999999999997 100-104 23.215 25.31 25.255 26.22 105-109 24.175 25.45 24.445 25.929999999999996 110-114 23.805 25.61 25.064999999999998 25.52 115-119 24.14 25.724999999999998 24.92 25.215 120-124 24.455 24.63 25.374999999999996 25.540000000000003 125-129 23.895 25.44 24.83 25.835 130-134 23.94 25.669999999999998 24.565 25.825 135-139 23.805 25.785000000000004 24.759999999999998 25.650000000000002 140-144 24.845 25.41 24.685000000000002 25.06 145-149 23.79 25.840000000000003 24.490000000000002 25.88 150-151 23.1375 25.9875 24.712500000000002 26.1625 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.5 7 0.5 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 0.0 22 0.0 23 0.0 24 0.0 25 1.0 26 4.5 27 5.0 28 5.5 29 6.0 30 8.5 31 13.0 32 10.5 33 15.5 34 26.5 35 33.5 36 47.5 37 63.0 38 82.0 39 98.0 40 117.0 41 146.0 42 164.5 43 184.5 44 199.5 45 192.0 46 206.0 47 218.0 48 207.0 49 188.0 50 150.0 51 142.0 52 142.0 53 121.0 54 113.5 55 92.5 56 88.5 57 93.5 58 80.5 59 77.0 60 68.0 61 72.0 62 73.0 63 59.0 64 49.5 65 56.0 66 57.5 67 45.5 68 42.0 69 32.5 70 27.5 71 22.5 72 14.0 73 14.0 74 8.0 75 2.5 76 0.5 77 3.0 78 3.0 79 1.0 80 1.0 81 1.0 82 1.0 83 0.5 84 1.0 85 0.5 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 0.35000000000000003 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 86.425 #Duplication Level Percentage of deduplicated Percentage of total 1 86.72259184263812 74.95 2 11.13682383569569 19.25 3 1.851316170089673 4.8 4 0.2892681515765114 1.0 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 0.025 4 0.0 0.0 0.0 0.0 0.025 5 0.0 0.0 0.0 0.0 0.025 6 0.0 0.0 0.0 0.0 0.025 7 0.0 0.0 0.0 0.0 0.025 8 0.0 0.0 0.0 0.0 0.025 9 0.0 0.0 0.0 0.0 0.025 10-11 0.0 0.0 0.0 0.0 0.025 12-13 0.0 0.0 0.0 0.0 0.025 14-15 0.0 0.0 0.0 0.0 0.025 16-17 0.0 0.0 0.0 0.0 0.025 18-19 0.0 0.0 0.0 0.0 0.025 20-21 0.0 0.0 0.0 0.0 0.025 22-23 0.0 0.0 0.0 0.0 0.025 24-25 0.0 0.0 0.0 0.0 0.025 26-27 0.0 0.0 0.0 0.0 0.025 28-29 0.0 0.0 0.0 0.0 0.025 30-31 0.0 0.0 0.0 0.0 0.025 32-33 0.0 0.0 0.0 0.0 0.025 34-35 0.0 0.0 0.0 0.0 0.025 36-37 0.0 0.0 0.0 0.0 0.025 38-39 0.0 0.0 0.0 0.0 0.025 40-41 0.0 0.0 0.0 0.0 0.025 42-43 0.0 0.0 0.0 0.0 0.025 44-45 0.0 0.0 0.0 0.0 0.025 46-47 0.0 0.0 0.0 0.0 0.025 48-49 0.0 0.0 0.0 0.0 0.025 50-51 0.0 0.0 0.0 0.0 0.025 52-53 0.0 0.0 0.0 0.0 0.025 54-55 0.0 0.0 0.0 0.0 0.025 56-57 0.0 0.0 0.0 0.0 0.025 58-59 0.0 0.0 0.0 0.0 0.025 60-61 0.0 0.0 0.0 0.0 0.025 62-63 0.0 0.0 0.0 0.0 0.025 64-65 0.0 0.0 0.025 0.0 0.025 66-67 0.0 0.0 0.025 0.0 0.025 68-69 0.0125 0.0 0.025 0.0 0.025 70-71 0.025 0.0 0.025 0.0 0.025 72-73 0.025 0.0 0.025 0.0 0.025 74-75 0.025 0.0 0.025 0.0 0.025 76-77 0.025 0.0 0.025 0.0 0.025 78-79 0.025 0.0 0.025 0.0 0.025 80-81 0.037500000000000006 0.0 0.025 0.0 0.025 82-83 0.0625 0.0 0.025 0.0 0.025 84-85 0.1 0.0 0.025 0.0 0.025 86-87 0.125 0.0 0.025 0.0 0.025 88-89 0.15 0.0 0.025 0.0 0.025 90-91 0.16249999999999998 0.0 0.025 0.0 0.025 92-93 0.175 0.0 0.025 0.0 0.025 94-95 0.2125 0.0 0.025 0.0 0.025 96-97 0.275 0.0 0.025 0.0 0.025 98-99 0.3125 0.0 0.025 0.0 0.025 100-101 0.375 0.0 0.025 0.0 0.025 102-103 0.525 0.0 0.025 0.0 0.025 104-105 0.625 0.0 0.025 0.0 0.025 106-107 0.825 0.0 0.025 0.0 0.025 108-109 0.9624999999999999 0.0 0.025 0.0 0.025 110-111 1.1124999999999998 0.0 0.025 0.0 0.025 112-113 1.2625000000000002 0.0 0.025 0.0 0.025 114-115 1.5125000000000002 0.0 0.025 0.0 0.025 116-117 1.7875 0.0 0.025 0.0 0.025 118-119 2.1 0.0 0.025 0.0 0.025 120-121 2.3499999999999996 0.0 0.025 0.0 0.025 122-123 2.6125 0.0 0.025 0.0 0.025 124-125 2.9124999999999996 0.0 0.025 0.0 0.025 126-127 3.3 0.0 0.025 0.0 0.025 128-129 3.65 0.0 0.025 0.0 0.025 130-131 3.95 0.0 0.025 0.0 0.025 132-133 4.35 0.0 0.025 0.0 0.025 134-135 4.775 0.0 0.025 0.0 0.025 136-137 5.2125 0.0 0.025 0.0 0.025 138-139 5.7625 0.0 0.025 0.0 0.025 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTTCCAC 10 0.006830828 145.0 8 >>END_MODULE SRR18694443 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR18694443_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 34.2215 37.0 37.0 37.0 25.0 37.0 2 35.245 37.0 37.0 37.0 25.0 37.0 3 35.363 37.0 37.0 37.0 37.0 37.0 4 35.287 37.0 37.0 37.0 25.0 37.0 5 35.2305 37.0 37.0 37.0 25.0 37.0 6 35.246 37.0 37.0 37.0 25.0 37.0 7 35.3565 37.0 37.0 37.0 37.0 37.0 8 35.6135 37.0 37.0 37.0 37.0 37.0 9 35.5195 37.0 37.0 37.0 37.0 37.0 10-14 35.5789 37.0 37.0 37.0 37.0 37.0 15-19 35.6872 37.0 37.0 37.0 37.0 37.0 20-24 35.4425 37.0 37.0 37.0 34.6 37.0 25-29 35.608 37.0 37.0 37.0 34.6 37.0 30-34 35.809799999999996 37.0 37.0 37.0 37.0 37.0 35-39 35.703199999999995 37.0 37.0 37.0 37.0 37.0 40-44 35.403000000000006 37.0 37.0 37.0 29.8 37.0 45-49 35.6001 37.0 37.0 37.0 37.0 37.0 50-54 34.9627 37.0 37.0 37.0 32.2 37.0 55-59 34.425000000000004 37.0 37.0 37.0 25.0 37.0 60-64 35.075 37.0 37.0 37.0 27.4 37.0 65-69 34.2921 37.0 34.6 37.0 27.4 37.0 70-74 33.070800000000006 37.0 29.8 37.0 25.0 37.0 75-79 33.6736 37.0 34.6 37.0 22.2 37.0 80-84 34.6321 37.0 37.0 37.0 25.0 37.0 85-89 32.653800000000004 37.0 32.2 37.0 19.4 37.0 90-94 34.0932 37.0 37.0 37.0 25.0 37.0 95-99 34.065599999999996 37.0 37.0 37.0 25.0 37.0 100-104 33.434599999999996 37.0 34.6 37.0 25.0 37.0 105-109 34.3045 37.0 37.0 37.0 25.0 37.0 110-114 34.5909 37.0 37.0 37.0 25.0 37.0 115-119 34.513999999999996 37.0 37.0 37.0 25.0 37.0 120-124 34.0846 37.0 37.0 37.0 25.0 37.0 125-129 34.02669999999999 37.0 37.0 37.0 25.0 37.0 130-134 33.7666 37.0 34.6 37.0 25.0 37.0 135-139 32.179100000000005 37.0 27.4 37.0 13.8 37.0 140-144 31.6813 37.0 25.0 37.0 11.0 37.0 145-149 31.1817 37.0 25.0 37.0 13.8 37.0 150-151 30.95525 37.0 25.0 37.0 18.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 16 1.0 17 1.0 18 2.0 19 1.0 20 2.0 21 1.0 22 3.0 23 7.0 24 4.0 25 8.0 26 11.0 27 16.0 28 23.0 29 34.0 30 86.0 31 125.0 32 272.0 33 567.0 34 1201.0 35 1425.0 36 210.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.525 21.075 7.875 31.525 2 30.7 23.474999999999998 27.35 18.475 3 23.400000000000002 25.074999999999996 28.075 23.45 4 27.05 29.799999999999997 21.25 21.9 5 26.924999999999997 34.075 19.425 19.575 6 23.05 34.75 20.549999999999997 21.65 7 23.25 17.625 36.9 22.225 8 20.674999999999997 22.325 27.400000000000002 29.599999999999998 9 22.55 21.275 29.175 27.0 10-14 25.575 24.83 23.775 25.82 15-19 25.715 24.29 25.135 24.86 20-24 25.885 24.474999999999998 25.069999999999997 24.57 25-29 26.040000000000003 24.82 24.37 24.77 30-34 26.235000000000003 24.665 24.635 24.465 35-39 25.009999999999998 26.27 24.37 24.349999999999998 40-44 25.905 25.2 24.635 24.26 45-49 25.69 25.435000000000002 24.915000000000003 23.96 50-54 24.69 25.03 26.119999999999997 24.16 55-59 25.335 25.545 24.775 24.345 60-64 26.13 25.259999999999998 25.035 23.575 65-69 26.21 24.9 24.815 24.075 70-74 25.919999999999998 24.82 24.745 24.515 75-79 26.640000000000004 24.575 24.715 24.07 80-84 26.32 25.06 25.069999999999997 23.549999999999997 85-89 24.05 28.215 24.375 23.36 90-94 26.515 25.069999999999997 24.84 23.575 95-99 25.785000000000004 25.145 24.75 24.32 100-104 26.135 25.540000000000003 24.525 23.799999999999997 105-109 25.64 25.705 24.015 24.64 110-114 26.334999999999997 25.495 24.6 23.57 115-119 26.46 25.224999999999998 24.535 23.78 120-124 25.974999999999998 25.580000000000002 25.005 23.44 125-129 26.724999999999998 25.729999999999997 24.64 22.905 130-134 26.745 25.324999999999996 24.985 22.945 135-139 26.384999999999998 25.869999999999997 25.27 22.475 140-144 26.540000000000003 26.05 24.415 22.994999999999997 145-149 27.27 25.66 24.375 22.695 150-151 25.15 26.200000000000003 25.874999999999996 22.775000000000002 >>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 1.0 6 1.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.5 15 0.5 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.5 23 2.0 24 1.5 25 1.0 26 1.5 27 0.5 28 4.0 29 4.5 30 4.5 31 13.0 32 22.0 33 23.5 34 26.0 35 37.5 36 46.5 37 55.0 38 80.5 39 102.5 40 116.0 41 136.5 42 159.0 43 166.5 44 169.5 45 190.5 46 188.0 47 170.0 48 171.0 49 170.5 50 155.0 51 134.0 52 126.0 53 123.0 54 114.0 55 114.0 56 104.5 57 86.0 58 91.5 59 101.0 60 89.5 61 78.5 62 76.0 63 72.0 64 65.5 65 56.5 66 55.5 67 55.5 68 52.5 69 50.0 70 37.5 71 27.0 72 20.5 73 13.0 74 8.5 75 7.0 76 5.5 77 3.5 78 2.0 79 0.5 80 0.5 81 0.5 82 1.0 83 0.5 84 0.5 85 0.5 86 0.0 87 0.0 88 1.0 89 1.0 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 1.0 >>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 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 87.175 #Duplication Level Percentage of deduplicated Percentage of total 1 87.84055061657585 76.575 2 10.065959277315745 17.549999999999997 3 1.749354746200172 4.575 4 0.2294235732721537 0.8 5 0.11471178663607685 0.5 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 CAGAGAGTTGAGCGTCTGTACGTGCTAGACTGAGGGAAAAATCAAGATGG 5 0.125 No Hit CCTCTTGTTAGCTATCTACGTACGTGTACGATGGCTCCCACAGTGATGTC 5 0.125 No Hit AGCACACACAAGCCTAGAAGCCTTCAGCTTAATCTTCTTCCTAAGCAAGT 5 0.125 No Hit GTTGGCTTCTCCTCCCCCTCACTAGTCCTCGGTTCCGGTTCCGGTTCGTT 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 0.0125 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 0.025 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 0.075 0.0 0.0 0.0 0.0 86-87 0.1 0.0 0.0 0.0 0.0 88-89 0.125 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 0.1875 0.0 0.0 0.0 0.0 96-97 0.25 0.0 0.0 0.0 0.0 98-99 0.2875 0.0 0.0 0.0 0.0 100-101 0.35 0.0 0.0 0.0 0.0 102-103 0.5 0.0 0.0 0.0 0.0 104-105 0.6000000000000001 0.0 0.0 0.0 0.0 106-107 0.7875 0.0 0.0 0.0 0.0 108-109 0.9125 0.0 0.0 0.0 0.0 110-111 1.0625 0.0 0.0 0.0 0.0 112-113 1.2125 0.0 0.0 0.0 0.0 114-115 1.4625 0.0 0.0 0.0 0.0 116-117 1.7374999999999998 0.0 0.0 0.0 0.0 118-119 2.025 0.0 0.0 0.0 0.0 120-121 2.3 0.0 0.0 0.0 0.0 122-123 2.5625 0.0 0.0 0.0 0.0 124-125 2.85 0.0 0.0 0.0 0.0 126-127 3.2249999999999996 0.0 0.0 0.0 0.0 128-129 3.5374999999999996 0.0 0.0 0.0 0.0 130-131 3.825 0.0 0.0 0.0 0.0 132-133 4.225 0.0 0.0 0.0 0.0 134-135 4.65 0.0 0.0 0.0 0.0 136-137 5.0875 0.0 0.0 0.0 0.0 138-139 5.6125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AACATTG 10 0.006830828 145.0 3 >>END_MODULE Read 699562 spots for SRR18694443.sra Written 699562 spots for SRR18694443.sra Read 699562 spots for SRR18694443.sra Written 699562 spots for SRR18694443.sra Read 699562 spots for SRR18694443.sra Written 699562 spots for SRR18694443.sra Read 699562 spots for SRR18694443.sra Written 699562 spots for SRR18694443.sra Read 699562 spots for SRR18694443.sra Written 699562 spots for SRR18694443.sra Read 699562 spots for SRR18694443.sra Written 699562 spots for SRR18694443.sra Read 699562 spots for SRR18694443.sra Written 699562 spots for SRR18694443.sra Read 699562 spots for SRR18694443.sra Written 699562 spots for SRR18694443.sra Read 699562 spots for SRR18694443.sra Written 699562 spots for SRR18694443.sra Read 699562 spots for SRR18694443.sra Written 699562 spots for SRR18694443.sra Read 699562 spots for SRR18694443.sra Written 699562 spots for SRR18694443.sra Read 699562 spots for SRR18694443.sra Written 699562 spots for SRR18694443.sra Read 699562 spots for SRR18694443.sra Written 699562 spots for SRR18694443.sra Read 699574 spots for SRR18694443.sra Written 699574 spots for SRR18694443.sra Read 699562 spots for SRR18694443.sra Written 699562 spots for SRR18694443.sra Read 699562 spots for SRR18694443.sra Written 699562 spots for SRR18694443.sra Read 699562 spots for SRR18694443.sra Written 699562 spots for SRR18694443.sra Read 699562 spots for SRR18694443.sra Written 699562 spots for SRR18694443.sra Read 699562 spots for SRR18694443.sra Written 699562 spots for SRR18694443.sra Read 699562 spots for SRR18694443.sra Written 699562 spots for SRR18694443.sra SRR ids: ['SRR18694443.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_jhcapnhi SRR18694443.sra spots: 13991252 blocks: [[1, 699562], [699563, 1399124], [1399125, 2098686], [2098687, 2798248], [2798249, 3497810], [3497811, 4197372], [4197373, 4896934], [4896935, 5596496], [5596497, 6296058], [6296059, 6995620], [6995621, 7695182], [7695183, 8394744], [8394745, 9094306], [9094307, 9793868], [9793869, 10493430], [10493431, 11192992], [11192993, 11892554], [11892555, 12592116], [12592117, 13291678], [13291679, 13991252]] SRR18694443 file size 4733139 SRR18694443 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 SRR18694443 SRR18694443_1.fastq SRR18694443_2.fastq Input file: SRR18694443_1.fastq Paired file: SRR18694443_2.fastq trimmed: SRR18694443-trimmed-pair1.fastq, SRR18694443-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 Tue Dec 10 06:53:45 2024 >> started Tue Dec 10 06:54:03 2024 >> done (17.927s) 13991252 read pairs processed; of these: 144 ( 0.00%) short read pairs filtered out after trimming by size control 1292 ( 0.01%) empty read pairs filtered out after trimming by size control 13989816 (99.99%) read pairs available; of these: 1279701 ( 9.15%) trimmed read pairs available after processing 12710115 (90.85%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 10 0.00% 19 16 0.00% 20 19 0.00% 21 16 0.00% 22 21 0.00% 23 23 0.00% 24 25 0.00% 25 28 0.00% 26 20 0.00% 27 22 0.00% 28 32 0.00% 29 29 0.00% 30 36 0.00% 31 31 0.00% 32 27 0.00% 33 31 0.00% 34 29 0.00% 35 34 0.00% 36 29 0.00% 37 26 0.00% 38 48 0.00% 39 35 0.00% 40 39 0.00% 41 51 0.00% 42 35 0.00% 43 50 0.00% 44 44 0.00% 45 54 0.00% 46 78 0.00% 47 41 0.00% 48 79 0.00% 49 64 0.00% 50 69 0.00% 51 74 0.00% 52 94 0.00% 53 79 0.00% 54 68 0.00% 55 110 0.00% 56 111 0.00% 57 119 0.00% 58 129 0.00% 59 150 0.00% 60 209 0.00% 61 245 0.00% 62 233 0.00% 63 236 0.00% 64 288 0.00% 65 309 0.00% 66 374 0.00% 67 357 0.00% 68 365 0.00% 69 447 0.00% 70 512 0.00% 71 538 0.00% 72 728 0.01% 73 699 0.00% 74 813 0.01% 75 912 0.01% 76 1031 0.01% 77 1140 0.01% 78 1283 0.01% 79 1409 0.01% 80 1561 0.01% 81 1790 0.01% 82 2190 0.02% 83 2224 0.02% 84 2454 0.02% 85 2691 0.02% 86 2965 0.02% 87 3055 0.02% 88 3416 0.02% 89 3611 0.03% 90 3842 0.03% 91 4321 0.03% 92 4559 0.03% 93 4920 0.04% 94 5364 0.04% 95 5982 0.04% 96 6251 0.04% 97 6407 0.05% 98 6667 0.05% 99 7009 0.05% 100 7645 0.05% 101 7977 0.06% 102 8523 0.06% 103 9057 0.06% 104 9458 0.07% 105 9909 0.07% 106 10446 0.07% 107 10871 0.08% 108 11089 0.08% 109 11807 0.08% 110 12570 0.09% 111 12884 0.09% 112 13534 0.10% 113 14237 0.10% 114 15073 0.11% 115 15450 0.11% 116 16314 0.12% 117 16849 0.12% 118 17027 0.12% 119 17592 0.13% 120 18779 0.13% 121 19107 0.14% 122 19969 0.14% 123 20876 0.15% 124 21910 0.16% 125 22473 0.16% 126 23213 0.17% 127 23852 0.17% 128 24179 0.17% 129 25373 0.18% 130 25911 0.19% 131 26156 0.19% 132 27631 0.20% 133 28241 0.20% 134 29392 0.21% 135 29813 0.21% 136 31152 0.22% 137 31355 0.22% 138 31747 0.23% 139 33194 0.24% 140 33597 0.24% 141 34521 0.25% 142 35202 0.25% 143 36527 0.26% 144 37332 0.27% 145 38770 0.28% 146 38937 0.28% 147 40851 0.29% 148 41256 0.29% 149 41875 0.30% 150 42666 0.30% 151 12710115 90.85% 13989816 reads passed initial QC criterion=sequence-density sequence-density=0.45 sequence-density-rank=1 fanout-score=3.15 fanout-score-rank=17 prefix-density=0.48 prefix-fanout=2.9 sequence=GGTGTTGTCGAAGCCGATGATGCGGACATAGGCGTC criterion=fanout-score sequence-density=0.03 sequence-density-rank=31 fanout-score=143.38 fanout-score-rank=1 prefix-density=0.38 prefix-fanout=9.9 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.75 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=32 prefix-density=0.75 prefix-fanout=2.0 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.27 sequence-density-rank=9 fanout-score=11.86 fanout-score-rank=1 prefix-density=0.53 prefix-fanout=6.1 sequence=AAGAAGGAGTACCC SRR18694443 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 10 06:54:55 Started mapping on | Dec 10 06:54:55 Finished on | Dec 10 06:56:23 Mapping speed, Million of reads per hour | 572.31 Number of input reads | 13989816 Average input read length | 297 UNIQUE READS: Uniquely mapped reads number | 13203448 Uniquely mapped reads % | 94.38% Average mapped length | 296.34 Number of splices: Total | 13925408 Number of splices: Annotated (sjdb) | 13033548 Number of splices: GT/AG | 13725798 Number of splices: GC/AG | 169276 Number of splices: AT/AC | 5804 Number of splices: Non-canonical | 24530 Mismatch rate per base, % | 0.44% Deletion rate per base | 0.01% Deletion average length | 2.42 Insertion rate per base | 0.01% Insertion average length | 2.43 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 180555 % of reads mapped to multiple loci | 1.29% Number of reads mapped to too many loci | 17325 % of reads mapped to too many loci | 0.12% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.03% % of reads unmapped: other | 1.17% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 605813 605813 605813 N_multimapping 180555 180555 180555 N_noFeature 702822 12840560 811865 N_ambiguous 305944 1926 52645 UnstrandedReadsAssigned:12194682 PositiveStrandReadsAssigned:360962 NegativeStrandReadsAssigned:12338938 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR18694443 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: SRR18694443-trimmed-pair1.fastq SRR18694443-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,989,816 reads, 12,518,860 reads pseudoaligned [quant] estimated average fragment length: 262.851 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,113 rounds 52973 SRR18694443.ke.tsv 35125 SRR18694443.se.tsv 88098 total ==> SRR18694443.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 674.676 0 0 PNS24247 1044 782.149 48.0073 7.12117 PNS24249 1928 1666.15 22.8549 1.59147 PNS24246 1044 782.149 48.0073 7.12117 PNS24248 1044 782.149 48.0073 7.12117 PNS24244 1471 1209.15 71.1232 6.82441 PNS24243 293 91.9899 0 0 KQK14069 1603 1341.15 756.476 65.4413 KQK14071 474 233.929 17.7631 8.80982 ==> SRR18694443.se.tsv <== BRADI_1g14170v3 846 BRADI_1g53295v3 69 BRADI_1g59795v3 800 BRADI_1g07683v3 0 BRADI_1g00485v3 2 BRADI_1g20270v3 524 BRADI_1g74790v3 165 BRADI_1g09890v3 0 BRADI_1g77505v3 154 BRADI_1g48960v3 0 SRR18694443 completed mapping pipeline successfully