Starting /dee2/code/volunteer_pipeline.sh SRR12919372 current disk space = 3051075985408 free memory = 1414327652 SRR12919372 SRAfilesize 872d9a2ba2c5a72dde76a6a0b362d532 SRR12919372.sra SRR12919372.sra file validated SRR12919372 is paired end SRR12919372 is conventional basespace SRR12919372 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12919372_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.615 37.0 37.0 37.0 37.0 37.0 2 36.3855 37.0 37.0 37.0 37.0 37.0 3 36.611 37.0 37.0 37.0 37.0 37.0 4 36.5875 37.0 37.0 37.0 37.0 37.0 5 36.584 37.0 37.0 37.0 37.0 37.0 6 36.6465 37.0 37.0 37.0 37.0 37.0 7 36.5775 37.0 37.0 37.0 37.0 37.0 8 36.605 37.0 37.0 37.0 37.0 37.0 9 36.6255 37.0 37.0 37.0 37.0 37.0 10-14 36.6509 37.0 37.0 37.0 37.0 37.0 15-19 36.585 37.0 37.0 37.0 37.0 37.0 20-24 36.5712 37.0 37.0 37.0 37.0 37.0 25-29 36.542500000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.506499999999996 37.0 37.0 37.0 37.0 37.0 35-39 36.4628 37.0 37.0 37.0 37.0 37.0 40-44 36.47559999999999 37.0 37.0 37.0 37.0 37.0 45-49 36.4912 37.0 37.0 37.0 37.0 37.0 50-54 36.447900000000004 37.0 37.0 37.0 37.0 37.0 55-59 36.4303 37.0 37.0 37.0 37.0 37.0 60-64 36.411500000000004 37.0 37.0 37.0 37.0 37.0 65-69 36.364 37.0 37.0 37.0 37.0 37.0 70-74 36.3134 37.0 37.0 37.0 37.0 37.0 75-79 36.2922 37.0 37.0 37.0 37.0 37.0 80-84 36.3426 37.0 37.0 37.0 37.0 37.0 85-89 36.2708 37.0 37.0 37.0 37.0 37.0 90-94 36.2187 37.0 37.0 37.0 37.0 37.0 95-99 36.2205 37.0 37.0 37.0 37.0 37.0 100-104 36.23879999999999 37.0 37.0 37.0 37.0 37.0 105-109 36.148199999999996 37.0 37.0 37.0 37.0 37.0 110-114 36.1296 37.0 37.0 37.0 37.0 37.0 115-119 36.08860000000001 37.0 37.0 37.0 37.0 37.0 120-124 36.1045 37.0 37.0 37.0 37.0 37.0 125-129 35.9846 37.0 37.0 37.0 37.0 37.0 130-134 35.9629 37.0 37.0 37.0 37.0 37.0 135-139 35.8731 37.0 37.0 37.0 37.0 37.0 140-144 35.7863 37.0 37.0 37.0 37.0 37.0 145-149 35.8848 37.0 37.0 37.0 37.0 37.0 150-151 35.55275 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 17 1.0 18 0.0 19 0.0 20 0.0 21 0.0 22 3.0 23 3.0 24 0.0 25 2.0 26 5.0 27 9.0 28 9.0 29 16.0 30 25.0 31 39.0 32 42.0 33 62.0 34 82.0 35 320.0 36 2931.0 37 451.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 37.35 13.525 7.1499999999999995 41.975 2 19.512807634354594 13.837267704671019 36.71521848317428 29.934706177800102 3 16.400000000000002 18.7 29.15 35.75 4 21.0 24.025 25.3 29.675 5 22.7 30.049999999999997 25.074999999999996 22.175 6 20.1 33.675 23.974999999999998 22.25 7 14.825 28.375 39.35 17.45 8 16.75 27.525 32.05 23.674999999999997 9 17.9 25.124999999999996 34.825 22.15 10-14 19.09 31.535000000000004 27.04 22.335 15-19 19.45 28.595 27.905 24.05 20-24 19.525000000000002 29.580000000000002 28.044999999999998 22.85 25-29 19.1 29.095 28.015 23.79 30-34 19.03 29.185 27.71 24.075 35-39 20.145 28.749999999999996 27.68 23.425 40-44 19.445 29.365000000000002 27.55 23.64 45-49 19.11 29.025000000000002 28.075 23.79 50-54 20.064999999999998 29.32 27.685 22.93 55-59 19.470000000000002 29.84 27.435 23.255 60-64 19.84 29.654999999999998 26.575 23.93 65-69 19.515 29.425 27.025 24.035 70-74 19.38 29.375 27.389999999999997 23.855 75-79 20.05 29.404999999999998 27.16 23.385 80-84 19.98 29.4 27.015 23.605 85-89 19.975 28.73 28.055000000000003 23.24 90-94 19.689999999999998 29.330000000000002 27.115000000000002 23.865 95-99 19.814999999999998 28.015 27.785 24.385 100-104 20.085 28.505000000000003 27.450000000000003 23.96 105-109 20.0 29.18 27.045 23.775 110-114 20.075000000000003 28.775000000000002 27.339999999999996 23.810000000000002 115-119 20.765 28.265 27.465 23.505000000000003 120-124 19.86 28.505000000000003 27.310000000000002 24.325 125-129 20.54 28.535 27.29 23.635 130-134 21.59 28.9 26.040000000000003 23.47 135-139 21.02 28.59 26.55 23.84 140-144 21.9 28.470000000000002 26.86 22.770000000000003 145-149 21.060000000000002 28.485 26.445 24.01 150-151 20.95 28.5875 26.237500000000004 24.224999999999998 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 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 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 1.5 22 1.5 23 1.5 24 3.0 25 3.5 26 3.5 27 5.0 28 9.0 29 14.0 30 22.5 31 34.0 32 42.5 33 55.5 34 69.5 35 87.5 36 102.5 37 122.5 38 148.5 39 173.5 40 198.5 41 220.0 42 243.0 43 259.5 44 263.0 45 273.0 46 280.0 47 243.0 48 208.0 49 177.5 50 145.0 51 131.0 52 102.5 53 79.0 54 68.0 55 55.5 56 39.0 57 27.5 58 23.0 59 13.5 60 7.5 61 7.5 62 11.5 63 9.0 64 5.5 65 4.5 66 1.5 67 0.5 68 0.5 69 0.0 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.5 78 0.5 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.44999999999999996 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 91.25 #Duplication Level Percentage of deduplicated Percentage of total 1 91.45205479452055 83.45 2 7.6438356164383565 13.950000000000001 3 0.7671232876712328 2.1 4 0.136986301369863 0.5 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 0.0125 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 0.037500000000000006 0.0 0.0 0.0 0.0 82-83 0.0625 0.0 0.0 0.0 0.0 84-85 0.125 0.0 0.0 0.0 0.0 86-87 0.2 0.0 0.0 0.0 0.0 88-89 0.25 0.0 0.0 0.0 0.0 90-91 0.32499999999999996 0.0 0.0 0.0 0.0 92-93 0.4375 0.0 0.0 0.0 0.0 94-95 0.5625 0.0 0.0 0.0 0.0 96-97 0.5874999999999999 0.0 0.0 0.0 0.0 98-99 0.6625 0.0 0.0 0.0 0.0 100-101 0.7875 0.0 0.0 0.0 0.0 102-103 0.9 0.0 0.0 0.0 0.0 104-105 1.1 0.0 0.0 0.0 0.0 106-107 1.325 0.0 0.0 0.0 0.0 108-109 1.6375 0.0 0.0 0.0 0.0 110-111 1.875 0.0 0.0 0.0 0.0 112-113 2.05 0.0 0.0 0.0 0.0 114-115 2.3 0.0 0.0 0.0 0.0 116-117 2.625 0.0 0.0 0.0 0.0 118-119 2.9125 0.0 0.0 0.0 0.0 120-121 3.125 0.0 0.0 0.0 0.0 122-123 3.3375 0.0 0.0 0.0 0.0 124-125 3.6375 0.0 0.0 0.0 0.0 126-127 4.012499999999999 0.0 0.0 0.0 0.0 128-129 4.3875 0.0 0.0 0.0 0.0 130-131 4.85 0.0 0.0 0.0 0.0 132-133 5.375 0.0 0.0 0.0 0.0 134-135 5.7125 0.0 0.0 0.0 0.0 136-137 6.225 0.0 0.0 0.0 0.0 138-139 6.7 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAGTCTC 10 0.006830828 145.0 9 >>END_MODULE SRR12919372 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12919372_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.32 37.0 37.0 37.0 37.0 37.0 2 36.196 37.0 37.0 37.0 37.0 37.0 3 36.197 37.0 37.0 37.0 37.0 37.0 4 36.133 37.0 37.0 37.0 37.0 37.0 5 36.2855 37.0 37.0 37.0 37.0 37.0 6 36.2525 37.0 37.0 37.0 37.0 37.0 7 36.186 37.0 37.0 37.0 37.0 37.0 8 36.1975 37.0 37.0 37.0 37.0 37.0 9 36.2995 37.0 37.0 37.0 37.0 37.0 10-14 36.3134 37.0 37.0 37.0 37.0 37.0 15-19 36.2673 37.0 37.0 37.0 37.0 37.0 20-24 36.2538 37.0 37.0 37.0 37.0 37.0 25-29 36.201800000000006 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 36.166599999999995 37.0 37.0 37.0 37.0 37.0 40-44 36.1255 37.0 37.0 37.0 37.0 37.0 45-49 36.152100000000004 37.0 37.0 37.0 37.0 37.0 50-54 36.0954 37.0 37.0 37.0 37.0 37.0 55-59 36.0914 37.0 37.0 37.0 37.0 37.0 60-64 36.0697 37.0 37.0 37.0 37.0 37.0 65-69 36.0329 37.0 37.0 37.0 37.0 37.0 70-74 35.9654 37.0 37.0 37.0 37.0 37.0 75-79 35.9755 37.0 37.0 37.0 37.0 37.0 80-84 35.9163 37.0 37.0 37.0 37.0 37.0 85-89 35.943400000000004 37.0 37.0 37.0 37.0 37.0 90-94 35.8614 37.0 37.0 37.0 37.0 37.0 95-99 35.903800000000004 37.0 37.0 37.0 37.0 37.0 100-104 35.847 37.0 37.0 37.0 37.0 37.0 105-109 35.819599999999994 37.0 37.0 37.0 37.0 37.0 110-114 35.8091 37.0 37.0 37.0 37.0 37.0 115-119 35.762 37.0 37.0 37.0 37.0 37.0 120-124 35.696 37.0 37.0 37.0 37.0 37.0 125-129 35.640699999999995 37.0 37.0 37.0 37.0 37.0 130-134 35.62 37.0 37.0 37.0 37.0 37.0 135-139 35.4647 37.0 37.0 37.0 37.0 37.0 140-144 35.3751 37.0 37.0 37.0 34.6 37.0 145-149 35.2399 37.0 37.0 37.0 34.6 37.0 150-151 35.12425 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 2.0 14 3.0 15 0.0 16 0.0 17 1.0 18 0.0 19 1.0 20 2.0 21 3.0 22 4.0 23 4.0 24 5.0 25 8.0 26 3.0 27 16.0 28 16.0 29 18.0 30 25.0 31 45.0 32 56.0 33 89.0 34 210.0 35 554.0 36 2690.0 37 245.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.45 25.525 9.9 26.125 2 28.349999999999998 27.625 28.349999999999998 15.675 3 19.75 29.049999999999997 31.474999999999998 19.725 4 22.975 33.95 23.625 19.45 5 25.724999999999998 35.375 22.0 16.900000000000002 6 22.0 38.3 22.6 17.1 7 20.8 22.625 38.125 18.45 8 21.9 26.275 27.500000000000004 24.325 9 21.475 24.825 30.625000000000004 23.075000000000003 10-14 23.72 28.910000000000004 26.275 21.095 15-19 23.36 28.64 27.705000000000002 20.294999999999998 20-24 23.400000000000002 28.560000000000002 27.3 20.74 25-29 23.94 28.435 26.939999999999998 20.685000000000002 30-34 22.645 28.525 27.595 21.235 35-39 23.27 28.610000000000003 27.195000000000004 20.925 40-44 23.52 28.244999999999997 27.97 20.265 45-49 23.294999999999998 27.96 27.57 21.175 50-54 23.205000000000002 27.839999999999996 28.349999999999998 20.605 55-59 23.724999999999998 27.525 28.025 20.724999999999998 60-64 23.345 27.925 28.1 20.630000000000003 65-69 23.635 27.250000000000004 27.49 21.625 70-74 23.665 27.655 28.475 20.205000000000002 75-79 23.419999999999998 28.13 27.834999999999997 20.615 80-84 23.395 28.349999999999998 27.55 20.705000000000002 85-89 24.025 27.865000000000002 27.725 20.385 90-94 23.685000000000002 27.994999999999997 28.470000000000002 19.85 95-99 23.14 27.075 28.46 21.325 100-104 23.485 27.72 28.435 20.36 105-109 23.845 27.345000000000002 28.165000000000003 20.645 110-114 23.965 28.12 28.215 19.7 115-119 24.115000000000002 27.935 28.18 19.77 120-124 24.525 27.73 27.634999999999998 20.11 125-129 25.009999999999998 27.76 27.18 20.05 130-134 25.0 27.96 27.46 19.580000000000002 135-139 25.03 27.465 27.785 19.72 140-144 25.28 27.825 27.375 19.52 145-149 26.16 26.965 27.48 19.395 150-151 26.3125 27.1375 27.712500000000002 18.8375 >>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 0.5 10 0.5 11 0.0 12 0.5 13 0.5 14 0.0 15 0.5 16 0.5 17 1.0 18 1.0 19 0.5 20 0.5 21 1.0 22 2.0 23 1.0 24 0.5 25 2.0 26 3.5 27 4.5 28 5.5 29 8.0 30 10.0 31 16.0 32 27.0 33 35.5 34 43.0 35 59.5 36 82.0 37 105.5 38 139.0 39 176.5 40 211.0 41 246.5 42 277.5 43 270.0 44 264.0 45 274.0 46 264.0 47 249.5 48 224.5 49 199.5 50 169.0 51 136.5 52 113.0 53 78.5 54 59.0 55 54.5 56 42.5 57 28.0 58 19.5 59 19.0 60 15.0 61 11.5 62 11.0 63 8.5 64 4.5 65 3.5 66 2.5 67 2.0 68 1.5 69 1.0 70 2.0 71 1.5 72 0.5 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.5 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 0.5 98 1.5 99 1.0 100 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 91.5 #Duplication Level Percentage of deduplicated Percentage of total 1 91.5846994535519 83.8 2 7.6775956284152995 14.05 3 0.6010928961748634 1.6500000000000001 4 0.1366120218579235 0.5 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 0.0125 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 0.037500000000000006 0.0 0.0 0.0 0.0 82-83 0.0625 0.0 0.0 0.0 0.0 84-85 0.125 0.0 0.0 0.0 0.0 86-87 0.2 0.0 0.0 0.0 0.0 88-89 0.25 0.0 0.0 0.0 0.0 90-91 0.32499999999999996 0.0 0.0 0.0 0.0 92-93 0.425 0.0 0.0 0.0 0.0 94-95 0.5375000000000001 0.0 0.0 0.0 0.0 96-97 0.5625 0.0 0.0 0.0 0.0 98-99 0.6375 0.0 0.0 0.0 0.0 100-101 0.7625 0.0 0.0 0.0 0.0 102-103 0.875 0.0 0.0 0.0 0.0 104-105 1.075 0.0 0.0 0.0 0.0 106-107 1.3125 0.0 0.0 0.0 0.0 108-109 1.6375 0.0 0.0 0.0 0.0 110-111 1.875 0.0 0.0 0.0 0.0 112-113 2.05 0.0 0.0 0.0 0.0 114-115 2.3 0.0 0.0 0.0 0.0 116-117 2.625 0.0 0.0 0.0 0.0 118-119 2.9 0.0 0.0 0.0 0.0 120-121 3.0999999999999996 0.0 0.0 0.0 0.0 122-123 3.3125 0.0 0.0 0.0 0.0 124-125 3.6375 0.0 0.0 0.0 0.0 126-127 3.9875 0.0 0.0 0.0 0.0 128-129 4.4375 0.0 0.0 0.0 0.0 130-131 4.9 0.0 0.0 0.0 0.0 132-133 5.449999999999999 0.0 0.0 0.0 0.0 134-135 5.8375 0.0 0.0 0.0 0.0 136-137 6.35 0.0 0.0 0.0 0.0 138-139 6.8375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGTTGTT 10 0.006830828 145.0 145 ACACGAT 10 0.006830828 145.0 8 CACGATC 10 0.006830828 145.0 9 GAGACAC 10 0.006830828 145.0 5 >>END_MODULE Read 1014578 spots for SRR12919372.sra Written 1014578 spots for SRR12919372.sra Read 1014578 spots for SRR12919372.sra Written 1014578 spots for SRR12919372.sra Read 1014578 spots for SRR12919372.sra Written 1014578 spots for SRR12919372.sra Read 1014578 spots for SRR12919372.sra Written 1014578 spots for SRR12919372.sra Read 1014578 spots for SRR12919372.sra Written 1014578 spots for SRR12919372.sra Read 1014578 spots for SRR12919372.sra Written 1014578 spots for SRR12919372.sra Read 1014578 spots for SRR12919372.sra Written 1014578 spots for SRR12919372.sra Read 1014578 spots for SRR12919372.sra Written 1014578 spots for SRR12919372.sra Read 1014578 spots for SRR12919372.sra Written 1014578 spots for SRR12919372.sra Read 1014578 spots for SRR12919372.sra Written 1014578 spots for SRR12919372.sra Read 1014578 spots for SRR12919372.sra Written 1014578 spots for SRR12919372.sra Read 1014578 spots for SRR12919372.sra Written 1014578 spots for SRR12919372.sra Read 1014578 spots for SRR12919372.sra Written 1014578 spots for SRR12919372.sra Read 1014578 spots for SRR12919372.sra Written 1014578 spots for SRR12919372.sra Read 1014578 spots for SRR12919372.sra Written 1014578 spots for SRR12919372.sra Read 1014578 spots for SRR12919372.sra Written 1014578 spots for SRR12919372.sra Read 1014578 spots for SRR12919372.sra Written 1014578 spots for SRR12919372.sra Read 1014592 spots for SRR12919372.sra Written 1014592 spots for SRR12919372.sra Read 1014578 spots for SRR12919372.sra Written 1014578 spots for SRR12919372.sra Read 1014578 spots for SRR12919372.sra Written 1014578 spots for SRR12919372.sra SRR ids: ['SRR12919372.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd__3iocsrp SRR12919372.sra spots: 20291574 blocks: [[1, 1014578], [1014579, 2029156], [2029157, 3043734], [3043735, 4058312], [4058313, 5072890], [5072891, 6087468], [6087469, 7102046], [7102047, 8116624], [8116625, 9131202], [9131203, 10145780], [10145781, 11160358], [11160359, 12174936], [12174937, 13189514], [13189515, 14204092], [14204093, 15218670], [15218671, 16233248], [16233249, 17247826], [17247827, 18262404], [18262405, 19276982], [19276983, 20291574]] SRR12919372 file size 6874264 SRR12919372 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 SRR12919372 SRR12919372_1.fastq SRR12919372_2.fastq Input file: SRR12919372_1.fastq Paired file: SRR12919372_2.fastq trimmed: SRR12919372-trimmed-pair1.fastq, SRR12919372-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Wed Feb 12 20:55:18 2025 >> started Wed Feb 12 20:55:53 2025 >> done (34.869s) 20291574 read pairs processed; of these: 28 ( 0.00%) short read pairs filtered out after trimming by size control 794 ( 0.00%) empty read pairs filtered out after trimming by size control 20290752 (100.00%) read pairs available; of these: 2287256 (11.27%) trimmed read pairs available after processing 18003496 (88.73%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 3 0.00% 20 3 0.00% 21 3 0.00% 22 5 0.00% 23 4 0.00% 24 0 0.00% 25 5 0.00% 26 7 0.00% 27 9 0.00% 28 4 0.00% 29 11 0.00% 30 10 0.00% 31 14 0.00% 32 9 0.00% 33 11 0.00% 34 9 0.00% 35 14 0.00% 36 20 0.00% 37 6 0.00% 38 18 0.00% 39 28 0.00% 40 21 0.00% 41 20 0.00% 42 19 0.00% 43 17 0.00% 44 22 0.00% 45 24 0.00% 46 27 0.00% 47 33 0.00% 48 35 0.00% 49 43 0.00% 50 66 0.00% 51 68 0.00% 52 54 0.00% 53 66 0.00% 54 61 0.00% 55 95 0.00% 56 86 0.00% 57 110 0.00% 58 126 0.00% 59 137 0.00% 60 202 0.00% 61 208 0.00% 62 227 0.00% 63 260 0.00% 64 264 0.00% 65 297 0.00% 66 372 0.00% 67 397 0.00% 68 453 0.00% 69 516 0.00% 70 636 0.00% 71 806 0.00% 72 846 0.00% 73 1041 0.01% 74 1148 0.01% 75 1320 0.01% 76 1480 0.01% 77 1649 0.01% 78 1794 0.01% 79 1976 0.01% 80 2219 0.01% 81 2544 0.01% 82 3043 0.01% 83 3538 0.02% 84 4096 0.02% 85 4372 0.02% 86 4725 0.02% 87 5240 0.03% 88 5591 0.03% 89 6149 0.03% 90 6695 0.03% 91 7583 0.04% 92 8314 0.04% 93 9567 0.05% 94 10216 0.05% 95 11303 0.06% 96 12174 0.06% 97 12540 0.06% 98 13196 0.07% 99 14366 0.07% 100 15059 0.07% 101 16427 0.08% 102 17305 0.09% 103 19082 0.09% 104 20663 0.10% 105 21515 0.11% 106 22464 0.11% 107 23628 0.12% 108 23765 0.12% 109 25334 0.12% 110 25599 0.13% 111 26851 0.13% 112 28040 0.14% 113 29760 0.15% 114 31086 0.15% 115 33235 0.16% 116 33540 0.17% 117 34541 0.17% 118 35238 0.17% 119 35863 0.18% 120 36149 0.18% 121 37442 0.18% 122 38496 0.19% 123 40034 0.20% 124 41671 0.21% 125 43536 0.21% 126 44777 0.22% 127 45251 0.22% 128 45607 0.22% 129 46703 0.23% 130 46823 0.23% 131 47552 0.23% 132 48544 0.24% 133 50108 0.25% 134 50993 0.25% 135 52469 0.26% 136 54346 0.27% 137 54465 0.27% 138 55219 0.27% 139 54924 0.27% 140 56471 0.28% 141 57254 0.28% 142 57937 0.29% 143 58613 0.29% 144 60190 0.30% 145 61794 0.30% 146 62456 0.31% 147 62837 0.31% 148 63480 0.31% 149 63467 0.31% 150 63965 0.32% 151 18003496 88.73% 20290752 reads passed initial QC criterion=sequence-density sequence-density=0.60 sequence-density-rank=1 fanout-score=3.47 fanout-score-rank=13 prefix-density=0.77 prefix-fanout=2.7 sequence=TGAACTTGTTTCACCAGCTACATTTGAAACACCTTGGAACACCACGAAGAGCTTTTCATTTGACAAAGATGTCAAAGCTACAGAAGCACTTGCTGTATCGGCAGTTTTTGCATCA criterion=fanout-score sequence-density=0.01 sequence-density-rank=29 fanout-score=180.07 fanout-score-rank=1 prefix-density=0.17 prefix-fanout=14.0 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTG criterion=sequence-density sequence-density=0.45 sequence-density-rank=1 fanout-score=2.32 fanout-score-rank=24 prefix-density=0.49 prefix-fanout=2.2 sequence=AATGCCTGCCCGGAAAACCCAAAGTTGTCTTTGGATCGAAGAGTTCTACTTCTGATTTTTACGTTCGAAATAAAGC criterion=fanout-score sequence-density=0.07 sequence-density-rank=25 fanout-score=36.05 fanout-score-rank=1 prefix-density=0.24 prefix-fanout=10.0 sequence=AAGGCCAAGATCCAGGACAAGGA SRR12919372 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 12 20:56:51 Started mapping on | Feb 12 20:56:51 Finished on | Feb 12 21:00:36 Mapping speed, Million of reads per hour | 324.65 Number of input reads | 20290752 Average input read length | 296 UNIQUE READS: Uniquely mapped reads number | 18689220 Uniquely mapped reads % | 92.11% Average mapped length | 295.36 Number of splices: Total | 16945256 Number of splices: Annotated (sjdb) | 16513098 Number of splices: GT/AG | 16638414 Number of splices: GC/AG | 235231 Number of splices: AT/AC | 20955 Number of splices: Non-canonical | 50656 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.03% Deletion average length | 2.85 Insertion rate per base | 0.03% Insertion average length | 2.40 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 484516 % of reads mapped to multiple loci | 2.39% Number of reads mapped to too many loci | 153714 % of reads mapped to too many loci | 0.76% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.55% % of reads unmapped: other | 0.20% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1117016 1117016 1117016 N_multimapping 484516 484516 484516 N_noFeature 668232 18457416 760518 N_ambiguous 255079 1477 114782 UnstrandedReadsAssigned:17765909 PositiveStrandReadsAssigned:230327 NegativeStrandReadsAssigned:17813920 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12919372 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR12919372-trimmed-pair1.fastq SRR12919372-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 20,290,752 reads, 17,888,792 reads pseudoaligned [quant] estimated average fragment length: 254.23 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,159 rounds 52401 SRR12919372.ke.tsv 34699 SRR12919372.se.tsv 87100 total ==> SRR12919372.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1764.77 622 19.3746 Potri.005G024800.1.v4.1 1035 781.77 423 29.7435 Potri.004G059700.1.v4.1 961 707.921 49 3.80489 Potri.007G009000.2.v4.1 1416 1162.77 0 0 Potri.003G141000.2.v4.1 2943 2689.77 765.959 15.6539 Potri.016G087400.1.v4.1 270 85.714 2538.64 1628.1 Potri.015G069301.1.v4.1 564 322.729 0 0 Potri.010G195200.1.v4.1 1773 1519.77 216 7.8128 Potri.012G127500.1.v4.1 977 723.853 4613 350.319 ==> SRR12919372.se.tsv <== Potri.001G166300.v4.1 2 Potri.001G448400.v4.1 139 Potri.001G233950.v4.1 3 Potri.001G122700.v4.1 281 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 12 Potri.001G452600.v4.1 7 SRR12919372 completed mapping pipeline successfully