Starting /dee2/code/volunteer_pipeline.sh SRR23047993 current disk space = 3050117095424 free memory = 1580390716 SRR23047993 SRAfilesize 55e2286b4adf3a84db0aa8aab3eac18e SRR23047993.sra SRR23047993.sra file validated SRR23047993 is paired end SRR23047993 is conventional basespace SRR23047993 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR23047993_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.00525 37.0 37.0 37.0 37.0 37.0 2 36.1445 37.0 37.0 37.0 37.0 37.0 3 36.2315 37.0 37.0 37.0 37.0 37.0 4 36.267 37.0 37.0 37.0 37.0 37.0 5 36.457 37.0 37.0 37.0 37.0 37.0 6 36.3595 37.0 37.0 37.0 37.0 37.0 7 36.197 37.0 37.0 37.0 37.0 37.0 8 36.257 37.0 37.0 37.0 37.0 37.0 9 36.3925 37.0 37.0 37.0 37.0 37.0 10-14 36.386700000000005 37.0 37.0 37.0 37.0 37.0 15-19 36.3294 37.0 37.0 37.0 37.0 37.0 20-24 36.32289999999999 37.0 37.0 37.0 37.0 37.0 25-29 36.2716 37.0 37.0 37.0 37.0 37.0 30-34 36.173 37.0 37.0 37.0 37.0 37.0 35-39 36.1174 37.0 37.0 37.0 37.0 37.0 40-44 36.1209 37.0 37.0 37.0 37.0 37.0 45-49 36.183800000000005 37.0 37.0 37.0 37.0 37.0 50-54 36.098400000000005 37.0 37.0 37.0 37.0 37.0 55-59 36.1376 37.0 37.0 37.0 37.0 37.0 60-64 36.0791 37.0 37.0 37.0 37.0 37.0 65-69 36.029399999999995 37.0 37.0 37.0 37.0 37.0 70-74 35.993399999999994 37.0 37.0 37.0 37.0 37.0 75-79 36.0127 37.0 37.0 37.0 37.0 37.0 80-84 35.9904 37.0 37.0 37.0 37.0 37.0 85-89 35.93429999999999 37.0 37.0 37.0 37.0 37.0 90-94 35.9166 37.0 37.0 37.0 37.0 37.0 95-99 35.8078 37.0 37.0 37.0 37.0 37.0 100-104 35.8424 37.0 37.0 37.0 37.0 37.0 105-109 35.8164 37.0 37.0 37.0 37.0 37.0 110-114 35.8101 37.0 37.0 37.0 37.0 37.0 115-119 35.8625 37.0 37.0 37.0 37.0 37.0 120-124 35.718399999999995 37.0 37.0 37.0 37.0 37.0 125-129 35.7306 37.0 37.0 37.0 37.0 37.0 130-134 35.705 37.0 37.0 37.0 37.0 37.0 135-139 35.730999999999995 37.0 37.0 37.0 37.0 37.0 140-144 35.5518 37.0 37.0 37.0 37.0 37.0 145-149 35.534800000000004 37.0 37.0 37.0 37.0 37.0 150 35.6935 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 1.0 24 0.0 25 0.0 26 7.0 27 7.0 28 12.0 29 24.0 30 44.0 31 54.0 32 82.0 33 110.0 34 195.0 35 454.0 36 2852.0 37 158.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 38.655250566607904 8.662805338705617 9.34273482749937 43.33920926718711 2 20.3 12.725 38.824999999999996 28.15 3 23.674999999999997 15.225 22.8 38.3 4 26.150000000000002 24.425 18.775 30.65 5 24.15 29.925 23.175 22.75 6 19.925 32.5 27.525 20.05 7 13.8 27.425 40.725 18.05 8 19.400000000000002 22.875 32.4 25.324999999999996 9 19.15 22.175 35.425000000000004 23.25 10-14 19.994999999999997 30.025000000000002 27.415 22.564999999999998 15-19 20.36 27.74 27.595 24.305 20-24 19.950000000000003 28.275 27.500000000000004 24.275 25-29 20.76 27.589999999999996 28.050000000000004 23.599999999999998 30-34 20.73 28.355000000000004 26.935 23.98 35-39 20.09 27.884999999999998 26.945000000000004 25.080000000000002 40-44 20.765 28.060000000000002 27.325 23.849999999999998 45-49 21.075 27.785 27.055 24.085 50-54 20.380000000000003 28.01 27.439999999999998 24.169999999999998 55-59 20.380000000000003 27.72 27.860000000000003 24.04 60-64 20.71 27.060000000000002 27.665 24.565 65-69 21.09 27.744999999999997 27.36 23.805 70-74 20.405 27.845 27.345000000000002 24.404999999999998 75-79 21.46 27.87 26.8 23.87 80-84 21.085 26.935 28.060000000000002 23.919999999999998 85-89 21.42 27.515 27.095000000000002 23.97 90-94 21.615000000000002 27.74 26.900000000000002 23.745 95-99 21.555 27.615000000000002 26.724999999999998 24.104999999999997 100-104 21.115000000000002 27.825 27.27 23.79 105-109 20.97 27.400000000000002 27.87 23.76 110-114 21.115000000000002 27.384999999999998 27.66 23.84 115-119 21.7 27.750000000000004 26.75 23.799999999999997 120-124 21.305 27.42 27.245 24.03 125-129 20.91 27.055 27.765 24.27 130-134 21.82 26.905 27.375 23.9 135-139 20.835 27.355 27.58 24.23 140-144 21.2 27.73 27.415 23.655 145-149 20.93 27.93 27.3 23.84 150 21.925 26.674999999999997 28.349999999999998 23.05 >>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 0.5 13 0.5 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 0.5 23 0.5 24 0.5 25 1.5 26 2.5 27 6.0 28 9.0 29 10.0 30 14.5 31 13.5 32 23.0 33 32.0 34 35.0 35 51.5 36 74.0 37 85.5 38 103.5 39 129.5 40 162.5 41 179.5 42 218.5 43 257.5 44 269.0 45 280.5 46 261.5 47 254.0 48 251.0 49 233.5 50 187.0 51 153.5 52 144.5 53 123.0 54 99.0 55 77.5 56 57.5 57 48.5 58 36.5 59 23.5 60 22.5 61 17.0 62 12.5 63 11.5 64 5.5 65 2.0 66 3.5 67 3.5 68 2.5 69 2.0 70 1.5 71 0.5 72 1.0 73 1.5 74 0.5 75 0.5 76 0.5 77 0.0 78 0.0 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 0.7250000000000001 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 88.575 #Duplication Level Percentage of deduplicated Percentage of total 1 88.2867626305391 78.2 2 10.640699971775332 18.85 3 0.9596387242449902 2.55 4 0.11289867344058707 0.4 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 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 114-115 0.0 0.0 0.0 0.0 0.0 116-117 0.0 0.0 0.0 0.0 0.0 118-119 0.0 0.0 0.0 0.0 0.0 120-121 0.0 0.0 0.0 0.0 0.0 122-123 0.0 0.0 0.0 0.0 0.0 124-125 0.0 0.0 0.0 0.0 0.0 126-127 0.0 0.0 0.0 0.0 0.0 128-129 0.0 0.0 0.0 0.0 0.0 130-131 0.0 0.0 0.0 0.0 0.0 132-133 0.0 0.0 0.0 0.0 0.0 134-135 0.0 0.0 0.0 0.0 0.0 136-137 0.0 0.0 0.0 0.0 0.0 138 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGCACCA 10 0.006973645 144.0 4 GCGAAGA 10 0.006973645 144.0 2 CGAAGAT 10 0.006973645 144.0 3 GGCGAAG 10 0.006973645 144.0 1 TAGTCAT 10 0.006973645 144.0 9 ATAGTCA 10 0.006973645 144.0 8 CTGCACC 10 0.006973645 144.0 3 ATTTCTA 10 0.006973645 144.0 4 >>END_MODULE SRR23047993 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR23047993_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.3335 37.0 37.0 37.0 37.0 37.0 2 35.707 37.0 37.0 37.0 37.0 37.0 3 35.6615 37.0 37.0 37.0 37.0 37.0 4 35.8455 37.0 37.0 37.0 37.0 37.0 5 36.084 37.0 37.0 37.0 37.0 37.0 6 35.876 37.0 37.0 37.0 37.0 37.0 7 35.755 37.0 37.0 37.0 37.0 37.0 8 35.983 37.0 37.0 37.0 37.0 37.0 9 35.9475 37.0 37.0 37.0 37.0 37.0 10-14 35.9841 37.0 37.0 37.0 37.0 37.0 15-19 35.9093 37.0 37.0 37.0 37.0 37.0 20-24 35.791999999999994 37.0 37.0 37.0 37.0 37.0 25-29 35.8215 37.0 37.0 37.0 37.0 37.0 30-34 35.8239 37.0 37.0 37.0 37.0 37.0 35-39 35.7759 37.0 37.0 37.0 37.0 37.0 40-44 35.7173 37.0 37.0 37.0 37.0 37.0 45-49 35.6452 37.0 37.0 37.0 37.0 37.0 50-54 35.72089999999999 37.0 37.0 37.0 37.0 37.0 55-59 35.5766 37.0 37.0 37.0 37.0 37.0 60-64 35.5434 37.0 37.0 37.0 37.0 37.0 65-69 35.5751 37.0 37.0 37.0 37.0 37.0 70-74 35.534800000000004 37.0 37.0 37.0 37.0 37.0 75-79 35.4829 37.0 37.0 37.0 37.0 37.0 80-84 35.3997 37.0 37.0 37.0 34.6 37.0 85-89 35.3014 37.0 37.0 37.0 32.2 37.0 90-94 35.3127 37.0 37.0 37.0 32.2 37.0 95-99 35.2853 37.0 37.0 37.0 29.8 37.0 100-104 35.3571 37.0 37.0 37.0 32.2 37.0 105-109 35.075900000000004 37.0 37.0 37.0 27.4 37.0 110-114 35.2376 37.0 37.0 37.0 29.8 37.0 115-119 35.124900000000004 37.0 37.0 37.0 25.0 37.0 120-124 35.140499999999996 37.0 37.0 37.0 27.4 37.0 125-129 35.072799999999994 37.0 37.0 37.0 25.0 37.0 130-134 35.0967 37.0 37.0 37.0 25.0 37.0 135-139 34.9464 37.0 37.0 37.0 25.0 37.0 140-144 34.9118 37.0 37.0 37.0 25.0 37.0 145-149 35.0202 37.0 37.0 37.0 25.0 37.0 150 34.913 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 3.0 22 4.0 23 8.0 24 8.0 25 5.0 26 6.0 27 19.0 28 24.0 29 39.0 30 49.0 31 61.0 32 102.0 33 167.0 34 318.0 35 997.0 36 2152.0 37 38.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 34.386143657666835 21.54865002547122 13.066734589913398 30.998471726948544 2 18.6 35.425000000000004 31.775 14.2 3 21.45 32.175 25.15 21.224999999999998 4 24.625 36.9 20.125 18.35 5 23.925 37.824999999999996 20.9 17.349999999999998 6 19.175 40.300000000000004 23.125 17.4 7 18.675 21.3 39.025 21.0 8 20.95 23.9 28.325 26.825 9 23.724999999999998 24.7 28.549999999999997 23.025000000000002 10-14 23.31 29.635 24.795 22.259999999999998 15-19 22.725 29.544999999999998 26.33 21.4 20-24 23.625 28.994999999999997 26.11 21.27 25-29 23.23 29.01 26.384999999999998 21.375 30-34 23.66 28.305000000000003 26.405 21.63 35-39 23.565 28.895 26.105 21.435000000000002 40-44 23.150000000000002 28.84 25.965 22.045 45-49 23.080000000000002 28.194999999999997 26.805 21.92 50-54 23.055 28.335 27.115000000000002 21.495 55-59 23.555 27.66 26.71 22.075 60-64 24.005000000000003 28.48 26.279999999999998 21.235 65-69 23.255 28.71 25.82 22.215 70-74 23.57 27.54 26.545 22.345000000000002 75-79 23.5 27.965 26.71 21.825 80-84 23.86 27.705000000000002 26.52 21.915000000000003 85-89 24.355 27.83 26.009999999999998 21.805 90-94 23.974999999999998 27.589999999999996 26.235000000000003 22.2 95-99 23.16 28.050000000000004 26.515 22.275 100-104 23.68 27.810000000000002 26.400000000000002 22.11 105-109 24.07 27.525 26.529999999999998 21.875 110-114 23.935000000000002 27.58 26.834999999999997 21.65 115-119 24.665 27.315 26.945000000000004 21.075 120-124 23.555 27.455000000000002 27.3 21.69 125-129 23.66 27.3 26.99 22.05 130-134 24.075 27.32 26.834999999999997 21.77 135-139 23.865 27.384999999999998 27.275 21.475 140-144 23.97 28.299999999999997 26.38 21.349999999999998 145-149 23.580000000000002 28.015 26.85 21.555 150 24.45 27.975 26.55 21.025 >>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 0.5 7 0.5 8 0.5 9 0.5 10 1.5 11 1.5 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 1.0 18 1.0 19 0.0 20 0.0 21 0.5 22 0.5 23 1.5 24 4.0 25 6.0 26 3.5 27 2.0 28 4.5 29 7.0 30 7.0 31 13.0 32 21.0 33 25.0 34 31.5 35 43.5 36 61.0 37 86.5 38 112.0 39 140.0 40 172.5 41 206.5 42 239.0 43 247.0 44 249.0 45 270.5 46 281.5 47 269.5 48 244.0 49 228.0 50 207.5 51 162.0 52 135.0 53 113.0 54 85.0 55 67.5 56 59.0 57 47.5 58 36.5 59 28.0 60 19.0 61 15.5 62 12.5 63 9.5 64 5.5 65 3.0 66 2.5 67 1.0 68 0.5 69 1.0 70 0.5 71 0.0 72 0.0 73 0.0 74 0.5 75 0.5 76 0.0 77 0.0 78 0.5 79 1.0 80 0.5 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 0.5 100 0.5 >>END_MODULE >>Per base N content pass #Base N-Count 1 1.8499999999999999 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 88.875 #Duplication Level Percentage of deduplicated Percentage of total 1 88.9451476793249 79.05 2 9.90154711673699 17.599999999999998 3 0.9282700421940928 2.475 4 0.14064697609001406 0.5 5 0.08438818565400844 0.375 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 GTAAGAGAAAAGCAGAGCAAGCAACTTAGAGGCAGCATTAACAAAGAAGA 5 0.125 No Hit CTTCAATCGTAAATCACAAATACATACACGTTTACTCATCAGCTCGAAAA 5 0.125 No Hit AAAAAATCTTAACTGCACCCGCTCATCCAGCAATGGCAGCAGCAACAATG 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 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 114-115 0.0 0.0 0.0 0.0 0.0 116-117 0.0 0.0 0.0 0.0 0.0 118-119 0.0 0.0 0.0 0.0 0.0 120-121 0.0 0.0 0.0 0.0 0.0 122-123 0.0 0.0 0.0 0.0 0.0 124-125 0.0 0.0 0.0 0.0 0.0 126-127 0.0 0.0 0.0 0.0 0.0 128-129 0.0 0.0 0.0 0.0 0.0 130-131 0.0 0.0 0.0 0.0 0.0 132-133 0.0 0.0 0.0 0.0 0.0 134-135 0.0 0.0 0.0 0.0 0.0 136-137 0.0 0.0 0.0 0.0 0.0 138 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGCAGG 10 0.0069754543 143.9875 8 AGAGGGC 10 0.0069754543 143.9875 5 CTCCACA 10 0.0069754543 143.9875 3 CCACAAT 10 0.0069754543 143.9875 5 GAGGGCA 10 0.0069754543 143.9875 6 >>END_MODULE Read 1871026 spots for SRR23047993.sra Written 1871026 spots for SRR23047993.sra Read 1871026 spots for SRR23047993.sra Written 1871026 spots for SRR23047993.sra Read 1871026 spots for SRR23047993.sra Written 1871026 spots for SRR23047993.sra Read 1871026 spots for SRR23047993.sra Written 1871026 spots for SRR23047993.sra Read 1871026 spots for SRR23047993.sra Written 1871026 spots for SRR23047993.sra Read 1871026 spots for SRR23047993.sra Written 1871026 spots for SRR23047993.sra Read 1871026 spots for SRR23047993.sra Written 1871026 spots for SRR23047993.sra Read 1871026 spots for SRR23047993.sra Written 1871026 spots for SRR23047993.sra Read 1871026 spots for SRR23047993.sra Written 1871026 spots for SRR23047993.sra Read 1871026 spots for SRR23047993.sra Written 1871026 spots for SRR23047993.sra Read 1871026 spots for SRR23047993.sra Written 1871026 spots for SRR23047993.sra Read 1871026 spots for SRR23047993.sra Written 1871026 spots for SRR23047993.sra Read 1871026 spots for SRR23047993.sra Written 1871026 spots for SRR23047993.sra Read 1871026 spots for SRR23047993.sra Written 1871026 spots for SRR23047993.sra Read 1871026 spots for SRR23047993.sra Written 1871026 spots for SRR23047993.sra Read 1871026 spots for SRR23047993.sra Written 1871026 spots for SRR23047993.sra Read 1871026 spots for SRR23047993.sra Written 1871026 spots for SRR23047993.sra Read 1871026 spots for SRR23047993.sra Written 1871026 spots for SRR23047993.sra Read 1871027 spots for SRR23047993.sra Written 1871027 spots for SRR23047993.sra Read 1871026 spots for SRR23047993.sra Written 1871026 spots for SRR23047993.sra SRR ids: ['SRR23047993.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_63b60qng SRR23047993.sra spots: 37420521 blocks: [[1, 1871026], [1871027, 3742052], [3742053, 5613078], [5613079, 7484104], [7484105, 9355130], [9355131, 11226156], [11226157, 13097182], [13097183, 14968208], [14968209, 16839234], [16839235, 18710260], [18710261, 20581286], [20581287, 22452312], [22452313, 24323338], [24323339, 26194364], [26194365, 28065390], [28065391, 29936416], [29936417, 31807442], [31807443, 33678468], [33678469, 35549494], [35549495, 37420521]] SRR23047993 file size 12622342 SRR23047993 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 SRR23047993 SRR23047993_1.fastq SRR23047993_2.fastq Input file: SRR23047993_1.fastq Paired file: SRR23047993_2.fastq trimmed: SRR23047993-trimmed-pair1.fastq, SRR23047993-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 07:06:13 2025 >> started Wed Feb 12 07:07:05 2025 >> done (52.872s) 37420521 read pairs processed; of these: 0 ( 0.00%) short read pairs filtered out after trimming by size control 0 ( 0.00%) empty read pairs filtered out after trimming by size control 37420521 (100.00%) read pairs available; of these: 89301 ( 0.24%) trimmed read pairs available after processing 37331220 (99.76%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 25 1 0.00% 26 0 0.00% 27 0 0.00% 28 1 0.00% 29 0 0.00% 30 1 0.00% 31 1 0.00% 32 1 0.00% 33 1 0.00% 34 1 0.00% 35 1 0.00% 36 1 0.00% 37 1 0.00% 38 2 0.00% 39 0 0.00% 40 1 0.00% 41 2 0.00% 42 0 0.00% 43 2 0.00% 44 2 0.00% 45 2 0.00% 46 1 0.00% 47 3 0.00% 48 0 0.00% 49 4 0.00% 50 1 0.00% 51 2 0.00% 52 5 0.00% 53 3 0.00% 54 1 0.00% 55 3 0.00% 56 3 0.00% 57 3 0.00% 58 5 0.00% 59 3 0.00% 60 5 0.00% 61 3 0.00% 62 5 0.00% 63 5 0.00% 64 4 0.00% 65 4 0.00% 66 5 0.00% 67 6 0.00% 68 2 0.00% 69 2 0.00% 70 1 0.00% 71 2 0.00% 72 7 0.00% 73 3 0.00% 74 7 0.00% 75 9 0.00% 76 5 0.00% 77 5 0.00% 78 4 0.00% 79 2 0.00% 80 4 0.00% 81 5 0.00% 82 3 0.00% 83 5 0.00% 84 6 0.00% 85 9 0.00% 86 4 0.00% 87 10 0.00% 88 3 0.00% 89 5 0.00% 90 7 0.00% 91 8 0.00% 92 10 0.00% 93 7 0.00% 94 9 0.00% 95 5 0.00% 96 10 0.00% 97 10 0.00% 98 5 0.00% 99 7 0.00% 100 5 0.00% 101 9 0.00% 102 5 0.00% 103 6 0.00% 104 11 0.00% 105 6 0.00% 106 7 0.00% 107 4 0.00% 108 5 0.00% 109 5 0.00% 110 10 0.00% 111 4 0.00% 112 5 0.00% 113 8 0.00% 114 10 0.00% 115 7 0.00% 116 10 0.00% 117 6 0.00% 118 14 0.00% 119 6 0.00% 120 7 0.00% 121 10 0.00% 122 13 0.00% 123 16 0.00% 124 18 0.00% 125 7 0.00% 126 4 0.00% 127 2 0.00% 128 11 0.00% 129 3 0.00% 130 11 0.00% 131 20 0.00% 132 22 0.00% 133 16 0.00% 134 11 0.00% 135 19 0.00% 136 7 0.00% 137 16 0.00% 138 0 0.00% 139 0 0.00% 140 12 0.00% 141 68 0.00% 142 37 0.00% 143 60 0.00% 144 0 0.00% 145 234 0.00% 146 20882 0.06% 147 21574 0.06% 148 22477 0.06% 149 23325 0.06% 150 37331220 99.76% 37420521 reads passed initial QC criterion=sequence-density sequence-density=0.34 sequence-density-rank=1 fanout-score=8.19 fanout-score-rank=9 prefix-density=0.53 prefix-fanout=5.3 sequence=CCAGCAGTGTCCCAGCCGTAGTCACCAGGGAACTCACCAGTCAAGTAGGATGGGGGCTCACCAGAGAACGGGCCCAAGTATTTAACACGGTCTGGTCCGTACCATGGGCTCCCGGAGGGAACAGGCTTGGTGGTTTTCCTCATGGAGACACGGCCATTGCCCATGATCTCAGAGGAGGAGGGGTTGAGCTTCACC criterion=fanout-score sequence-density=0.01 sequence-density-rank=41 fanout-score=353.23 fanout-score-rank=1 prefix-density=0.22 prefix-fanout=16.6 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAAC criterion=sequence-density sequence-density=0.33 sequence-density-rank=1 fanout-score=1.97 fanout-score-rank=37 prefix-density=0.33 prefix-fanout=2.0 sequence=TCCCCTTCGCTAGCCGGAAAGGCGGTGAAGCTCAACCCCTCCTCCTCTGAGATCATGGGCAATGGCCGTGTCTCCATGAGGAAAACCACCAAGCCTGTTCCCTCCGGGAGCCCATGGTACGGACCAGACCGTGTTAAATACTTGGGCCCGTTCTCTGGTGAGCCCCCATCCTACTTGACTGGTGAGTTCCCTGGTGACTACGGCTGGGACACTGCTGG criterion=fanout-score sequence-density=0.02 sequence-density-rank=31 fanout-score=176.64 fanout-score-rank=1 prefix-density=0.24 prefix-fanout=13.2 sequence=AGAGGAGAAAAGGAGTGAGATATTCAAGAGAAATACGTTTAGAAATCAAGAGAGAGAG SRR23047993 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 12 07:07:47 Started mapping on | Feb 12 07:07:47 Finished on | Feb 12 07:11:26 Mapping speed, Million of reads per hour | 615.13 Number of input reads | 37420521 Average input read length | 299 UNIQUE READS: Uniquely mapped reads number | 35251478 Uniquely mapped reads % | 94.20% Average mapped length | 299.17 Number of splices: Total | 35200178 Number of splices: Annotated (sjdb) | 34686153 Number of splices: GT/AG | 34593386 Number of splices: GC/AG | 514468 Number of splices: AT/AC | 25472 Number of splices: Non-canonical | 66852 Mismatch rate per base, % | 0.26% Deletion rate per base | 0.02% Deletion average length | 2.72 Insertion rate per base | 0.01% Insertion average length | 2.10 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1010746 % of reads mapped to multiple loci | 2.70% Number of reads mapped to too many loci | 648740 % of reads mapped to too many loci | 1.73% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 0.94% % of reads unmapped: other | 0.42% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1158297 1158297 1158297 N_multimapping 1010746 1010746 1010746 N_noFeature 784484 34935944 878543 N_ambiguous 430808 1911 208132 UnstrandedReadsAssigned:34036186 PositiveStrandReadsAssigned:313623 NegativeStrandReadsAssigned:34164803 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=150 echo kmer=145 SRR23047993 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: SRR23047993-trimmed-pair1.fastq SRR23047993-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 37,420,521 reads, 35,279,452 reads pseudoaligned [quant] estimated average fragment length: 294.135 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,170 rounds 52401 SRR23047993.ke.tsv 34699 SRR23047993.se.tsv 87100 total ==> SRR23047993.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1724.87 2779 33.7406 Potri.005G024800.1.v4.1 1035 741.865 1649 46.5495 Potri.004G059700.1.v4.1 961 667.89 35 1.09745 Potri.007G009000.2.v4.1 1416 1122.87 0 0 Potri.003G141000.2.v4.1 2943 2649.87 1181.24 9.33543 Potri.016G087400.1.v4.1 270 47.3768 1765.57 780.441 Potri.015G069301.1.v4.1 564 272.415 0 0 Potri.010G195200.1.v4.1 1773 1479.87 302 4.27371 Potri.012G127500.1.v4.1 977 683.89 11484 351.663 ==> SRR23047993.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 83 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 344 Potri.001G212900.v4.1 106 Potri.001G182400.v4.1 4 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 47 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 17 SRR23047993 completed mapping pipeline successfully